From ec9647cd397b53f17984229bf0ec1a7e0ed87001 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 1 Mar 2024 08:14:33 +0100 Subject: [PATCH 001/206] Implement correct handling of samplesheet --- README.md | 9 ++++-- assets/samplesheet.csv | 10 +++++-- assets/schema_input.json | 23 +++++++-------- .../utils_nfcore_tfactivity_pipeline/main.nf | 29 +++++++------------ 4 files changed, 35 insertions(+), 36 deletions(-) diff --git a/README.md b/README.md index 3e76380..348c49f 100644 --- a/README.md +++ b/README.md @@ -47,8 +47,13 @@ First, prepare a samplesheet with your input data that looks as follows: `samplesheet.csv`: ```csv -sample,fastq_1,fastq_2 -CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz +state,assay,peak_file +condition1,H3K27ac,condition1_H3K27ac_1.broadPeak +condition1,H3K27ac,condition1_H3K27ac_2.broadPeak +condition1,H3K4me3,condition1_H3K4me3.broadPeak +condition2,H3K27ac,condition2_H3K27ac.broadPeak +condition3,H3K27ac,condition3_H3K27ac.broadPeak +condition3,H3K4me3,condition3_H3K4me3.broadPeak ``` Each row represents a fastq file (single-end) or a pair of fastq files (paired end). diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv index 5f653ab..adade57 100644 --- a/assets/samplesheet.csv +++ b/assets/samplesheet.csv @@ -1,3 +1,7 @@ -sample,fastq_1,fastq_2 -SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz -SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz, +state,assay,peak_file +condition1,H3K27ac,condition1_H3K27ac_1.broadPeak +condition1,H3K27ac,condition1_H3K27ac_2.broadPeak +condition1,H3K4me3,condition1_H3K4me3.broadPeak +condition2,H3K27ac,condition2_H3K27ac.broadPeak +condition3,H3K27ac,condition3_H3K27ac.broadPeak +condition3,H3K4me3,condition3_H3K4me3.broadPeak diff --git a/assets/schema_input.json b/assets/schema_input.json index 4cac086..859aae9 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -7,27 +7,26 @@ "items": { "type": "object", "properties": { - "sample": { + "state": { "type": "string", "pattern": "^\\S+$", - "errorMessage": "Sample name must be provided and cannot contain spaces", - "meta": ["id"] + "errorMessage": "State name must be provided and cannot contain spaces", + "meta": ["state"] }, - "fastq_1": { + "assay": { "type": "string", - "format": "file-path", - "exists": true, - "pattern": "^\\S+\\.f(ast)?q\\.gz$", - "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" + "pattern": "^\\S+$", + "errorMessage": "Assay name must be provided and cannot contain spaces", + "meta": ["assay"] }, - "fastq_2": { + "peak_file": { "type": "string", "format": "file-path", "exists": true, - "pattern": "^\\S+\\.f(ast)?q\\.gz$", - "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" + "pattern": "^\\S+\\.(bed|broadPeak)$", + "errorMessage": "Peak file must be provided and must be a .bed or .broadPeak file", } }, - "required": ["sample", "fastq_1"] + "required": ["state", "assay", "peak_file"] } } diff --git a/subworkflows/local/utils_nfcore_tfactivity_pipeline/main.nf b/subworkflows/local/utils_nfcore_tfactivity_pipeline/main.nf index 2b8a879..40056ba 100644 --- a/subworkflows/local/utils_nfcore_tfactivity_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_tfactivity_pipeline/main.nf @@ -75,29 +75,19 @@ workflow PIPELINE_INITIALISATION { // // Custom validation for pipeline parameters // - validateInputParameters() + // validateInputParameters() // // Create channel from input file provided through params.input // Channel .fromSamplesheet("input") - .map { - meta, fastq_1, fastq_2 -> - if (!fastq_2) { - return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ] - } else { - return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ] - } - } + .map { meta, peak_file -> [ [id: meta.state + "_" + meta.assay] + meta, peak_file]} .groupTuple() .map { validateInputSamplesheet(it) } - .map { - meta, fastqs -> - return [ meta, fastqs.flatten() ] - } + .view() .set { ch_samplesheet } emit: @@ -158,15 +148,16 @@ def validateInputParameters() { // Validate channels from input samplesheet // def validateInputSamplesheet(input) { - def (metas, fastqs) = input[1..2] + print(input[1]) + def (meta, peak_files) = input[0..1] // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end - def endedness_ok = metas.collect{ it.single_end }.unique().size == 1 - if (!endedness_ok) { - error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}") - } + // def endedness_ok = metas.collect{ it.single_end }.unique().size == 1 + // if (!endedness_ok) { + // error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}") + // } - return [ metas[0], fastqs ] + return [ meta, peak_files ] } // // Get attribute from genome config file e.g. fasta From ae66a0a2bfbd6f2ed4bce0028586ef9c5722d9bb Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 1 Mar 2024 08:21:09 +0100 Subject: [PATCH 002/206] Remove template processes --- .../utils_nfcore_tfactivity_pipeline/main.nf | 2 - workflows/tfactivity.nf | 46 +++++++++---------- 2 files changed, 22 insertions(+), 26 deletions(-) diff --git a/subworkflows/local/utils_nfcore_tfactivity_pipeline/main.nf b/subworkflows/local/utils_nfcore_tfactivity_pipeline/main.nf index 40056ba..0cf8ae7 100644 --- a/subworkflows/local/utils_nfcore_tfactivity_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_tfactivity_pipeline/main.nf @@ -87,7 +87,6 @@ workflow PIPELINE_INITIALISATION { .map { validateInputSamplesheet(it) } - .view() .set { ch_samplesheet } emit: @@ -148,7 +147,6 @@ def validateInputParameters() { // Validate channels from input samplesheet // def validateInputSamplesheet(input) { - print(input[1]) def (meta, peak_files) = input[0..1] // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end diff --git a/workflows/tfactivity.nf b/workflows/tfactivity.nf index f6cefc8..cd0ed0a 100644 --- a/workflows/tfactivity.nf +++ b/workflows/tfactivity.nf @@ -5,7 +5,7 @@ */ include { FASTQC } from '../modules/nf-core/fastqc/main' -include { MULTIQC } from '../modules/nf-core/multiqc/main' +// include { MULTIQC } from '../modules/nf-core/multiqc/main' include { paramsSummaryMap } from 'plugin/nf-validation' include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' @@ -25,16 +25,14 @@ workflow TFACTIVITY { main: ch_versions = Channel.empty() - ch_multiqc_files = Channel.empty() + // ch_multiqc_files = Channel.empty() // // MODULE: Run FastQC // - FASTQC ( - ch_samplesheet - ) - ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}) - ch_versions = ch_versions.mix(FASTQC.out.versions.first()) + + // ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}) + // ch_versions = ch_versions.mix(FASTQC.out.versions.first()) // // Collate and save software versions @@ -46,26 +44,26 @@ workflow TFACTIVITY { // // MODULE: MultiQC // - ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) - ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty() - ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty() - summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") - ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) - ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) - ch_methods_description = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description)) - ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) - ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false)) + // ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) + // ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty() + // ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty() + // summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") + // ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) + // ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) + // ch_methods_description = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description)) + // ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) + // ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) + // ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false)) - MULTIQC ( - ch_multiqc_files.collect(), - ch_multiqc_config.toList(), - ch_multiqc_custom_config.toList(), - ch_multiqc_logo.toList() - ) + // MULTIQC ( + // ch_multiqc_files.collect(), + // ch_multiqc_config.toList(), + // ch_multiqc_custom_config.toList(), + // ch_multiqc_logo.toList() + // ) emit: - multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html + multiqc_report = Channel.empty() // MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html versions = ch_versions // channel: [ path(versions.yml) ] } From c90d7c8269ed42bf66266786014b1ec866b4d8f9 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 1 Mar 2024 09:37:19 +0100 Subject: [PATCH 003/206] Start implementing PREPARE_GENOME --- conf/modules.config | 4 +- main.nf | 13 +++-- modules.json | 5 ++ .../gtf2featureannotation/environment.yml | 7 +++ .../gtf2featureannotation/main.nf | 40 ++++++++++++++ .../gtf2featureannotation/meta.yml | 54 +++++++++++++++++++ nextflow.config | 1 - nextflow_schema.json | 10 ++++ subworkflows/local/prepare_genome.nf | 26 +++++++++ workflows/tfactivity.nf | 10 ++-- 10 files changed, 158 insertions(+), 12 deletions(-) create mode 100644 modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/environment.yml create mode 100644 modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/main.nf create mode 100644 modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/meta.yml create mode 100644 subworkflows/local/prepare_genome.nf diff --git a/conf/modules.config b/conf/modules.config index e3ea8fa..a23ca68 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -18,8 +18,8 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] - withName: FASTQC { - ext.args = '--quiet' + withName: 'PREPARE_GENOME:EXTRACT_ID_SYMBOL_MAP' { + ext.args = "-l \"gene_id,gene_name\"" } withName: CUSTOM_DUMPSOFTWAREVERSIONS { diff --git a/main.nf b/main.nf index 79a5d33..7ccf8e2 100644 --- a/main.nf +++ b/main.nf @@ -22,6 +22,7 @@ include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_tfac include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_tfactivity_pipeline' include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_tfactivity_pipeline' +include { PREPARE_GENOME } from './subworkflows/local/prepare_genome' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -29,10 +30,8 @@ include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_tfac ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -// TODO nf-core: Remove this line if you don't need a FASTA file -// This is an example of how to use getGenomeAttribute() to fetch parameters -// from igenomes.config using `--genome` params.fasta = getGenomeAttribute('fasta') +params.gtf = getGenomeAttribute('gtf') /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -50,6 +49,14 @@ workflow NFCORE_TFACTIVITY { main: + // + // SUBWORKFLOW: Prepare genome + // + PREPARE_GENOME ( + params.fasta, + params.gtf + ) + // // WORKFLOW: Run pipeline // diff --git a/modules.json b/modules.json index 6b3ee82..ca62461 100644 --- a/modules.json +++ b/modules.json @@ -5,6 +5,11 @@ "https://github.com/nf-core/modules.git": { "modules": { "nf-core": { + "atlasgeneannotationmanipulation/gtf2featureannotation": { + "branch": "master", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": ["modules"] + }, "fastqc": { "branch": "master", "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c", diff --git a/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/environment.yml b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/environment.yml new file mode 100644 index 0000000..67d88a4 --- /dev/null +++ b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/environment.yml @@ -0,0 +1,7 @@ +name: atlasgeneannotationmanipulation_gtf2featureannotation +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::atlas-gene-annotation-manipulation=1.1.0 diff --git a/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/main.nf b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/main.nf new file mode 100644 index 0000000..c8abbc5 --- /dev/null +++ b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/main.nf @@ -0,0 +1,40 @@ +process ATLASGENEANNOTATIONMANIPULATION_GTF2FEATUREANNOTATION { + tag "${meta.id}" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/atlas-gene-annotation-manipulation%3A1.1.0--hdfd78af_0': + 'biocontainers/atlas-gene-annotation-manipulation:1.1.0--hdfd78af_0' }" + + input: + tuple val(meta), path(gtf) + tuple val(meta2), path(fasta) + + output: + tuple val(meta), path("*.anno.tsv") , emit: feature_annotation + tuple val(meta), path("*.fa.gz") , emit: filtered_cdna, optional: true + path("versions.yml") , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: meta.id + def reference_cdna = fasta ? "--parse-cdnas $fasta" : "" + + """ + gtf2featureAnnotation.R \\ + --gtf-file $gtf \\ + --output-file ${prefix}.anno.tsv \\ + $reference_cdna \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//') + atlas-gene-annotation-manipulation: 1.1.0 + END_VERSIONS + """ +} diff --git a/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/meta.yml b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/meta.yml new file mode 100644 index 0000000..10aa536 --- /dev/null +++ b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/meta.yml @@ -0,0 +1,54 @@ +name: "atlasgeneannotationmanipulation_gtf2featureannotation" +description: Generate tables of feature metadata from GTF files +keywords: + - gtf + - annotation +tools: + - "atlasgeneannotationmanipulation": + description: "Scripts for manipulating gene annotation" + homepage: "https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation" + documentation: "https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation" + tool_dev_url: "https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation" + licence: "['Apache-2.0']" +input: + - meta: + type: map + description: | + Groovy Map containing information on input GTF file + e.g. [ id:'test' ] + - meta2: + type: map + description: | + Groovy Map containing information in input FASTA file + e.g. [ id:'test' ] + - gtf: + type: file + description: gtf annotation file + pattern: "*.{gtf}" + - fasta: + type: file + description: | + An optional cDNA file for extracting meta info and/or filtering. + pattern: "*.{gtf}" +output: + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - feature_annotation: + type: file + description: TSV file with feature annotation + pattern: "*.{tsv}" + - filtered_cdna: + type: file + description: | + Where --parse-cdnas is specified in ext.args and an input fasta file is + provided, filtered sequences are output to the specified file. No file + will be output if this is not specified (for example for use of + --dummy-from-cdnas only). See documentation at + https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation. + pattern: "*.{tsv}" +authors: + - "@pinin4fjords" +maintainers: + - "@pinin4fjords" diff --git a/nextflow.config b/nextflow.config index 8768916..a242ea3 100644 --- a/nextflow.config +++ b/nextflow.config @@ -16,7 +16,6 @@ params { genome = null igenomes_base = 's3://ngi-igenomes/igenomes/' igenomes_ignore = false - fasta = null// MultiQC options multiqc_config = null multiqc_title = null multiqc_logo = null diff --git a/nextflow_schema.json b/nextflow_schema.json index c5c0c76..22b3e1f 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -65,6 +65,16 @@ "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.", "fa_icon": "far fa-file-code" }, + "gtf": { + "type": "string", + "format": "file-path", + "exists": true, + "mimetype": "text/plain", + "pattern": "^\\S+\\.gtf(\\.gz)?$", + "description": "Path to GTF gene annotation file.", + "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a STAR index available this will be generated for you automatically. Combine with `--save_reference` to save STAR index for future runs.", + "fa_icon": "far fa-file-code" + }, "igenomes_ignore": { "type": "boolean", "description": "Do not load the iGenomes reference config.", diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf new file mode 100644 index 0000000..af9380d --- /dev/null +++ b/subworkflows/local/prepare_genome.nf @@ -0,0 +1,26 @@ +include { ATLASGENEANNOTATIONMANIPULATION_GTF2FEATUREANNOTATION as EXTRACT_ID_SYMBOL_MAP } from '../../modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/main.nf' + +workflow PREPARE_GENOME { + + take: + fasta + gtf + + main: + + ch_versions = Channel.empty() + + ch_fasta = Channel.value([[id: 'fasta'], file(fasta)]) + ch_gtf = Channel.value([[id: 'gtf'], file(gtf)]) + + // TODO nf-core: substitute modules here for the modules of your subworkflow + + EXTRACT_ID_SYMBOL_MAP(ch_gtf, [[], []]) + ch_versions = ch_versions.mix(EXTRACT_ID_SYMBOL_MAP.out.versions) + + emit: + // TODO nf-core: edit emitted channels + + versions = ch_versions // channel: [ versions.yml ] +} + diff --git a/workflows/tfactivity.nf b/workflows/tfactivity.nf index cd0ed0a..69ca982 100644 --- a/workflows/tfactivity.nf +++ b/workflows/tfactivity.nf @@ -4,13 +4,14 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { FASTQC } from '../modules/nf-core/fastqc/main' -// include { MULTIQC } from '../modules/nf-core/multiqc/main' +// include { MULTIQC } from '../modules/nf-core/multiqc/main' include { paramsSummaryMap } from 'plugin/nf-validation' include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_tfactivity_pipeline' +include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome' + /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ RUN MAIN WORKFLOW @@ -22,14 +23,11 @@ workflow TFACTIVITY { take: ch_samplesheet // channel: samplesheet read in from --input + main: ch_versions = Channel.empty() // ch_multiqc_files = Channel.empty() - - // - // MODULE: Run FastQC - // // ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}) // ch_versions = ch_versions.mix(FASTQC.out.versions.first()) From 720c7e7af315566cc090538b9d7d3dbd71be1942 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 1 Mar 2024 10:20:04 +0100 Subject: [PATCH 004/206] Implement fai creation --- conf/modules.config | 6 ++ modules.json | 10 +++ modules/nf-core/gawk/environment.yml | 7 +++ modules/nf-core/gawk/main.nf | 54 ++++++++++++++++ modules/nf-core/gawk/meta.yml | 50 +++++++++++++++ .../nf-core/samtools/faidx/environment.yml | 8 +++ modules/nf-core/samtools/faidx/main.nf | 50 +++++++++++++++ modules/nf-core/samtools/faidx/meta.yml | 61 +++++++++++++++++++ subworkflows/local/peaks.nf | 36 +++++++++++ subworkflows/local/prepare_genome.nf | 21 +++++-- 10 files changed, 299 insertions(+), 4 deletions(-) create mode 100644 modules/nf-core/gawk/environment.yml create mode 100644 modules/nf-core/gawk/main.nf create mode 100644 modules/nf-core/gawk/meta.yml create mode 100644 modules/nf-core/samtools/faidx/environment.yml create mode 100644 modules/nf-core/samtools/faidx/main.nf create mode 100644 modules/nf-core/samtools/faidx/meta.yml create mode 100644 subworkflows/local/peaks.nf diff --git a/conf/modules.config b/conf/modules.config index a23ca68..e083246 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -22,6 +22,12 @@ process { ext.args = "-l \"gene_id,gene_name\"" } + withName: REMOVE_GENE_VERSIONS { + ext.args = {"'{sub(/\\.[0-9]+/, \"\", \$1); print \$1 \"\t\" \$2}'"} + ext.prefix = {"${meta.id}.no_version"} + ext.suffix = "tsv" + } + withName: CUSTOM_DUMPSOFTWAREVERSIONS { publishDir = [ path: { "${params.outdir}/pipeline_info" }, diff --git a/modules.json b/modules.json index ca62461..a731299 100644 --- a/modules.json +++ b/modules.json @@ -15,10 +15,20 @@ "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c", "installed_by": ["modules"] }, + "gawk": { + "branch": "master", + "git_sha": "dc3527855e7358c6d8400828754c0caa5f11698f", + "installed_by": ["modules"] + }, "multiqc": { "branch": "master", "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", "installed_by": ["modules"] + }, + "samtools/faidx": { + "branch": "master", + "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "installed_by": ["modules"] } } }, diff --git a/modules/nf-core/gawk/environment.yml b/modules/nf-core/gawk/environment.yml new file mode 100644 index 0000000..34513c7 --- /dev/null +++ b/modules/nf-core/gawk/environment.yml @@ -0,0 +1,7 @@ +name: gawk +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - anaconda::gawk=5.1.0 diff --git a/modules/nf-core/gawk/main.nf b/modules/nf-core/gawk/main.nf new file mode 100644 index 0000000..f856a1f --- /dev/null +++ b/modules/nf-core/gawk/main.nf @@ -0,0 +1,54 @@ +process GAWK { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gawk:5.1.0' : + 'biocontainers/gawk:5.1.0' }" + + input: + tuple val(meta), path(input) + path(program_file) + + output: + tuple val(meta), path("${prefix}.${suffix}"), emit: output + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' // args is used for the main arguments of the tool + def args2 = task.ext.args2 ?: '' // args2 is used to specify a program when no program file has been given + prefix = task.ext.prefix ?: "${meta.id}" + suffix = task.ext.suffix ?: "${input.getExtension()}" + + program = program_file ? "-f ${program_file}" : "${args2}" + + """ + awk \\ + ${args} \\ + ${program} \\ + ${input} \\ + > ${prefix}.${suffix} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gawk: \$(awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//') + END_VERSIONS + """ + + stub: + prefix = task.ext.prefix ?: "${meta.id}" + suffix = task.ext.suffix ?: "${input.getExtension}" + + """ + touch ${prefix}.${suffix} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gawk: \$(awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/gawk/meta.yml b/modules/nf-core/gawk/meta.yml new file mode 100644 index 0000000..2b6033b --- /dev/null +++ b/modules/nf-core/gawk/meta.yml @@ -0,0 +1,50 @@ +name: "gawk" +description: | + If you are like many computer users, you would frequently like to make changes in various text files + wherever certain patterns appear, or extract data from parts of certain lines while discarding the rest. + The job is easy with awk, especially the GNU implementation gawk. +keywords: + - gawk + - awk + - txt + - text + - file parsing +tools: + - "gawk": + description: "GNU awk" + homepage: "https://www.gnu.org/software/gawk/" + documentation: "https://www.gnu.org/software/gawk/manual/" + tool_dev_url: "https://www.gnu.org/prep/ftp.html" + licence: ["GPL v3"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: The input file - Specify the logic that needs to be executed on this file on the `ext.args2` or in the program file + pattern: "*" + - program_file: + type: file + description: Optional file containing logic for awk to execute. If you don't wish to use a file, you can use `ext.args2` to specify the logic. + pattern: "*" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - output: + type: file + description: The output file - specify the name of this file using `ext.prefix` and the extension using `ext.suffix` + pattern: "*" +authors: + - "@nvnieuwk" +maintainers: + - "@nvnieuwk" diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml new file mode 100644 index 0000000..3e95dd7 --- /dev/null +++ b/modules/nf-core/samtools/faidx/environment.yml @@ -0,0 +1,8 @@ +name: samtools_faidx +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.19.2 + - bioconda::htslib=1.19.1 diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf new file mode 100644 index 0000000..cfe7ad9 --- /dev/null +++ b/modules/nf-core/samtools/faidx/main.nf @@ -0,0 +1,50 @@ +process SAMTOOLS_FAIDX { + tag "$fasta" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : + 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" + + input: + tuple val(meta), path(fasta) + tuple val(meta2), path(fai) + + output: + tuple val(meta), path ("*.{fa,fasta}") , emit: fa , optional: true + tuple val(meta), path ("*.fai") , emit: fai, optional: true + tuple val(meta), path ("*.gzi") , emit: gzi, optional: true + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + """ + samtools \\ + faidx \\ + $fasta \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ + + stub: + def match = (task.ext.args =~ /-o(?:utput)?\s(.*)\s?/).findAll() + def fastacmd = match[0] ? "touch ${match[0][1]}" : '' + """ + ${fastacmd} + touch ${fasta}.fai + + cat <<-END_VERSIONS > versions.yml + + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml new file mode 100644 index 0000000..e189af2 --- /dev/null +++ b/modules/nf-core/samtools/faidx/meta.yml @@ -0,0 +1,61 @@ +name: samtools_faidx +description: Index FASTA file +keywords: + - index + - fasta + - faidx +tools: + - samtools: + description: | + SAMtools is a set of utilities for interacting with and post-processing + short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. + These files are generated as output by short read aligners like BWA. + homepage: http://www.htslib.org/ + documentation: http://www.htslib.org/doc/samtools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fa,fasta}" + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fai: + type: file + description: FASTA index file + pattern: "*.{fai}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fai: + type: file + description: FASTA index file + pattern: "*.{fai}" + - gzi: + type: file + description: Optional gzip index file for compressed inputs + pattern: "*.gzi" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@drpatelh" + - "@ewels" + - "@phue" +maintainers: + - "@drpatelh" + - "@ewels" + - "@phue" diff --git a/subworkflows/local/peaks.nf b/subworkflows/local/peaks.nf new file mode 100644 index 0000000..2383659 --- /dev/null +++ b/subworkflows/local/peaks.nf @@ -0,0 +1,36 @@ +// TODO nf-core: If in doubt look at other nf-core/subworkflows to see how we are doing things! :) +// https://github.com/nf-core/modules/tree/master/subworkflows +// You can also ask for help via your pull request or on the #subworkflows channel on the nf-core Slack workspace: +// https://nf-co.re/join +// TODO nf-core: A subworkflow SHOULD import at least two modules + +include { SAMTOOLS_SORT } from '../../../modules/nf-core/samtools/sort/main' +include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main' + +workflow PEAKS { + + take: + // TODO nf-core: edit input (take) channels + ch_bam // channel: [ val(meta), [ bam ] ] + + main: + + ch_versions = Channel.empty() + + // TODO nf-core: substitute modules here for the modules of your subworkflow + + SAMTOOLS_SORT ( ch_bam ) + ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions.first()) + + SAMTOOLS_INDEX ( SAMTOOLS_SORT.out.bam ) + ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) + + emit: + // TODO nf-core: edit emitted channels + bam = SAMTOOLS_SORT.out.bam // channel: [ val(meta), [ bam ] ] + bai = SAMTOOLS_INDEX.out.bai // channel: [ val(meta), [ bai ] ] + csi = SAMTOOLS_INDEX.out.csi // channel: [ val(meta), [ csi ] ] + + versions = ch_versions // channel: [ versions.yml ] +} + diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index af9380d..51c82b6 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -1,4 +1,6 @@ include { ATLASGENEANNOTATIONMANIPULATION_GTF2FEATUREANNOTATION as EXTRACT_ID_SYMBOL_MAP } from '../../modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/main.nf' +include { GAWK as REMOVE_GENE_VERSIONS } from '../../modules/nf-core/gawk/main' +include { SAMTOOLS_FAIDX } from '../../modules/nf-core/samtools/faidx/main' workflow PREPARE_GENOME { @@ -13,14 +15,25 @@ workflow PREPARE_GENOME { ch_fasta = Channel.value([[id: 'fasta'], file(fasta)]) ch_gtf = Channel.value([[id: 'gtf'], file(gtf)]) - // TODO nf-core: substitute modules here for the modules of your subworkflow + // Prepare gene map EXTRACT_ID_SYMBOL_MAP(ch_gtf, [[], []]) - ch_versions = ch_versions.mix(EXTRACT_ID_SYMBOL_MAP.out.versions) + REMOVE_GENE_VERSIONS(EXTRACT_ID_SYMBOL_MAP.out.feature_annotation, []) + + ch_versions = ch_versions.mix( + EXTRACT_ID_SYMBOL_MAP.out.versions, + REMOVE_GENE_VERSIONS.out.versions + ) + + SAMTOOLS_FAIDX(ch_fasta, [[], []]) + + ch_versions = ch_versions.mix( + SAMTOOLS_FAIDX.out.versions + ) emit: - // TODO nf-core: edit emitted channels + gene_map = REMOVE_GENE_VERSIONS.out.output + fai = SAMTOOLS_FAIDX.out.fai versions = ch_versions // channel: [ versions.yml ] } - From 44753f33558d505d7d3217cdb5682d66e308f704 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 1 Mar 2024 11:19:43 +0100 Subject: [PATCH 005/206] Implement sample merging --- README.md | 14 +- assets/samplesheet.csv | 14 +- assets/schema_input.json | 14 +- conf/modules.config | 26 +++ modules.json | 15 ++ .../nf-core/bedtools/merge/environment.yml | 7 + modules/nf-core/bedtools/merge/main.nf | 47 +++++ modules/nf-core/bedtools/merge/meta.yml | 45 +++++ modules/nf-core/bedtools/sort/environment.yml | 7 + modules/nf-core/bedtools/sort/main.nf | 54 ++++++ modules/nf-core/bedtools/sort/meta.yml | 54 ++++++ modules/nf-core/cat/cat/environment.yml | 7 + modules/nf-core/cat/cat/main.nf | 79 ++++++++ modules/nf-core/cat/cat/meta.yml | 36 ++++ modules/nf-core/cat/cat/tests/main.nf.test | 178 ++++++++++++++++++ .../nf-core/cat/cat/tests/main.nf.test.snap | 121 ++++++++++++ .../cat/tests/nextflow_unzipped_zipped.config | 6 + .../cat/tests/nextflow_zipped_unzipped.config | 8 + modules/nf-core/cat/cat/tests/tags.yml | 2 + nextflow.config | 5 + nextflow_schema.json | 24 +++ subworkflows/local/merge_samples.nf | 45 +++++ subworkflows/local/peaks.nf | 35 ++-- .../utils_nfcore_tfactivity_pipeline/main.nf | 2 - workflows/tfactivity.nf | 6 +- 25 files changed, 810 insertions(+), 41 deletions(-) create mode 100644 modules/nf-core/bedtools/merge/environment.yml create mode 100644 modules/nf-core/bedtools/merge/main.nf create mode 100644 modules/nf-core/bedtools/merge/meta.yml create mode 100644 modules/nf-core/bedtools/sort/environment.yml create mode 100644 modules/nf-core/bedtools/sort/main.nf create mode 100644 modules/nf-core/bedtools/sort/meta.yml create mode 100644 modules/nf-core/cat/cat/environment.yml create mode 100644 modules/nf-core/cat/cat/main.nf create mode 100644 modules/nf-core/cat/cat/meta.yml create mode 100644 modules/nf-core/cat/cat/tests/main.nf.test create mode 100644 modules/nf-core/cat/cat/tests/main.nf.test.snap create mode 100644 modules/nf-core/cat/cat/tests/nextflow_unzipped_zipped.config create mode 100644 modules/nf-core/cat/cat/tests/nextflow_zipped_unzipped.config create mode 100644 modules/nf-core/cat/cat/tests/tags.yml create mode 100644 subworkflows/local/merge_samples.nf diff --git a/README.md b/README.md index 348c49f..9408d37 100644 --- a/README.md +++ b/README.md @@ -47,13 +47,13 @@ First, prepare a samplesheet with your input data that looks as follows: `samplesheet.csv`: ```csv -state,assay,peak_file -condition1,H3K27ac,condition1_H3K27ac_1.broadPeak -condition1,H3K27ac,condition1_H3K27ac_2.broadPeak -condition1,H3K4me3,condition1_H3K4me3.broadPeak -condition2,H3K27ac,condition2_H3K27ac.broadPeak -condition3,H3K27ac,condition3_H3K27ac.broadPeak -condition3,H3K4me3,condition3_H3K4me3.broadPeak +sample,condition,assay,peak_file +condition1_H3K27ac_1,condition1,H3K27ac,condition1_H3K27ac_1.broadPeak +condition1_H3K27ac_2,condition1,H3K27ac,condition1_H3K27ac_2.broadPeak +condition1_H3K4me3,condition1,H3K4me3,condition1_H3K4me3.broadPeak +condition2_H3K27ac,condition2,H3K27ac,condition2_H3K27ac.broadPeak +condition3_H3K27ac,condition3,H3K27ac,condition3_H3K27ac.broadPeak +condition3_H3K4me3,condition3,H3K4me3,condition3_H3K4me3.broadPeak ``` Each row represents a fastq file (single-end) or a pair of fastq files (paired end). diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv index adade57..b220117 100644 --- a/assets/samplesheet.csv +++ b/assets/samplesheet.csv @@ -1,7 +1,7 @@ -state,assay,peak_file -condition1,H3K27ac,condition1_H3K27ac_1.broadPeak -condition1,H3K27ac,condition1_H3K27ac_2.broadPeak -condition1,H3K4me3,condition1_H3K4me3.broadPeak -condition2,H3K27ac,condition2_H3K27ac.broadPeak -condition3,H3K27ac,condition3_H3K27ac.broadPeak -condition3,H3K4me3,condition3_H3K4me3.broadPeak +sample,condition,assay,peak_file +condition1_H3K27ac_1,condition1,H3K27ac,condition1_H3K27ac_1.broadPeak +condition1_H3K27ac_2,condition1,H3K27ac,condition1_H3K27ac_2.broadPeak +condition1_H3K4me3,condition1,H3K4me3,condition1_H3K4me3.broadPeak +condition2_H3K27ac,condition2,H3K27ac,condition2_H3K27ac.broadPeak +condition3_H3K27ac,condition3,H3K27ac,condition3_H3K27ac.broadPeak +condition3_H3K4me3,condition3,H3K4me3,condition3_H3K4me3.broadPeak diff --git a/assets/schema_input.json b/assets/schema_input.json index 859aae9..8e0a9a5 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -7,11 +7,17 @@ "items": { "type": "object", "properties": { - "state": { + "sample": { "type": "string", "pattern": "^\\S+$", - "errorMessage": "State name must be provided and cannot contain spaces", - "meta": ["state"] + "errorMessage": "Sample name must be provided and cannot contain spaces", + "meta": ["id"] + }, + "condition": { + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "Condition name must be provided and cannot contain spaces", + "meta": ["condition"] }, "assay": { "type": "string", @@ -27,6 +33,6 @@ "errorMessage": "Peak file must be provided and must be a .bed or .broadPeak file", } }, - "required": ["state", "assay", "peak_file"] + "required": ["sample", "condition", "assay", "peak_file"] } } diff --git a/conf/modules.config b/conf/modules.config index e083246..f636cdf 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -28,6 +28,32 @@ process { ext.suffix = "tsv" } + withName: CLEAN_BED { + ext.args = {"'{print \$1 \"\\t\" \$2 \"\\t\" \$3}'"} + ext.prefix = {"${meta.id}.clean"} + ext.suffix = "bed" + } + + withName: BEDTOOLS_SORT { + ext.prefix = {"${meta.id}.sorted"} + } + + withName: BEDTOOLS_MERGE { + ext.prefix = {"${meta.id}.merged"} + } + + withName: ANNOTATE_SAMPLES { + ext.args = {"'{print \$0 \"\\t\" \"${meta.id}\"}'"} + } + + withName: CONCAT_SAMPLES { + ext.prefix = {"${meta.id}.concatenated"} + } + + withName: FILTER_MIN_OCCURRENCE { + ext.args = "'\$NF >= ${params.min_peak_occurrence}'" + } + withName: CUSTOM_DUMPSOFTWAREVERSIONS { publishDir = [ path: { "${params.outdir}/pipeline_info" }, diff --git a/modules.json b/modules.json index a731299..e93dd73 100644 --- a/modules.json +++ b/modules.json @@ -10,6 +10,21 @@ "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, + "bedtools/merge": { + "branch": "master", + "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83", + "installed_by": ["modules"] + }, + "bedtools/sort": { + "branch": "master", + "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83", + "installed_by": ["modules"] + }, + "cat/cat": { + "branch": "master", + "git_sha": "9437e6053dccf4aafa022bfd6e7e9de67e625af8", + "installed_by": ["modules"] + }, "fastqc": { "branch": "master", "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c", diff --git a/modules/nf-core/bedtools/merge/environment.yml b/modules/nf-core/bedtools/merge/environment.yml new file mode 100644 index 0000000..9970787 --- /dev/null +++ b/modules/nf-core/bedtools/merge/environment.yml @@ -0,0 +1,7 @@ +name: bedtools_merge +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/merge/main.nf b/modules/nf-core/bedtools/merge/main.nf new file mode 100644 index 0000000..5310647 --- /dev/null +++ b/modules/nf-core/bedtools/merge/main.nf @@ -0,0 +1,47 @@ +process BEDTOOLS_MERGE { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bedtools:2.31.1--hf5e1c6e_0' : + 'biocontainers/bedtools:2.31.1--hf5e1c6e_0' }" + + input: + tuple val(meta), path(bed) + + output: + tuple val(meta), path('*.bed'), emit: bed + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + if ("$bed" == "${prefix}.bed") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + bedtools \\ + merge \\ + -i $bed \\ + $args \\ + > ${prefix}.bed + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.bed + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS + """ +} diff --git a/modules/nf-core/bedtools/merge/meta.yml b/modules/nf-core/bedtools/merge/meta.yml new file mode 100644 index 0000000..d7463e3 --- /dev/null +++ b/modules/nf-core/bedtools/merge/meta.yml @@ -0,0 +1,45 @@ +name: bedtools_merge +description: combines overlapping or “book-ended” features in an interval file into a single feature which spans all of the combined features. +keywords: + - bed + - merge + - bedtools + - overlapped bed +tools: + - bedtools: + description: | + A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. + documentation: https://bedtools.readthedocs.io/en/latest/content/tools/merge.html + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Input BED file + pattern: "*.{bed}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Overlapped bed file with combined features + pattern: "*.{bed}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@edmundmiller" + - "@sruthipsuresh" + - "@drpatelh" +maintainers: + - "@edmundmiller" + - "@sruthipsuresh" + - "@drpatelh" diff --git a/modules/nf-core/bedtools/sort/environment.yml b/modules/nf-core/bedtools/sort/environment.yml new file mode 100644 index 0000000..87b2e42 --- /dev/null +++ b/modules/nf-core/bedtools/sort/environment.yml @@ -0,0 +1,7 @@ +name: bedtools_sort +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/sort/main.nf b/modules/nf-core/bedtools/sort/main.nf new file mode 100644 index 0000000..b833150 --- /dev/null +++ b/modules/nf-core/bedtools/sort/main.nf @@ -0,0 +1,54 @@ +process BEDTOOLS_SORT { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bedtools:2.31.1--hf5e1c6e_0' : + 'biocontainers/bedtools:2.31.1--hf5e1c6e_0' }" + + input: + tuple val(meta), path(intervals) + path genome_file + + output: + tuple val(meta), path("*.${extension}"), emit: sorted + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def genome_cmd = genome_file ? "-g $genome_file" : "" + extension = task.ext.suffix ?: intervals.extension + if ("$intervals" == "${prefix}.${extension}") { + error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + } + """ + bedtools \\ + sort \\ + -i $intervals \\ + $genome_cmd \\ + $args \\ + > ${prefix}.${extension} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + extension = task.ext.suffix ?: intervals.extension + """ + touch ${prefix}.${extension} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS + """ +} diff --git a/modules/nf-core/bedtools/sort/meta.yml b/modules/nf-core/bedtools/sort/meta.yml new file mode 100644 index 0000000..7c915f5 --- /dev/null +++ b/modules/nf-core/bedtools/sort/meta.yml @@ -0,0 +1,54 @@ +name: bedtools_sort +description: Sorts a feature file by chromosome and other criteria. +keywords: + - bed + - sort + - bedtools + - chromosome +tools: + - bedtools: + description: | + A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. + documentation: https://bedtools.readthedocs.io/en/latest/content/tools/sort.html + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intervals: + type: file + description: BED/BEDGRAPH + pattern: "*.{bed|bedGraph}" + - genome_file: + type: file + description: | + Optional reference genome 2 column file that defines the expected chromosome order. + pattern: "*.{fai,txt,chromsizes}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sorted: + type: file + description: Sorted output file + pattern: "*.${extension}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@edmundmiller" + - "@sruthipsuresh" + - "@drpatelh" + - "@chris-cheshire" + - "@adamrtalbot" +maintainers: + - "@edmundmiller" + - "@sruthipsuresh" + - "@drpatelh" + - "@chris-cheshire" + - "@adamrtalbot" diff --git a/modules/nf-core/cat/cat/environment.yml b/modules/nf-core/cat/cat/environment.yml new file mode 100644 index 0000000..17a04ef --- /dev/null +++ b/modules/nf-core/cat/cat/environment.yml @@ -0,0 +1,7 @@ +name: cat_cat +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::pigz=2.3.4 diff --git a/modules/nf-core/cat/cat/main.nf b/modules/nf-core/cat/cat/main.nf new file mode 100644 index 0000000..adbdbd7 --- /dev/null +++ b/modules/nf-core/cat/cat/main.nf @@ -0,0 +1,79 @@ +process CAT_CAT { + tag "$meta.id" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pigz:2.3.4' : + 'biocontainers/pigz:2.3.4' }" + + input: + tuple val(meta), path(files_in) + + output: + tuple val(meta), path("${prefix}"), emit: file_out + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + def file_list = files_in.collect { it.toString() } + + // choose appropriate concatenation tool depending on input and output format + + // | input | output | command1 | command2 | + // |-----------|------------|----------|----------| + // | gzipped | gzipped | cat | | + // | ungzipped | ungzipped | cat | | + // | gzipped | ungzipped | zcat | | + // | ungzipped | gzipped | cat | pigz | + + // Use input file ending as default + prefix = task.ext.prefix ?: "${meta.id}${getFileSuffix(file_list[0])}" + out_zip = prefix.endsWith('.gz') + in_zip = file_list[0].endsWith('.gz') + command1 = (in_zip && !out_zip) ? 'zcat' : 'cat' + command2 = (!in_zip && out_zip) ? "| pigz -c -p $task.cpus $args2" : '' + if(file_list.contains(prefix.trim())) { + error "The name of the input file can't be the same as for the output prefix in the " + + "module CAT_CAT (currently `$prefix`). Please choose a different one." + } + """ + $command1 \\ + $args \\ + ${file_list.join(' ')} \\ + $command2 \\ + > ${prefix} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' ) + END_VERSIONS + """ + + stub: + def file_list = files_in.collect { it.toString() } + prefix = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}" + if(file_list.contains(prefix.trim())) { + error "The name of the input file can't be the same as for the output prefix in the " + + "module CAT_CAT (currently `$prefix`). Please choose a different one." + } + """ + touch $prefix + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' ) + END_VERSIONS + """ +} + +// for .gz files also include the second to last extension if it is present. E.g., .fasta.gz +def getFileSuffix(filename) { + def match = filename =~ /^.*?((\.\w{1,5})?(\.\w{1,5}\.gz$))/ + return match ? match[0][1] : filename.substring(filename.lastIndexOf('.')) +} + diff --git a/modules/nf-core/cat/cat/meta.yml b/modules/nf-core/cat/cat/meta.yml new file mode 100644 index 0000000..00a8db0 --- /dev/null +++ b/modules/nf-core/cat/cat/meta.yml @@ -0,0 +1,36 @@ +name: cat_cat +description: A module for concatenation of gzipped or uncompressed files +keywords: + - concatenate + - gzip + - cat +tools: + - cat: + description: Just concatenation + documentation: https://man7.org/linux/man-pages/man1/cat.1.html + licence: ["GPL-3.0-or-later"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - files_in: + type: file + description: List of compressed / uncompressed files + pattern: "*" +output: + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - file_out: + type: file + description: Concatenated file. Will be gzipped if file_out ends with ".gz" + pattern: "${file_out}" +authors: + - "@erikrikarddaniel" + - "@FriederikeHanssen" +maintainers: + - "@erikrikarddaniel" + - "@FriederikeHanssen" diff --git a/modules/nf-core/cat/cat/tests/main.nf.test b/modules/nf-core/cat/cat/tests/main.nf.test new file mode 100644 index 0000000..fcee2d1 --- /dev/null +++ b/modules/nf-core/cat/cat/tests/main.nf.test @@ -0,0 +1,178 @@ +nextflow_process { + + name "Test Process CAT_CAT" + script "../main.nf" + process "CAT_CAT" + tag "modules" + tag "modules_nfcore" + tag "cat" + tag "cat/cat" + + test("test_cat_name_conflict") { + when { + params { + outdir = "${outputDir}" + } + process { + """ + input[0] = + [ + [ id:'genome', single_end:true ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true) + ] + ] + """ + } + } + then { + assertAll( + { assert !process.success }, + { assert process.stdout.toString().contains("The name of the input file can't be the same as for the output prefix") } + ) + } + } + + test("test_cat_unzipped_unzipped") { + when { + params { + outdir = "${outputDir}" + } + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true) + ] + ] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + + test("test_cat_zipped_zipped") { + when { + params { + outdir = "${outputDir}" + } + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) + ] + ] + """ + } + } + then { + def lines = path(process.out.file_out.get(0).get(1)).linesGzip + assertAll( + { assert process.success }, + { assert snapshot(lines[0..5]).match("test_cat_zipped_zipped_lines") }, + { assert snapshot(lines.size()).match("test_cat_zipped_zipped_size")} + ) + } + } + + test("test_cat_zipped_unzipped") { + config './nextflow_zipped_unzipped.config' + + when { + params { + outdir = "${outputDir}" + } + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("test_cat_unzipped_zipped") { + config './nextflow_unzipped_zipped.config' + when { + params { + outdir = "${outputDir}" + } + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true) + ] + ] + """ + } + } + then { + def lines = path(process.out.file_out.get(0).get(1)).linesGzip + assertAll( + { assert process.success }, + { assert snapshot(lines[0..5]).match("test_cat_unzipped_zipped_lines") }, + { assert snapshot(lines.size()).match("test_cat_unzipped_zipped_size")} + ) + } + } + + test("test_cat_one_file_unzipped_zipped") { + config './nextflow_unzipped_zipped.config' + when { + params { + outdir = "${outputDir}" + } + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + ] + """ + } + } + then { + def lines = path(process.out.file_out.get(0).get(1)).linesGzip + assertAll( + { assert process.success }, + { assert snapshot(lines[0..5]).match("test_cat_one_file_unzipped_zipped_lines") }, + { assert snapshot(lines.size()).match("test_cat_one_file_unzipped_zipped_size")} + ) + } + } +} diff --git a/modules/nf-core/cat/cat/tests/main.nf.test.snap b/modules/nf-core/cat/cat/tests/main.nf.test.snap new file mode 100644 index 0000000..423571b --- /dev/null +++ b/modules/nf-core/cat/cat/tests/main.nf.test.snap @@ -0,0 +1,121 @@ +{ + "test_cat_unzipped_zipped_size": { + "content": [ + 375 + ], + "timestamp": "2023-10-16T14:33:08.049445686" + }, + "test_cat_unzipped_unzipped": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.fasta:md5,f44b33a0e441ad58b2d3700270e2dbe2" + ] + ], + "1": [ + "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" + ], + "file_out": [ + [ + { + "id": "test", + "single_end": true + }, + "test.fasta:md5,f44b33a0e441ad58b2d3700270e2dbe2" + ] + ], + "versions": [ + "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" + ] + } + ], + "timestamp": "2023-10-16T14:32:18.500464399" + }, + "test_cat_zipped_unzipped": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "cat.txt:md5,c439d3b60e7bc03e8802a451a0d9a5d9" + ] + ], + "1": [ + "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" + ], + "file_out": [ + [ + { + "id": "test", + "single_end": true + }, + "cat.txt:md5,c439d3b60e7bc03e8802a451a0d9a5d9" + ] + ], + "versions": [ + "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" + ] + } + ], + "timestamp": "2023-10-16T14:32:49.642741302" + }, + "test_cat_zipped_zipped_lines": { + "content": [ + [ + "MT192765.1\tGenbank\ttranscript\t259\t29667\t.\t+\t.\tID=unknown_transcript_1;geneID=orf1ab;gene_name=orf1ab", + "MT192765.1\tGenbank\tgene\t259\t21548\t.\t+\t.\tParent=unknown_transcript_1", + "MT192765.1\tGenbank\tCDS\t259\t13461\t.\t+\t0\tParent=unknown_transcript_1;exception=\"ribosomal slippage\";gbkey=CDS;gene=orf1ab;note=\"pp1ab;translated=by -1 ribosomal frameshift\";product=\"orf1ab polyprotein\";protein_id=QIK50426.1", + "MT192765.1\tGenbank\tCDS\t13461\t21548\t.\t+\t0\tParent=unknown_transcript_1;exception=\"ribosomal slippage\";gbkey=CDS;gene=orf1ab;note=\"pp1ab;translated=by -1 ribosomal frameshift\";product=\"orf1ab polyprotein\";protein_id=QIK50426.1", + "MT192765.1\tGenbank\tCDS\t21556\t25377\t.\t+\t0\tParent=unknown_transcript_1;gbkey=CDS;gene=S;note=\"structural protein\";product=\"surface glycoprotein\";protein_id=QIK50427.1", + "MT192765.1\tGenbank\tgene\t21556\t25377\t.\t+\t.\tParent=unknown_transcript_1" + ] + ], + "timestamp": "2023-10-16T14:32:33.629048645" + }, + "test_cat_unzipped_zipped_lines": { + "content": [ + [ + ">MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/PC00101P/2020, complete genome", + "GTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGT", + "GTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAG", + "TAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGG", + "GTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTT", + "ACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAG" + ] + ], + "timestamp": "2023-10-16T14:33:08.038830506" + }, + "test_cat_one_file_unzipped_zipped_lines": { + "content": [ + [ + ">MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/PC00101P/2020, complete genome", + "GTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGT", + "GTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAG", + "TAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGG", + "GTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTT", + "ACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAG" + ] + ], + "timestamp": "2023-10-16T14:33:21.39642399" + }, + "test_cat_zipped_zipped_size": { + "content": [ + 78 + ], + "timestamp": "2023-10-16T14:32:33.641869244" + }, + "test_cat_one_file_unzipped_zipped_size": { + "content": [ + 374 + ], + "timestamp": "2023-10-16T14:33:21.4094373" + } +} \ No newline at end of file diff --git a/modules/nf-core/cat/cat/tests/nextflow_unzipped_zipped.config b/modules/nf-core/cat/cat/tests/nextflow_unzipped_zipped.config new file mode 100644 index 0000000..ec26b0f --- /dev/null +++ b/modules/nf-core/cat/cat/tests/nextflow_unzipped_zipped.config @@ -0,0 +1,6 @@ + +process { + withName: CAT_CAT { + ext.prefix = 'cat.txt.gz' + } +} diff --git a/modules/nf-core/cat/cat/tests/nextflow_zipped_unzipped.config b/modules/nf-core/cat/cat/tests/nextflow_zipped_unzipped.config new file mode 100644 index 0000000..fbc7978 --- /dev/null +++ b/modules/nf-core/cat/cat/tests/nextflow_zipped_unzipped.config @@ -0,0 +1,8 @@ + +process { + + withName: CAT_CAT { + ext.prefix = 'cat.txt' + } + +} diff --git a/modules/nf-core/cat/cat/tests/tags.yml b/modules/nf-core/cat/cat/tests/tags.yml new file mode 100644 index 0000000..37b578f --- /dev/null +++ b/modules/nf-core/cat/cat/tests/tags.yml @@ -0,0 +1,2 @@ +cat/cat: + - modules/nf-core/cat/cat/** diff --git a/nextflow.config b/nextflow.config index a242ea3..7560eea 100644 --- a/nextflow.config +++ b/nextflow.config @@ -12,6 +12,11 @@ params { // TODO nf-core: Specify your pipeline's command line flags // Input options input = null + + // Pipeline options + merge_samples = false + min_peak_occurrence = 1 + // References genome = null igenomes_base = 's3://ngi-igenomes/igenomes/' diff --git a/nextflow_schema.json b/nextflow_schema.json index 22b3e1f..574f41d 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -43,6 +43,27 @@ } } }, + "pipeline_options": { + "title": "Pipeline options", + "type": "object", + "fa_icon": "fas fa-cogs", + "description": "Options for the pipeline itself.", + "properties": { + "merge_samples": { + "type": "boolean", + "description": "Merge samples with the same condition and assay.", + "fa_icon": "fas fa-compress-arrows-alt", + "help_text": "If you have multiple samples with the same condition and assay, you can set this parameter to `true` to merge them into a single sample. This is useful if you have technical replicates and want to combine them into a single sample for analysis." + }, + "min_peak_occurrence": { + "type": "integer", + "default": 1, + "description": "Minimum number of samples that a peak has to occur in to keep it while merging.", + "fa_icon": "fas fa-compress-arrows-alt", + "help_text": "If you have multiple samples with the same condition and assay and use the `--merge_samples` parameter, you can set this parameter to the minimum number of samples that a peak has to occur in to keep it while merging." + } + } + }, "reference_genome_options": { "title": "Reference genome options", "type": "object", @@ -283,6 +304,9 @@ { "$ref": "#/definitions/input_output_options" }, + { + "$ref": "#/definitions/pipeline_options" + }, { "$ref": "#/definitions/reference_genome_options" }, diff --git a/subworkflows/local/merge_samples.nf b/subworkflows/local/merge_samples.nf new file mode 100644 index 0000000..60044bf --- /dev/null +++ b/subworkflows/local/merge_samples.nf @@ -0,0 +1,45 @@ +include { GAWK as ANNOTATE_SAMPLES } from '../../modules/nf-core/gawk/main' +include { CAT_CAT as CONCAT_SAMPLES } from '../../modules/nf-core/cat/cat/main' +include { BEDTOOLS_SORT } from '../../modules/nf-core/bedtools/sort/main' +include { BEDTOOLS_MERGE } from '../../modules/nf-core/bedtools/merge/main' +include { GAWK as FILTER_MIN_OCCURRENCE } from '../../modules/nf-core/gawk/main' +include { GAWK as CLEAN_BED } from '../../modules/nf-core/gawk/main' + +workflow MERGE_SAMPLES { + + take: + ch_peaks + + main: + + ch_versions = Channel.empty() + + ANNOTATE_SAMPLES(ch_peaks, []) + + ch_grouped = ANNOTATE_SAMPLES.out.output + .map{ meta, peak_file -> [meta + [id: meta.condition + "_" + meta.assay], peak_file]} + .groupTuple() + + // ch_grouped.view() + + CONCAT_SAMPLES(ch_grouped) + BEDTOOLS_SORT(CONCAT_SAMPLES.out.file_out, []) + BEDTOOLS_MERGE(BEDTOOLS_SORT.out.sorted) + FILTER_MIN_OCCURRENCE(BEDTOOLS_MERGE.out.bed, []) + CLEAN_BED(FILTER_MIN_OCCURRENCE.out.output, []) + + ch_versions = ch_versions.mix( + ANNOTATE_SAMPLES.out.versions, + CONCAT_SAMPLES.out.versions, + BEDTOOLS_SORT.out.versions, + BEDTOOLS_MERGE.out.versions, + FILTER_MIN_OCCURRENCE.out.versions, + CLEAN_BED.out.versions + ) + + emit: + merged = CLEAN_BED.out.output + + versions = ch_versions // channel: [ versions.yml ] +} + diff --git a/subworkflows/local/peaks.nf b/subworkflows/local/peaks.nf index 2383659..51b8d35 100644 --- a/subworkflows/local/peaks.nf +++ b/subworkflows/local/peaks.nf @@ -1,36 +1,31 @@ -// TODO nf-core: If in doubt look at other nf-core/subworkflows to see how we are doing things! :) -// https://github.com/nf-core/modules/tree/master/subworkflows -// You can also ask for help via your pull request or on the #subworkflows channel on the nf-core Slack workspace: -// https://nf-co.re/join -// TODO nf-core: A subworkflow SHOULD import at least two modules +// Modules +include { GAWK as CLEAN_BED } from '../../modules/nf-core/gawk/main' +include { BEDTOOLS_SORT as SORT_PEAKS } from '../../modules/nf-core/bedtools/sort/main' -include { SAMTOOLS_SORT } from '../../../modules/nf-core/samtools/sort/main' -include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main' +// Subworkflows +include { MERGE_SAMPLES as MERGE_SAMPLES } from './merge_samples' workflow PEAKS { take: - // TODO nf-core: edit input (take) channels - ch_bam // channel: [ val(meta), [ bam ] ] + ch_peaks // channel: [ val(meta), [ peaks ] ] + merge_samples main: ch_versions = Channel.empty() - // TODO nf-core: substitute modules here for the modules of your subworkflow + CLEAN_BED(ch_peaks, []) - SAMTOOLS_SORT ( ch_bam ) - ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions.first()) - - SAMTOOLS_INDEX ( SAMTOOLS_SORT.out.bam ) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) + if (merge_samples) { + MERGE_SAMPLES(CLEAN_BED.out.output) + ch_peaks = MERGE_SAMPLES.out.merged + } else { + SORT_PEAKS(CLEAN_BED.out.output, []) + ch_peaks = SORT_PEAKS.out.sorted + } emit: - // TODO nf-core: edit emitted channels - bam = SAMTOOLS_SORT.out.bam // channel: [ val(meta), [ bam ] ] - bai = SAMTOOLS_INDEX.out.bai // channel: [ val(meta), [ bai ] ] - csi = SAMTOOLS_INDEX.out.csi // channel: [ val(meta), [ csi ] ] versions = ch_versions // channel: [ versions.yml ] } - diff --git a/subworkflows/local/utils_nfcore_tfactivity_pipeline/main.nf b/subworkflows/local/utils_nfcore_tfactivity_pipeline/main.nf index 0cf8ae7..32ee9f9 100644 --- a/subworkflows/local/utils_nfcore_tfactivity_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_tfactivity_pipeline/main.nf @@ -82,8 +82,6 @@ workflow PIPELINE_INITIALISATION { // Channel .fromSamplesheet("input") - .map { meta, peak_file -> [ [id: meta.state + "_" + meta.assay] + meta, peak_file]} - .groupTuple() .map { validateInputSamplesheet(it) } diff --git a/workflows/tfactivity.nf b/workflows/tfactivity.nf index 69ca982..40da7b2 100644 --- a/workflows/tfactivity.nf +++ b/workflows/tfactivity.nf @@ -11,6 +11,7 @@ include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pi include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_tfactivity_pipeline' include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome' +include { PEAKS } from '../subworkflows/local/peaks' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -23,7 +24,6 @@ workflow TFACTIVITY { take: ch_samplesheet // channel: samplesheet read in from --input - main: ch_versions = Channel.empty() @@ -31,6 +31,10 @@ workflow TFACTIVITY { // ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}) // ch_versions = ch_versions.mix(FASTQC.out.versions.first()) + PEAKS( + ch_samplesheet, + params.merge_samples + ) // // Collate and save software versions From c7cbc9104b3a89874932db73c7e63d98dca98239 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 1 Mar 2024 11:24:33 +0100 Subject: [PATCH 006/206] Improve version capture --- main.nf | 7 ++++++- subworkflows/local/peaks.nf | 2 ++ workflows/tfactivity.nf | 4 +++- 3 files changed, 11 insertions(+), 2 deletions(-) diff --git a/main.nf b/main.nf index 7ccf8e2..1ca4f13 100644 --- a/main.nf +++ b/main.nf @@ -49,6 +49,8 @@ workflow NFCORE_TFACTIVITY { main: + ch_versions = Channel.empty() + // // SUBWORKFLOW: Prepare genome // @@ -57,11 +59,14 @@ workflow NFCORE_TFACTIVITY { params.gtf ) + ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions) + // // WORKFLOW: Run pipeline // TFACTIVITY ( - samplesheet + samplesheet, + ch_versions ) emit: diff --git a/subworkflows/local/peaks.nf b/subworkflows/local/peaks.nf index 51b8d35..431c2c2 100644 --- a/subworkflows/local/peaks.nf +++ b/subworkflows/local/peaks.nf @@ -20,9 +20,11 @@ workflow PEAKS { if (merge_samples) { MERGE_SAMPLES(CLEAN_BED.out.output) ch_peaks = MERGE_SAMPLES.out.merged + ch_versions = ch_versions.mix(MERGE_SAMPLES.out.versions) } else { SORT_PEAKS(CLEAN_BED.out.output, []) ch_peaks = SORT_PEAKS.out.sorted + ch_versions = ch_versions.mix(SORT_PEAKS.out.versions) } emit: diff --git a/workflows/tfactivity.nf b/workflows/tfactivity.nf index 40da7b2..fbb27d0 100644 --- a/workflows/tfactivity.nf +++ b/workflows/tfactivity.nf @@ -23,10 +23,10 @@ workflow TFACTIVITY { take: ch_samplesheet // channel: samplesheet read in from --input + ch_versions main: - ch_versions = Channel.empty() // ch_multiqc_files = Channel.empty() // ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}) @@ -36,6 +36,8 @@ workflow TFACTIVITY { params.merge_samples ) + ch_versions = ch_versions.mix(PEAKS.out.versions) + // // Collate and save software versions // From ed8138b895b97f40a664389f2969148a292eca5e Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 1 Mar 2024 19:20:38 +0100 Subject: [PATCH 007/206] Add footprinting samplesheet params --- assets/schema_input.json | 19 +++++++++++++++++++ .../utils_nfcore_tfactivity_pipeline/main.nf | 9 ++++----- 2 files changed, 23 insertions(+), 5 deletions(-) diff --git a/assets/schema_input.json b/assets/schema_input.json index 8e0a9a5..3289929 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -31,6 +31,25 @@ "exists": true, "pattern": "^\\S+\\.(bed|broadPeak)$", "errorMessage": "Peak file must be provided and must be a .bed or .broadPeak file", + }, + "footprints": { + "type": "boolean", + "default": true, + "errorMessage": "footprints must be a boolean value", + "meta": ["footprints"] + }, + "include_original": { + "type": "boolean", + "default": true, + "errorMessage": "include_original must be a boolean value", + "meta": ["include_original"] + }, + "max_peak_gap": { + "type": "integer", + "default": 500, + "minimum": 0, + "errorMessage": "max_peak_gap must be a positive integer", + "meta": ["max_peak_gap"] } }, "required": ["sample", "condition", "assay", "peak_file"] diff --git a/subworkflows/local/utils_nfcore_tfactivity_pipeline/main.nf b/subworkflows/local/utils_nfcore_tfactivity_pipeline/main.nf index 32ee9f9..f754108 100644 --- a/subworkflows/local/utils_nfcore_tfactivity_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_tfactivity_pipeline/main.nf @@ -147,11 +147,10 @@ def validateInputParameters() { def validateInputSamplesheet(input) { def (meta, peak_files) = input[0..1] - // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end - // def endedness_ok = metas.collect{ it.single_end }.unique().size == 1 - // if (!endedness_ok) { - // error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}") - // } + // Check that include_original is only set to false if footprinting is enabled + if ( !meta.footprinting && !meta.include_original ) { + error("The 'include_original' parameter can only be set to 'false' if 'footprinting' is enabled.") + } return [ meta, peak_files ] } From 42d1969cf96bba56bd9d5f322a1ab0791ef58984 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 1 Mar 2024 19:52:54 +0100 Subject: [PATCH 008/206] Implement footprinting --- assets/schema_input.json | 6 +-- conf/modules.config | 5 ++ modules.json | 5 ++ .../nf-core/bedtools/subtract/environment.yml | 7 +++ modules/nf-core/bedtools/subtract/main.nf | 50 +++++++++++++++++++ modules/nf-core/bedtools/subtract/meta.yml | 45 +++++++++++++++++ subworkflows/local/footprinting.nf | 46 +++++++++++++++++ subworkflows/local/peaks.nf | 13 +++-- 8 files changed, 171 insertions(+), 6 deletions(-) create mode 100644 modules/nf-core/bedtools/subtract/environment.yml create mode 100644 modules/nf-core/bedtools/subtract/main.nf create mode 100644 modules/nf-core/bedtools/subtract/meta.yml create mode 100644 subworkflows/local/footprinting.nf diff --git a/assets/schema_input.json b/assets/schema_input.json index 3289929..e94c015 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -32,11 +32,11 @@ "pattern": "^\\S+\\.(bed|broadPeak)$", "errorMessage": "Peak file must be provided and must be a .bed or .broadPeak file", }, - "footprints": { + "footprinting": { "type": "boolean", "default": true, - "errorMessage": "footprints must be a boolean value", - "meta": ["footprints"] + "errorMessage": "footprinting must be a boolean value", + "meta": ["footprinting"] }, "include_original": { "type": "boolean", diff --git a/conf/modules.config b/conf/modules.config index f636cdf..0a1733b 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -54,6 +54,11 @@ process { ext.args = "'\$NF >= ${params.min_peak_occurrence}'" } + withName: ".*:FOOTPRINTING:BEDTOOLS_MERGE" { + ext.args = {"-d ${meta.max_peak_gap}"} + ext.prefix = {"${meta.id}.merged"} + } + withName: CUSTOM_DUMPSOFTWAREVERSIONS { publishDir = [ path: { "${params.outdir}/pipeline_info" }, diff --git a/modules.json b/modules.json index e93dd73..ecf7fca 100644 --- a/modules.json +++ b/modules.json @@ -20,6 +20,11 @@ "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83", "installed_by": ["modules"] }, + "bedtools/subtract": { + "branch": "master", + "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668", + "installed_by": ["modules"] + }, "cat/cat": { "branch": "master", "git_sha": "9437e6053dccf4aafa022bfd6e7e9de67e625af8", diff --git a/modules/nf-core/bedtools/subtract/environment.yml b/modules/nf-core/bedtools/subtract/environment.yml new file mode 100644 index 0000000..083ba61 --- /dev/null +++ b/modules/nf-core/bedtools/subtract/environment.yml @@ -0,0 +1,7 @@ +name: bedtools_subtract +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/subtract/main.nf b/modules/nf-core/bedtools/subtract/main.nf new file mode 100644 index 0000000..c080844 --- /dev/null +++ b/modules/nf-core/bedtools/subtract/main.nf @@ -0,0 +1,50 @@ +process BEDTOOLS_SUBTRACT { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bedtools:2.31.1--hf5e1c6e_0' : + 'biocontainers/bedtools:2.31.1--hf5e1c6e_0' }" + + input: + tuple val(meta), path(intervals1), path(intervals2) + + output: + tuple val(meta), path("*.bed"), emit: bed + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + if ("$intervals1" == "${prefix}.bed" || + "$intervals2" == "${prefix}.bed") + error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + bedtools \\ + subtract \\ + -a $intervals1 \\ + -b $intervals2 \\ + $args \\ + > ${prefix}.bed + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.bed + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS + """ +} diff --git a/modules/nf-core/bedtools/subtract/meta.yml b/modules/nf-core/bedtools/subtract/meta.yml new file mode 100644 index 0000000..0226ff1 --- /dev/null +++ b/modules/nf-core/bedtools/subtract/meta.yml @@ -0,0 +1,45 @@ +name: bedtools_subtract +description: Finds overlaps between two sets of regions (A and B), removes the overlaps from A and reports the remaining portion of A. +keywords: + - bed + - gff + - vcf + - subtract +tools: + - bedtools: + description: | + A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. + documentation: https://bedtools.readthedocs.io/en/latest/content/tools/subtract.html + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intervals1: + type: file + description: BED/GFF/VCF + pattern: "*.{bed|gff|vcf}" + - intervals2: + type: file + description: BED/GFF/VCF + pattern: "*.{bed|gff|vcf}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: File containing the difference between the two sets of features + patters: "*.bed" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@sidorov-si" +maintainers: + - "@sidorov-si" diff --git a/subworkflows/local/footprinting.nf b/subworkflows/local/footprinting.nf new file mode 100644 index 0000000..d3c047f --- /dev/null +++ b/subworkflows/local/footprinting.nf @@ -0,0 +1,46 @@ +include { BEDTOOLS_MERGE } from '../../modules/nf-core/bedtools/merge/main' +include { BEDTOOLS_SUBTRACT } from '../../modules/nf-core/bedtools/subtract/main' + +workflow FOOTPRINTING { + + take: + ch_peaks + + main: + + ch_versions = Channel.empty() + + ch_footprint_split = ch_peaks.branch{ + meta, peaks -> + footprinting: meta.footprinting + as_is: !meta.footprinting + } + + BEDTOOLS_MERGE( ch_footprint_split.footprinting ) + + ch_include_original_split = BEDTOOLS_MERGE.out.bed + .branch{ + meta, bed -> + include: meta.include_original + subtract: !meta.include_original + } + + ch_subtract_pairs = ch_include_original_split.subtract + .join( ch_peaks ) + + BEDTOOLS_SUBTRACT( ch_subtract_pairs ) + + ch_versions = ch_versions.mix( + BEDTOOLS_MERGE.out.versions, + BEDTOOLS_SUBTRACT.out.versions + ) + + emit: + footprinted_peaks = ch_footprint_split.as_is.mix( + ch_include_original_split.include, + BEDTOOLS_SUBTRACT.out.bed + ) + + versions = ch_versions // channel: [ versions.yml ] +} + diff --git a/subworkflows/local/peaks.nf b/subworkflows/local/peaks.nf index 431c2c2..86b3e48 100644 --- a/subworkflows/local/peaks.nf +++ b/subworkflows/local/peaks.nf @@ -3,7 +3,8 @@ include { GAWK as CLEAN_BED } from '../../modules/nf-core/gawk/main' include { BEDTOOLS_SORT as SORT_PEAKS } from '../../modules/nf-core/bedtools/sort/main' // Subworkflows -include { MERGE_SAMPLES as MERGE_SAMPLES } from './merge_samples' +include { FOOTPRINTING } from './footprinting' +include { MERGE_SAMPLES } from './merge_samples' workflow PEAKS { @@ -17,12 +18,18 @@ workflow PEAKS { CLEAN_BED(ch_peaks, []) + ch_peaks = CLEAN_BED.out.output + + FOOTPRINTING(ch_peaks) + + ch_peaks = FOOTPRINTING.out.footprinted_peaks + if (merge_samples) { - MERGE_SAMPLES(CLEAN_BED.out.output) + MERGE_SAMPLES(ch_peaks) ch_peaks = MERGE_SAMPLES.out.merged ch_versions = ch_versions.mix(MERGE_SAMPLES.out.versions) } else { - SORT_PEAKS(CLEAN_BED.out.output, []) + SORT_PEAKS(ch_peaks, []) ch_peaks = SORT_PEAKS.out.sorted ch_versions = ch_versions.mix(SORT_PEAKS.out.versions) } From 94b81cf7ccd53ca8b515f548da71d53cfc988068 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 1 Mar 2024 20:07:46 +0100 Subject: [PATCH 009/206] Implement blacklist --- assets/blacklists/hg19-blacklist.txt | 834 +++++++ assets/blacklists/hg38-blacklist.bed | 636 +++++ assets/blacklists/mm10-blacklist.bed | 3435 ++++++++++++++++++++++++++ main.nf | 9 +- nextflow_schema.json | 14 +- subworkflows/local/peaks.nf | 11 +- workflows/tfactivity.nf | 5 +- 7 files changed, 4936 insertions(+), 8 deletions(-) create mode 100755 assets/blacklists/hg19-blacklist.txt create mode 100755 assets/blacklists/hg38-blacklist.bed create mode 100755 assets/blacklists/mm10-blacklist.bed diff --git a/assets/blacklists/hg19-blacklist.txt b/assets/blacklists/hg19-blacklist.txt new file mode 100755 index 0000000..03688d9 --- /dev/null +++ b/assets/blacklists/hg19-blacklist.txt @@ -0,0 +1,834 @@ +chr10 38726200 42489100 High Signal Region +chr10 42524900 42819200 High Signal Region +chr10 98560400 98562500 High 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806800 High Signal Region +chrY 924800 1005300 High Signal Region +chrY 1276400 1813700 High Signal Region +chrY 1834500 1940700 High Signal Region +chrY 1973200 1996400 High Signal Region +chrY 2017200 2068000 Low Mappability +chrY 2104700 2210800 High Signal Region +chrY 2280300 2288900 Low Mappability +chrY 2471300 3819300 High Signal Region +chrY 3880300 4177100 High Signal Region +chrY 4249500 4289100 High Signal Region +chrY 4432000 4956300 High Signal Region +chrY 5062400 5227700 High Signal Region +chrY 6376700 6382700 High Signal Region +chrY 6530200 6663200 High Signal Region +chrY 6760200 6835800 High Signal Region +chrY 6984100 8985400 High Signal Region +chrY 10638500 41003800 High Signal Region +chrY 41159200 91744600 High Signal Region diff --git a/main.nf b/main.nf index 1ca4f13..3459c57 100644 --- a/main.nf +++ b/main.nf @@ -30,8 +30,9 @@ include { PREPARE_GENOME } from './subworkflows/local/prepare_genome' ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -params.fasta = getGenomeAttribute('fasta') -params.gtf = getGenomeAttribute('gtf') +params.fasta = getGenomeAttribute('fasta') +params.gtf = getGenomeAttribute('gtf') +params.blacklist = getGenomeAttribute('blacklist') /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -66,7 +67,9 @@ workflow NFCORE_TFACTIVITY { // TFACTIVITY ( samplesheet, - ch_versions + ch_versions, + params.merge_samples, + params.blacklist ) emit: diff --git a/nextflow_schema.json b/nextflow_schema.json index 574f41d..0d95a3f 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -83,7 +83,7 @@ "mimetype": "text/plain", "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$", "description": "Path to FASTA genome file.", - "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.", + "help_text": "This parameter is *mandatory* if `--genome` is not specified.", "fa_icon": "far fa-file-code" }, "gtf": { @@ -93,7 +93,17 @@ "mimetype": "text/plain", "pattern": "^\\S+\\.gtf(\\.gz)?$", "description": "Path to GTF gene annotation file.", - "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a STAR index available this will be generated for you automatically. Combine with `--save_reference` to save STAR index for future runs.", + "help_text": "This parameter is *mandatory* if `--genome` is not specified.", + "fa_icon": "far fa-file-code" + }, + "blacklist": { + "type": "string", + "format": "file-path", + "exists": true, + "mimetype": "text/plain", + "pattern": "^\\S+\\.bed(\\.gz)?$", + "description": "Path to blacklist regions file.", + "help_text": "This parameter is *mandatory* if `--genome` is not specified.", "fa_icon": "far fa-file-code" }, "igenomes_ignore": { diff --git a/subworkflows/local/peaks.nf b/subworkflows/local/peaks.nf index 86b3e48..1d518a6 100644 --- a/subworkflows/local/peaks.nf +++ b/subworkflows/local/peaks.nf @@ -1,6 +1,7 @@ // Modules -include { GAWK as CLEAN_BED } from '../../modules/nf-core/gawk/main' -include { BEDTOOLS_SORT as SORT_PEAKS } from '../../modules/nf-core/bedtools/sort/main' +include { GAWK as CLEAN_BED } from '../../modules/nf-core/gawk/main' +include { BEDTOOLS_SORT as SORT_PEAKS } from '../../modules/nf-core/bedtools/sort/main' +include { BEDTOOLS_SUBTRACT as BLACKLIST } from '../../modules/nf-core/bedtools/subtract/main' // Subworkflows include { FOOTPRINTING } from './footprinting' @@ -11,6 +12,7 @@ workflow PEAKS { take: ch_peaks // channel: [ val(meta), [ peaks ] ] merge_samples + blacklist main: @@ -34,6 +36,11 @@ workflow PEAKS { ch_versions = ch_versions.mix(SORT_PEAKS.out.versions) } + if (blacklist) { + BLACKLIST( ch_peaks.map{ meta, peaks -> [meta, peaks, blacklist] } ) + ch_peaks = BLACKLIST.out.bed + } + emit: versions = ch_versions // channel: [ versions.yml ] diff --git a/workflows/tfactivity.nf b/workflows/tfactivity.nf index fbb27d0..e5f4cd9 100644 --- a/workflows/tfactivity.nf +++ b/workflows/tfactivity.nf @@ -24,6 +24,8 @@ workflow TFACTIVITY { take: ch_samplesheet // channel: samplesheet read in from --input ch_versions + merge_samples + blacklist main: @@ -33,7 +35,8 @@ workflow TFACTIVITY { // ch_versions = ch_versions.mix(FASTQC.out.versions.first()) PEAKS( ch_samplesheet, - params.merge_samples + merge_samples, + blacklist ) ch_versions = ch_versions.mix(PEAKS.out.versions) From fbdfb75dc3e06a4b9f57913ca4b687e8c6d4c3f0 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 1 Mar 2024 20:45:15 +0100 Subject: [PATCH 010/206] Implement STARE --- .../Jaspar_Hocomoco_Kellis_human_PSEMs.txt | 11200 ++++++++++++++++ .../Jaspar_Hocomoco_Kellis_mouse_PSEMs.txt | 6211 +++++++++ conf/igenomes.config | 6 + conf/modules.config | 1 + main.nf | 19 +- modules/local/stare/main.nf | 31 + nextflow.config | 2 + nextflow_schema.json | 24 + subworkflows/local/peaks.nf | 21 +- subworkflows/local/prepare_genome.nf | 8 +- workflows/tfactivity.nf | 18 +- 11 files changed, 17524 insertions(+), 17 deletions(-) create mode 100644 assets/PWMs/Jaspar_Hocomoco_Kellis_human_PSEMs.txt create mode 100644 assets/PWMs/Jaspar_Hocomoco_Kellis_mouse_PSEMs.txt create mode 100644 modules/local/stare/main.nf diff --git a/assets/PWMs/Jaspar_Hocomoco_Kellis_human_PSEMs.txt b/assets/PWMs/Jaspar_Hocomoco_Kellis_human_PSEMs.txt new file mode 100644 index 0000000..2bf8971 --- /dev/null +++ b/assets/PWMs/Jaspar_Hocomoco_Kellis_human_PSEMs.txt @@ -0,0 +1,11200 @@ +#/Lambda=0.7 /Regression_slope=0.584 /Regression_intercept=-5.66 /GC_content=0.41 +>MA0002.1 RUNX1 lnR0: 0.764 +0.124302 1.46047 1.0495 0 +0 1.57482 2.15405 0.114347 +1.56945 0.378062 2.35848 0 +3.60818 3.08823 4.07844 0 +3.49058 4.54008 0 4.06982 +2.478 0.388605 3.5275 0 +5.22829 4.70834 0 5.22829 +5.22829 4.70834 0 5.22829 +4.65442 3.14426 4.13447 0 +0.908555 1.95805 3.5275 0 +0 1.68069 0.950934 0.799451 +>MA0030.1 FOXF2 lnR0: 2.516 +2.9553 0 0.454934 0.656108 +0 -0.0650166 0.345958 0.865908 +0 1.30995 2.03971 1.82991 +0 0.690475 0.690475 1.21043 +2.0894 0 0.410974 4.06982 +1.89864 4.34932 0 4.86927 +4.76029 4.24034 4.24034 0 +0 4.24034 4.24034 4.76029 +0 4.24034 4.24034 4.76029 +0 4.24034 4.24034 4.76029 +5.17437 0 4.65442 3.60493 +0 4.24034 4.24034 4.76029 +0 1.2283 1.95805 1.48779 +0.454934 0.606417 0.125742 0 +>MA0031.1 FOXD1 lnR0: -0.988 +3.65884 3.13889 0 3.65884 +4.34932 3.82937 3.82937 0 +0 2.76946 3.75967 4.27962 +0 3.82937 3.82937 4.34932 +0 2.69618 2.69618 4.20634 +3.73608 0 4.20634 3.73608 +0 3.82937 3.82937 4.34932 +0.168261 1.0495 0.638521 0 +>MA0051.1 IRF2 lnR0: 4.852 +3.49058 0.671434 0 2.50037 +2.37607 3.42556 0 3.94552 +0 3.14426 3.14426 3.66421 +0 3.02992 3.02992 2.55966 +0 3.14426 3.14426 3.66421 +2.37607 3.42556 0 3.94552 +2.77987 0 2.77987 0 +4.18416 3.66421 0 4.18416 +0 3.14426 3.14426 3.66421 +0 3.14426 3.14426 3.66421 +0 3.14426 3.14426 3.66421 +3.29982 0 0 3.29982 +3.49058 0 1.40118 1.51016 +0 0.47026 0.0592853 0.99021 +0 2.25992 0.690475 0.480675 +0 1.26971 1.26971 0.480675 +0 0.47026 1.0495 0.260459 +1.3194 0 1.78966 1.73038 +>MA0059.1 MAX::MYC lnR0: 0.764 +0.838727 2.2992 0 1.51016 +0 2.45068 1.14169 2.97063 +2.23991 0 0 2.81915 +3.87906 0 4.34932 4.86927 +0 3.89582 3.89582 4.41577 +4.86927 0 4.34932 3.87906 +3.87906 4.34932 0 4.86927 +4.34932 2.83916 3.82937 0 +4.93573 4.41577 0 4.93573 +3.73608 3.21613 0 3.73608 +1.78966 0.690475 3.25013 0 +>MA0065.1 PPARG::RXRA lnR0: 6.02 +0.238649 0 0.693583 0 +0.799451 0 0.63119 0 +0 1.46047 0.979795 0.615404 +1.51016 3.77008 0 5.28024 +0.989242 4.59839 0 5.11834 +5.85948 5.33953 0 5.85948 +5.78978 5.26983 0 4.22033 +5.26983 3.18043 4.74988 0 +4.14706 0 3.62711 5.7165 +0 4.81958 4.81958 5.33953 +0 4.81958 4.81958 5.33953 +0 4.74988 3.18043 5.26983 +5.85948 5.33953 0 5.85948 +5.78978 5.26983 0 4.22033 +5.26983 3.18043 4.74988 0 +4.10896 0 4.16824 4.10896 +0 3.7235 3.14426 5.23366 +0.535276 -0.223323 1.14169 0 +0.71071 0 0.671434 2.18159 +0.693583 0.238649 0 0 +>MA0066.1 PPARG lnR0: 6.02 +2.40817 0.729751 0 2.40817 +2.674 4.13447 4.13447 0 +0 3.75967 0.47026 4.27962 +5.28024 3.77008 0 5.28024 +4.23808 4.70834 0 4.23808 +4.54008 3.02992 1.72093 0 +3.49058 0 2.55966 5.06003 +0 3.19818 4.18839 3.71813 +1.92114 0 1.66164 2.18159 +1.38586 0.454934 0 1.16564 +2.42709 2.6369 0 2.42709 +3.66421 4.13447 2.56503 0 +3.29982 1.78966 0 3.87906 +0 1.39967 3.95933 3.48907 +4.29003 0 4.76029 5.28024 +5.17437 0 4.65442 3.19395 +1.78966 -0.414082 3.25013 0 +0 1.39967 3.95933 3.48907 +1.62451 0 0.884342 1.62451 +1.37869 3.82937 2.83916 0 +>MA0069.1 PAX6 lnR0: 2.516 +3.46821 2.21851 2.21851 0 +3.70038 3.18043 4.74988 0 +2.92909 0 3.71813 1.56408 +0 3.18043 3.75967 4.27962 +3.6186 0 4.08886 3.03936 +4.86927 5.33953 0 4.86927 +4.72629 0 2.89735 4.72629 +0 2.32638 2.32638 0.209434 +4.20634 2.3774 3.68639 0 +3.60493 0.78578 0 3.60493 +0 4.6385 1.85863 4.16824 +0.740166 0.220215 0 1.15114 +4.08886 1.99946 2.5787 0 +3.66421 4.13447 0.00537058 0 +>MA0070.1 PBX1 lnR0: 1.348 +0.740166 0 1.21043 0.740166 +1.82894 0 1.30899 1.82894 +0 2.53729 2.53729 4.04745 +3.05724 2.53729 3.5275 0 +4.72629 0 4.20634 4.72629 +0 2.61894 3.60915 4.1291 +0 3.60915 3.60915 3.13889 +4.1291 3.60915 2.61894 0 +4.72629 0 4.20634 4.72629 +0 2.53729 3.5275 3.05724 +0 3.14426 2.15405 1.10456 +0 1.0495 1.0495 0.359021 +>MA0071.1 RORA(MA0071.1) lnR0: 0.18 +0 2.45068 1.87144 0.99021 +0.671434 2.45068 3.44089 0 +1.40429 0 1.36502 2.20374 +0 1.46047 0.47026 0.579236 +0 3.89582 1.59663 4.41577 +5.17437 4.65442 0 5.17437 +5.17437 4.65442 0 5.17437 +4.65442 4.13447 4.13447 0 +5.17437 0 4.65442 5.17437 +0 4.13447 4.13447 4.65442 +>MA0072.1 RORA(MA0072.1) lnR0: 2.516 +0.260459 -0.108976 -0.108976 0 +0 2.03971 0.638521 0.703538 +0.2455 3.68639 1.70597 0 +0 3.60915 4.59936 5.11931 +0 4.02013 4.02013 0.769995 +2.72059 0.105869 0 1.00063 +5.15845 4.6385 4.6385 0 +0 4.29047 1.15158 4.81042 +5.6784 5.15845 0 5.6784 +5.6784 5.15845 0 5.6784 +5.15845 4.6385 4.6385 0 +5.6784 0 5.15845 5.6784 +0 4.6385 4.6385 5.15845 +0 0.661019 0.0153258 1.40118 +>MA0073.1 RREB1 lnR0: 6.02 +1.67842 0 3.13889 3.65884 +2.9553 0 3.42556 3.94552 +1.67842 0 3.13889 3.65884 +4.06982 0 3.54987 4.06982 +0 0.151483 2.45068 2.97063 +0 1.20001 2.76946 3.28941 +0 0.638521 2.61894 3.13889 +1.00063 0 2.77987 2.30961 +4.06982 0 3.54987 4.06982 +0 3.02992 3.02992 3.54987 +1.19138 0 2.97063 3.49058 +2.9553 0 3.42556 3.94552 +1.67842 0 3.13889 3.65884 +1.00063 0 1.78966 3.29982 +2.23991 0 3.28941 3.80936 +0.78041 0 2.55966 1.51016 +0.78041 0 1.56945 2.0894 +1.00063 0 2.77987 2.30961 +2.50037 0 0.99021 3.49058 +0 0 0.729751 1.30899 +>MA0074.1 RXRA::VDR lnR0: 3.1 +1.51016 2.97063 0 3.49058 +3.94552 3.42556 0 3.94552 +3.80936 3.28941 0 2.81915 +3.42556 2.90561 2.90561 0 +3.80936 0 3.28941 2.81915 +0 2.76946 1.77925 3.28941 +0 0.2098 1.77925 0 +1.2497 0 0.729751 1.2497 +2.0894 3.13889 0 3.65884 +0 2.55966 0 2.55966 +3.94552 3.42556 0 3.94552 +3.42556 2.90561 2.90561 0 +2.2992 2.76946 2.76946 0 +3.80936 0 3.28941 2.81915 +0 1.46047 0.881234 2.97063 +>MA0077.1 SOX9 lnR0: -0.404 +4.29003 0 2.4611 2.98105 +2.61472 0 2.45379 1.15522 +0 4.59936 5.58957 3.81033 +4.54008 4.59936 4.02013 0 +3.01459 5.46527 3.16607 0 +5.07973 4.55978 0 6.64918 +2.07898 5.32911 3.02992 0 +2.43535 2.23418 2.42494 0 +1.60236 0 1.98042 0.872608 +>MA0084.1 SRY lnR0: -0.404 +1.38586 0.865908 0 0.806623 +0.63119 1.26971 0.950934 0 +0 3.44089 1.46047 0.535276 +0 1.70597 1.70597 1.90714 +0 4.13447 4.13447 2.674 +5.22829 0 4.70834 3.65884 +0 4.29047 4.29047 4.81042 +0 4.24034 3.25013 4.76029 +1.30899 3.75967 2.19022 0 +>MA0091.1 TAL1::TCF3 lnR0: 1.348 +0.618512 0 0.729751 1.09919 +1.57986 0.923753 0 2.30961 +0 4.74988 2.76946 3.70038 +0.769027 0 4.59839 5.11834 +5.92594 0 4.41577 5.92594 +0 4.91814 4.91814 5.43809 +4.99501 3.48485 0.925194 0 +1.85075 0 4.99501 5.51496 +5.43809 4.91814 4.91814 0 +5.92594 5.40599 0 4.93573 +4.41577 1.9154 -0.453493 0 +2.77987 2.25992 2.98967 0 +>MA0101.1 REL lnR0: 0.18 +3.65884 0.579236 0 1.35965 +4.48079 2.97063 0 3.49058 +3.49058 3.96084 0 3.49058 +1.2497 2.2992 0 2.23991 +0 -0.299735 0.279501 0.799451 +0.865908 1.9154 1.9154 0 +3.05724 3.5275 3.5275 0 +2.39139 3.44089 3.44089 0 +4.48079 0 3.96084 2.91135 +3.57719 0 4.04745 4.5674 +>MA0107.1 RELA lnR0: 0.18 +4.06982 1.25067 0 2.0894 +4.64905 4.1291 0 3.65884 +4.72629 4.20634 0 4.72629 +0 3.02992 0.0592853 3.54987 +0 0.925194 0.606417 2.43535 +2.478 3.5275 3.5275 0 +4.20634 3.68639 3.68639 0 +4.04745 1.95805 3.5275 0 +4.72629 0 4.20634 4.72629 +4.72629 0 4.20634 4.72629 +>MA0115.1 NR1H2::RXRA lnR0: 4.268 +0 1.0495 3.60915 2.14868 +0 2.61894 1.0495 2.55966 +0 3.82937 1.26971 4.34932 +5.17437 4.65442 0 5.17437 +5.11834 4.59839 0 4.12813 +4.65442 4.13447 4.13447 0 +5.17437 0 4.65442 5.17437 +0 4.13447 4.13447 4.65442 +0 4.07844 4.07844 3.60818 +0 4.13447 4.13447 4.65442 +5.17437 4.65442 0 5.17437 +5.17437 4.65442 0 5.17437 +4.65442 4.13447 4.13447 0 +5.17437 0 4.65442 5.17437 +0 4.13447 4.13447 4.65442 +0 2.83916 2.25992 2.77987 +4.48079 0 1.18097 2.18159 +>MA0119.1 NFIC::TLX1 lnR0: 2.516 +4.04745 3.5275 3.5275 0 +4.5674 4.04745 0 4.5674 +4.5674 4.04745 0 4.5674 +4.5674 0 4.04745 4.5674 +0 2.35848 3.34869 2.87843 +2.0894 0 0.579236 2.66863 +2.0894 0 0.839695 2.0894 +0 1.46047 -0.108976 0.99021 +0.671434 0.47026 0.881234 0 +4.5674 4.04745 0 4.5674 +4.5674 0 4.04745 4.5674 +4.5674 0 4.04745 4.5674 +0 3.5275 3.5275 4.04745 +0 3.34869 2.35848 2.87843 +>MA0124.1 NKX3-1 lnR0: -1.572 +0 2.25992 1.26971 1.78966 +4.27962 2.76946 3.75967 0 +0 3.82937 3.82937 4.34932 +4.79957 0 4.27962 3.80936 +3.28941 3.75967 3.75967 0 +3.28941 3.75967 3.75967 0 +0 3.75967 2.76946 4.27962 +>MA0130.1 ZNF354C lnR0: -2.156 +0 -0.329191 0.47026 2.97063 +1.56945 1.46047 3.02992 0 +4.5674 0 4.04745 4.5674 +4.5674 0 4.04745 4.5674 +0 3.5275 3.5275 4.04745 +4.48079 0 2.97063 4.48079 +>MA0139.1 CTCF(MA0139.1) lnR0: 5.436 +2.3627 0.129296 2.03351 0 +1.81183 1.49239 0 1.65115 +1.18758 3.13889 0 2.23991 +4.29539 0 5.13545 4.91273 +7.1051 0 9.72404 8.67455 +0 5.15766 2.94252 2.98799 +4.1734 0 0.652654 5.92864 +2.50697 0 3.11603 0.933121 +0 5.56959 4.12445 5.43307 +7.68434 9.72404 0 8.26357 +1.27598 7.07724 0 6.2882 +3.68742 5.22801 0 1.07673 +6.55909 9.70335 0 7.08441 +4.2501 6.36704 0 3.91636 +3.29788 0 6.86679 3.91852 +0.961241 5.13061 0 5.29154 +3.03592 0 0.642738 4.15199 +1.73322 -0.225259 1.87987 0 +0 0.615664 0.068175 2.72085 +>MA0149.1 EWSR1-FLI1 lnR0: 4.852 +7.18201 6.66206 0 7.18201 +5.58535 6.63484 0 7.15479 +0 6.12856 5.13835 6.64851 +0 6.12856 5.13835 6.64851 +6.17826 6.64851 0 7.16847 +5.57155 6.62104 0 6.15078 +0 6.11489 4.54545 6.63484 +0 6.10109 4.12067 6.62104 +7.16847 6.64851 0 6.17826 +7.15479 5.0654 0 7.15479 +0 3.75967 4.48942 6.57881 +0 6.14211 6.14211 6.66206 +7.18201 6.66206 0 7.18201 +7.15479 5.0654 0 7.15479 +0 4.09266 6.07308 5.02358 +0 6.10109 4.53164 5.63083 +4.51025 6.54995 0 5.08948 +5.08948 4.56953 0 5.50046 +>MA0138.2 REST lnR0: 6.604 +1.96858 1.72263 0.664663 0 +4.21143 1.51879 2.38734 0 +4.62933 0 4.69793 4.17271 +0 4.97633 3.37649 5.69364 +5.90444 5.02547 0 7.55794 +3.4833 0 1.5797 2.91573 +0 7.02748 6.3339 6.85385 +9.06753 0 6.86379 8.4883 +5.83085 0 6.08089 4.86062 +0 1.63657 1.94302 1.45534 +1.99174 0.706129 2.27938 0 +5.74627 7.52551 0 8.04546 +6.69051 7.96022 0 9.47038 +0 3.08266 4.757 4.71139 +6.97186 0 2.42868 4.57411 +0 6.7078 7.02658 7.09159 +5.62349 6.7066 0 7.70722 +2.7883 0 2.4297 2.83769 +1.41978 4.38501 0 0.955322 +2.62495 0 1.53022 3.38166 +3.12517 0 4.82718 2.59436 +>MA0150.1 NFE2L2 lnR0: 0.764 +0 1.9154 -0.383793 3.42556 +4.34932 3.82937 3.82937 0 +4.79957 4.27962 0 3.80936 +0 3.82937 3.82937 4.34932 +4.64905 0 3.13889 3.07961 +0.769995 1.46047 2.03971 0 +1.38586 0 2.43535 1.64632 +0 3.5275 1.95805 2.478 +4.86927 4.34932 0 4.86927 +4.86927 0 4.34932 4.86927 +0 1.87144 1.87144 2.97063 +>MA0152.1 NFATC2 lnR0: -1.572 +2.3689 2.83916 2.25992 0 +3.42556 2.32638 2.32638 0 +3.60818 3.08823 4.07844 0 +4.70834 4.18839 4.18839 0 +4.18416 0 4.65442 5.17437 +5.22829 0 4.70834 5.22829 +0 1.70597 2.69618 1.90714 +>MA0155.1 INSM1 lnR0: 1.348 +3.28941 3.75967 1.46047 0 +4.86927 4.34932 0 2.57007 +3.77008 0.111239 1.26971 0 +1.70092 0 3.96084 2.50037 +0 3.5275 3.5275 0.908555 +5.11834 4.59839 0 5.11834 +5.06003 3.54987 0 5.06003 +5.11834 4.59839 0 5.11834 +5.11834 4.59839 0 5.11834 +4.5674 2.478 0 1.78753 +2.58698 0 4.04745 2.00774 +0.758599 3.66421 0 2.61472 +>MA0159.1 RARA::RXRA lnR0: 4.268 +0 3.14426 -0.405604 3.66421 +5.06003 4.54008 0 5.06003 +3.29982 3.77008 0 1.00063 +4.47928 3.95933 2.96912 0 +4.72629 0 2.22592 3.15685 +0 3.95933 2.96912 4.47928 +0.671434 0 0.410974 0 +1.2497 0.150515 0 2.81915 +1.51016 1.25067 0 2.0894 +0 2.25992 0.279501 2.20064 +1.62451 0.884342 0 4.18416 +0 1.62873 1.62873 4.1291 +3.87906 3.35911 0 3.87906 +4.5674 3.05724 0 1.78753 +2.55966 2.61894 1.62873 0 +3.65884 0 2.14868 3.07961 +0 3.89582 2.90561 3.42556 +>MA0163.1 PLAG1 lnR0: 2.516 +4.72629 4.20634 0 4.72629 +2.40817 3.86864 0 3.39838 +4.72629 4.20634 0 4.72629 +4.64905 4.1291 0 3.65884 +4.38859 0 1.56945 4.38859 +4.48079 0 2.97063 2.91135 +1.64632 0 2.43535 1.96509 +0 3.14426 3.14426 0.884342 +0 0.47026 1.46047 3.54987 +2.81915 3.86864 0 2.81915 +4.72629 4.20634 0 4.72629 +4.72629 4.20634 0 4.72629 +4.5674 4.04745 0 2.99795 +2.99795 4.04745 0 4.5674 +>MA0259.1 ARNT::HIF1A lnR0: -0.988 +1.34826 0.778182 0 6.10855 +2.17345 0.220215 0 0.647968 +0 4.15267 1.18204 5.25186 +7.15479 0 6.63484 6.16458 +7.16847 6.64851 0 7.16847 +6.64851 6.12856 6.12856 0 +7.16847 6.64851 0 7.16847 +1.95824 0 1.29532 2.20374 +>MA0468.1 DUX4 lnR0: 0.764 +1.89237 2.90515 4.24071 0 +0 14.5068 4.35803 15.0268 +0 14.553 14.553 15.0729 +1.86651 0.198968 2.71738 0 +13.8953 -0.495881 1.21306 0 +14.0084 -0.144955 1.03041 0 +0 3.05438 14.4387 9.34174 +0 14.553 14.553 15.0729 +15.0729 14.553 14.553 0 +15.5623 0 15.0424 5.99514 +0 14.3775 14.3775 2.90613 +>MA0476.1 FOS(MA0476.1) lnR0: 0.764 +0.492025 3.40436 -0.322864 0 +1.05099 0.0902842 0 4.06903 +14.6981 14.1781 14.1781 0 +15.1023 14.5823 0 4.05102 +0 14.1781 14.1781 14.6981 +4.2996 0 0.326024 2.67545 +14.6981 14.1781 14.1781 0 +15.218 0 14.6981 15.218 +0 14.1781 14.1781 14.6981 +6.33118 1.36421 3.26543 0 +1.19635 -0.353019 -0.292981 0 +>MA0478.1 FOSL2 lnR0: 0.764 +1.83031 1.0582 0 1.08421 +1.33932 2.16967 0 2.94768 +0 5.09994 -0.225548 5.20255 +12.2558 11.7358 11.7358 0 +12.7757 12.2558 0 12.7757 +0 6.02439 4.15089 12.189 +12.0881 0 0.829648 4.55528 +12.2558 11.7358 11.7358 0 +5.10832 0 12.1996 12.7196 +0 11.7358 11.7358 12.2558 +10.8491 -0.0197309 -0.481328 0 +>MA0479.1 FOXH1 lnR0: 0.764 +1.63044 -0.46956 0.451453 0 +1.07822 0 0.125304 0.627987 +2.24664 0 0.0467404 2.48903 +0 12.3563 12.3563 12.8762 +0 12.2358 4.46713 4.07342 +12.8762 12.3563 12.3563 0 +1.78905 0 12.373 6.92957 +2.76209 0 12.6063 13.1262 +0 12.3563 12.3563 12.8762 +13.3962 0 12.8762 13.3962 +0 12.1562 12.1562 2.70598 +>MA0488.1 JUN(MA0488.1) lnR0: 1.932 +0 1.00851 0.206937 0.656562 +0 0.743502 -0.0115901 0.26066 +1.09 2.32345 0 2.24825 +0 3.93677 1.61274 13.8754 +14.2154 13.6955 13.6955 0 +14.7272 14.2073 0 7.88798 +0 13.6954 13.6954 13.2252 +13.5345 1.38181 0.993546 0 +14.6933 5.01365 0 14.6933 +4.09471 1.68219 13.3531 0 +1.5363 0 13.6449 14.1649 +0 13.6955 13.6955 14.2154 +6.23585 1.57402 3.42091 0 +>MA0489.1 JUN(MA0489.1) lnR0: 2.516 +0 1.4167 0.256071 1.24017 +0.585002 1.61751 0 1.87162 +0.734515 1.92193 0 1.79504 +0 1.42993 -0.178413 1.14119 +0.542846 2.79898 0 1.58105 +0 2.03178 0.03067 12.4114 +13.2882 12.7682 12.7682 0 +13.8081 13.2882 0 13.8081 +0 12.7678 12.7678 11.3074 +4.37861 0 0.475076 3.3607 +5.69298 12.7421 12.7421 0 +3.87229 0 13.1578 13.6777 +0 12.7682 12.7682 13.2882 +3.80985 0.581626 0.506246 0 +>MA0492.1 JUND(MA0492.1) lnR0: 3.1 +0 0.870089 -0.0073278 0.213162 +0 1.51696 0.0974259 0.697375 +0 0.687392 -0.0510747 0.254384 +0.728926 2.65756 0 3.61731 +0 6.62956 1.107 14.4864 +14.8903 14.3704 14.3704 0 +15.4052 14.8852 0 8.55405 +0 14.3704 14.3704 14.8903 +13.731 -0.00352684 0.321716 0 +2.877 3.83212 0 15.0797 +14.7126 2.36702 14.1926 0 +1.99517 0 7.3695 14.9692 +0 14.3704 14.3704 14.8903 +6.50711 1.67826 2.85064 0 +0.599329 0 0.763797 1.32181 +>MA0497.1 MEF2C lnR0: 3.1 +0 0.601569 -0.460031 0.470191 +0.0365089 1.76603 -0.132185 0 +1.44071 2.0425 0 0.63184 +2.38486 0 4.12003 2.56341 +10.1581 -0.209894 9.63819 0 +0 2.10755 3.86696 2.58911 +0 5.11717 2.27084 2.85725 +0 10.4136 4.01742 6.97272 +0 10.4298 8.86034 4.7443 +0 10.4325 8.13327 4.86287 +5.14689 4.48397 10.4027 0 +0 10.4603 5.46527 10.9802 +2.59942 3.75141 0 6.26363 +0 -0.300467 2.16507 1.94001 +0 0.631818 2.44222 0.685649 +>MA0501.1 MAF::NFE2 lnR0: 3.1 +0 4.18446 0.586901 7.11356 +9.99264 9.47269 9.47269 0 +10.5021 9.98213 0 7.36319 +0 9.47269 9.47269 9.99264 +6.14506 0 2.36114 4.99596 +3.09386 8.3116 5.6376 0 +4.01895 0 5.29751 4.6521 +0 9.31795 3.67332 3.942 +7.30805 7.6278 0 5.25039 +10.4768 0 5.47757 7.91714 +0 5.11857 3.099 3.69834 +0 0.383653 -0.0889958 0.782807 +0.461377 1.76503 1.39349 0 +1.03815 2.01169 2.17304 0 +1.1998 0.262149 1.65664 0 +>MA0504.1 NR2C2(MA0504.1) lnR0: 3.1 +0 -0.486597 -0.0104149 1.33673 +1.92543 1.62857 0 3.75878 +0.534603 4.76029 0 7.0699 +8.95618 5.29734 0 4.54041 +5.48714 6.41234 0 4.15242 +6.233 7.69347 1.43343 0 +5.93518 0 2.47034 4.00672 +0 7.82382 2.26408 6.04458 +0.671225 7.63191 0 8.15186 +0 7.74266 1.63313 8.26261 +5.60272 8.50834 0 9.02829 +5.28449 8.3144 0 3.27461 +8.0497 2.76946 1.10145 0 +5.45303 0 3.10318 3.58399 +0 7.5848 1.10965 4.33467 +>MA0506.1 NRF1 lnR0: 0.764 +3.0914 3.24621 0 12.237 +3.17481 0 11.8494 12.3693 +4.9044 4.43613 0 12.4518 +12.3747 0 3.06813 5.30499 +0.81534 0 0.983326 3.06359 +11.735 2.64155 2.25644 0 +12.576 12.056 0 12.576 +12.4848 0 11.9649 4.39983 +12.4639 3.57549 0 12.4639 +6.38511 0 12.033 12.553 +0 0.945855 -0.0138636 11.0242 +>MA0517.1 STAT1::STAT2 lnR0: 3.1 +2.53218 2.14025 1.85764 0 +1.12729 0 1.42824 1.07162 +0 5.17529 0.968946 3.67086 +7.32306 1.63503 0 7.73403 +9.18301 7.09361 8.66306 0 +7.19565 7.08667 8.65612 0 +7.16043 4.85082 6.3217 0 +9.61491 0 9.09496 4.34508 +0 1.21497 -0.108976 1.34287 +1.15258 0.580676 0.0533943 0 +6.82492 4.83408 5.1786 0 +5.73418 7.07034 8.63979 0 +6.4059 0.839915 5.88595 0 +5.40826 0 5.55974 2.68034 +4.14186 0 3.27388 1.44158 +>MA0523.1 TCF7L2 lnR0: 2.516 +0 0.481538 -0.104601 0.980879 +0 0.574246 0.12225 2.19932 +0 3.92259 1.91122 2.82861 +5.02144 0.0440484 0 4.2363 +0 6.10878 10.8171 1.0212 +4.81749 11.3468 11.3468 0 +4.88186 0 2.15735 12.0959 +0 11.3946 11.3946 11.9146 +0 7.40452 5.27582 11.8853 +0 11.3882 7.10853 11.9081 +4.14644 6.59712 0 12.3136 +1.46605 1.22879 0 3.25089 +0 -0.207288 -0.313792 1.59521 +0 0.577546 0.702006 1.10269 +>MA0527.1 ZBTB33 lnR0: 3.1 +2.13457 0 0.798062 0.729092 +6.36335 2.61657 3.62826 0 +4.98416 0 5.72476 6.82395 +5.71766 2.19497 6.06362 0 +9.89083 0 9.37088 9.89083 +4.69248 9.29184 0 7.83137 +8.24448 0 9.29398 4.69461 +9.89083 9.37088 0 9.89083 +0 1.96736 1.41782 3.26488 +6.11173 2.93003 0 1.74737 +0 1.59321 1.01899 2.89393 +1.54149 -0.402306 0.356347 0 +4.52042 0 2.8741 0.577544 +2.19936 0.820009 1.22448 0 +2.05765 0.188468 0 1.69863 +>MA0007.2 AR lnR0: 3.1 +0 1.95147 0.511349 2.99959 +0 12.0218 -0.0602269 12.5418 +13.8404 13.3204 0 13.8404 +0 1.76561 1.82142 1.54795 +0 12.8005 12.8005 13.3204 +9.12038 0 7.32355 13.8287 +0 12.6974 6.00865 3.91275 +1.94982 0.430515 0 1.0742 +0 0.523745 0.48676 0.732707 +0 -0.492523 -0.510866 1.27722 +1.20178 5.14054 4.05377 0 +13.7718 4.30145 0 13.7718 +1.65599 1.93856 2.83997 0 +0.456351 0.0610443 0.0458714 0 +2.63511 0 4.51132 2.1304 +>MA0076.2 ELK4 lnR0: 0.764 +2.78433 0 0.710945 1.40359 +2.77924 0 1.72196 2.26461 +0 3.24383 0.440388 3.2377 +11.8013 0 7.23387 2.39443 +8.48596 11.1049 11.1049 0 +11.6282 11.1082 11.1082 0 +12.1481 0 11.6282 12.1481 +12.1481 0 11.6282 12.1481 +11.917 11.3971 0 3.00237 +11.8813 2.47767 0 5.55159 +2.60677 0 0.897585 0.562736 +>MA0258.2 ESR2 lnR0: 3.1 +0 5.22502 0.547 4.902 +4.53997 12.6826 0 3.96074 +7.53523 12.8643 0 8.04476 +6.48718 4.99619 2.2812 0 +13.2897 0 3.79771 6.86136 +0 11.3463 6.53584 6.46023 +3.55276 0 0.611722 2.8863 +1.14244 0 0.928859 1.903 +0.988389 0 0.205875 1.03331 +1.66287 1.85173 2.71326 0 +3.06403 4.02109 0 7.09 +0 0.146178 0.704045 1.09927 +4.3765 0 4.11111 3.21912 +2.893 0 12.3929 2.69312 +2.27191 0.0706656 2.20753 0 +>MA0050.2 IRF1 lnR0: 6.604 +0.534995 -0.00286922 0.260263 0 +1.18345 0.487697 0.663497 0 +1.8915 0.479024 1.08264 0 +2.19696 0.0603898 1.57776 0 +0 2.30327 0.493744 2.12749 +5.45845 0 0.639017 4.75174 +6.63379 9.77805 9.77805 0 +10.2778 4.80677 9.75782 0 +10.2463 3.95058 7.42717 0 +10.7069 0 10.187 3.94095 +0 3.94998 1.39629 2.37791 +5.69849 0 1.1758 2.40229 +6.24526 8.78254 9.77275 0 +7.31249 5.89453 7.20351 0 +6.68655 3.89142 9.71647 0 +6.29295 0 5.09168 2.2978 +0 0.532752 0.43187 0.582018 +1.59562 0 0.664691 0.771223 +2.62656 1.75303 2.44757 0 +2.11233 1.62873 2.57543 0 +2.07756 0.575975 1.69205 0 +>MA0137.3 STAT1 lnR0: 0.764 +2.22981 0.723545 0.621865 0 +11.6894 5.49757 11.1694 0 +11.6636 8.36376 4.41574 0 +3.66103 0 8.77785 12.0777 +4.67054 0 10.8656 0.926667 +0 10.1395 -0.433652 2.74901 +4.87878 11.6443 0 12.1643 +7.28887 8.65714 0 4.82777 +0 11.1865 7.89708 11.7064 +0 8.62841 11.1881 11.708 +0 2.0458 0.839302 1.38106 +>MA0144.2 STAT3 lnR0: 0.764 +2.64475 0 1.16139 0.746876 +4.83467 13.6917 13.6917 0 +5.85993 4.87731 0.841531 0 +4.75972 0 14.118 4.72746 +3.9117 0.213394 13.0126 0 +2.13732 13.3519 0 1.33561 +4.15399 14.1512 0 14.6711 +3.37484 14.0508 0 6.00087 +0 13.7392 13.7392 14.2592 +0 13.7392 13.7392 14.2592 +0 2.72149 -0.0238518 0.955953 +>MA0140.2 GATA1::TAL1 lnR0: 4.852 +1.38224 0 1.06426 1.79194 +4.15117 1.68573 3.99914 0 +3.82407 11.5401 11.5401 0 +0 11.6348 11.6348 12.1548 +12.1548 11.6348 11.6348 0 +12.6747 0 12.1548 12.6747 +0.439776 4.87227 5.06303 0 +2.25179 0.72653 0 2.0613 +0.664563 -0.18597 -0.220815 0 +0.868144 0.427031 0 0.959703 +0 0.12712 0.315895 0.742387 +1.23422 0.463927 0 1.33386 +0.635515 0.356519 0 1.07313 +0 0.338654 0.668179 0.62464 +0.963374 0.600615 0 2.55364 +5.90798 0 7.57585 12.6359 +0 11.5469 11.5469 3.93291 +4.93693 1.97278 0 3.77945 +>MA0095.2 YY1 lnR0: 1.348 +2.52425 0 2.49031 3.28432 +0 12.1232 4.68894 8.68235 +0 5.49568 4.08205 6.65318 +0.905195 1.53888 0 4.10461 +0 12.1628 12.1628 12.6828 +12.6804 8.49622 12.1604 0 +9.65066 12.6806 0 13.2005 +9.43005 12.6802 0 13.2001 +3.28646 0 7.10532 3.53119 +2.17562 0.710598 0 1.08761 +2.86783 2.38649 0 3.14169 +2.27975 0 3.50827 2.87137 +>MA0593.1 FOXP2 lnR0: 0.764 +0 1.00279 0.265542 1.29183 +0 4.84068 0.721532 0.291802 +2.41584 9.15504 0 9.67499 +3.52586 8.85497 8.85497 0 +0 8.96932 8.96932 9.48927 +0 8.96932 8.96932 9.48927 +0 8.96932 8.96932 9.48927 +9.99236 0 9.4724 6.70295 +0 8.96932 8.96932 9.48927 +0 0.413861 -0.500645 3.65943 +0 0.879805 0.319745 1.37708 +>MA0595.1 SREBF1(MA0595.1) lnR0: 0.18 +0 0.421829 0.243024 4.81042 +5.82505 5.3051 5.3051 0 +6.345 0 5.82505 6.345 +0 5.3051 5.3051 5.82505 +6.16458 0 2.674 6.16458 +2.97374 0 1.46358 4.7634 +5.95804 0 5.43809 2.0894 +4.41999 0 1.91962 5.98944 +0 5.3051 5.3051 5.82505 +5.22829 0 1.73771 0.573865 +>MA0596.1 SREBF2(MA0596.1) lnR0: 0.18 +0 0.789036 0.2098 4.59839 +5.53029 5.01034 5.01034 0 +5.95804 3.45767 0 5.95804 +2.29094 5.19655 0 5.7165 +3.7108 1.33473 0 2.14135 +4.10896 1.86905 0 5.6784 +5.53029 5.01034 5.01034 0 +6.05024 5.53029 0 6.05024 +0 5.01034 5.01034 5.53029 +3.19085 0.192894 2.6709 0 +>MA0599.1 KLF5 lnR0: 0.18 +2.90126 1.88502 0 2.05381 +13.9262 0 13.4063 3.28989 +13.9391 0 13.4192 3.39589 +1.96592 0 13.0948 4.55966 +14.1181 0 13.5982 14.1181 +0.556522 12.2188 0 1.1311 +14.1181 0 13.5982 14.1181 +14.1181 0 13.5982 14.1181 +14.0673 0 13.5473 5.25652 +1.02992 0 12.3283 0.963633 +>MA0610.1 DMRT3 lnR0: 0.764 +0 0.384764 1.0153 1.53525 +0 1.58189 1.58189 1.30239 +2.96394 4.64018 4.64018 0 +10.3882 9.86822 0 10.3882 +9.86822 9.34827 9.34827 0 +0 9.34827 9.34827 9.86822 +1.75815 8.82849 2.17998 0 +10.3882 0 9.86822 10.3882 +0 1.17485 2.1131 2.63305 +0 1.45488 1.45488 1.09479 +0.460029 -0.0599217 -0.0599217 0 +>MA0613.1 FOXG1 lnR0: -0.988 +1.24741 8.20429 0 8.72424 +8.87515 8.3552 8.3552 0 +0 8.3552 8.3552 8.87515 +0 8.3552 8.3552 8.87515 +0 8.3552 8.3552 8.87515 +9.3951 0 8.87515 9.3951 +0 8.3552 8.3552 8.87515 +0 1.03525 6.78575 0.573522 +>MA0618.1 LBX1 lnR0: -0.988 +1.12458 1.32133 0.918499 0 +9.79795 3.6894 9.278 0 +0 9.34827 9.34827 9.86822 +0 9.34827 9.34827 9.86822 +9.43614 0.955969 8.91619 0 +2.33641 8.91619 2.07692 0 +0 8.90259 0.910148 9.42254 +5.21054 2.77097 0 4.26876 +>MA0628.1 POU6F1(MA0628.1) lnR0: 0.18 +0 0.855226 0.728471 2.47239 +1.20774 -0.511857 0.745321 0 +4.80144 5.85093 6.13761 0 +0 3.11771 6.06836 5.52086 +0 4.17929 5.38971 5.90966 +5.90966 5.38971 4.17929 0 +5.52086 6.06836 3.11771 0 +0 6.13761 5.85093 4.80144 +0 0.745321 -0.511857 1.20774 +2.47239 0.728471 0.855226 0 +>MA0630.1 SHOX lnR0: -0.988 +0.982252 -0.276942 0.604025 0 +3.52908 4.27127 5.88756 0 +0 3.56139 3.37063 4.1716 +0 7.76735 6.77714 8.2873 +5.82505 5.3051 4.50565 0 +2.92853 3.35614 2.62639 0 +0.547098 3.0861 0 2.42508 +0.848157 1.00533 0 2.009 +>MA0634.1 ALX3 lnR0: 0.18 +1.4234 0.114473 1.13723 0 +2.28671 0 1.54861 1.05618 +2.4799 -0.102522 3.14839 0 +0 3.39908 2.60164 3.60873 +0 4.06545 5.2172 5.03585 +6.61146 6.16772 9.15806 0 +3.4623 2.87831 4.46746 0 +0 3.56945 5.90075 2.98046 +0 0.109651 -0.286292 0.879167 +0 -0.347996 0.347339 1.22726 +>MA0635.1 BARHL2 lnR0: 0.18 +0.914583 0.338918 0 1.85863 +0.810208 0 1.20321 0.661582 +4.27695 12.9966 12.9966 0 +0 12.9966 12.9966 2.67968 +0 12.9966 12.9966 13.5165 +0 6.19347 3.00918 1.65614 +5.32815 0 6.58505 1.24169 +3.52295 13.5165 0 3.75442 +0.951178 1.1434 0 1.66857 +1.54646 0.566086 1.78527 0 +>MA0636.1 BHLHE41 lnR0: 0.18 +1.4561 2.38909 0 6.99381 +5.75847 7.67387 1.06988 0 +11.2734 0 10.3425 11.8527 +0 8.13876 7.3872 10.3425 +11.8527 0 11.3327 10.2832 +11.2734 11.3327 0 12.8429 +8.04331 7.75553 7.75553 0 +11.8527 11.3327 0 12.8429 +0 1.63902 8.83234 7.78285 +6.67504 0 2.47484 2.01039 +>MA0638.1 CREB3 lnR0: 2.516 +0.948671 0.446691 0 1.59182 +3.07997 1.31297 1.36827 0 +4.69736 8.52673 0 2.09305 +1.66986 0 6.05561 3.79569 +5.39066 0 3.79389 5.39066 +0 7.6566 7.6566 7.18634 +8.38471 0 7.86476 8.38471 +7.26066 8.72113 0 7.67164 +7.48443 6.96448 7.95469 0 +4.95915 0 4.72587 6.08551 +0 6.06362 3.96885 5.37314 +4.29736 -0.0427989 1.93762 0 +2.18024 0 2.5262 2.3164 +0 0.70243 -0.245134 1.43329 +>MA0639.1 DBP lnR0: 1.348 +0.311214 -0.350486 -0.499835 0 +0 1.17594 -0.393931 5.24955 +10.1089 9.84941 10.5792 0 +10.3694 9.36874 3.00301 0 +0 12.1486 3.27346 10.3694 +11.6191 0 8.25278 1.92 +1.66715 8.53946 0 12.1983 +10.6881 3.15537 9.17798 0 +0 4.05371 9.17798 9.88869 +0 11.1584 10.5792 11.0991 +5.01901 0 1.25159 0.646356 +0 0.10896 0.0334455 1.18549 +>MA0641.1 ELF4 lnR0: 1.348 +0 1.90117 1.35699 1.61796 +0 2.70226 4.89009 2.21283 +2.72417 0 3.57932 3.61057 +6.24615 0 3.19325 9.38505 +4.66055 0 7.08549 10.3853 +9.69021 10.1605 0 10.6804 +10.6804 10.1605 0 9.11097 +0 8.91812 7.34868 7.86863 +0 6.3546 7.34481 7.13501 +5.25214 5.93183 0 7.87825 +7.54016 3.54362 4.50899 0 +0.717764 2.44153 0 2.52522 +>MA0136.2 ELF5 lnR0: 0.764 +0 2.70418 2.45127 1.59028 +1.42279 0 1.25353 1.91308 +1.81965 0 0.944382 5.12068 +1.30577 0 2.99858 5.93785 +10.1168 11.5773 0 7.74792 +9.54103 11.5807 0 7.44626 +0 7.21734 9.77699 8.98796 +0 4.84297 10.7389 3.39407 +2.185 4.15432 0 5.5417 +2.34681 1.24762 2.43173 0 +0 0.834392 -0.191843 0.526644 +>MA0027.2 EN1 lnR0: -0.988 +1.96267 0 0.611202 1.66813 +3.85772 -0.288264 7.42662 0 +0 4.28653 4.75582 11.3853 +0 6.05492 10.8653 11.3853 +11.3853 10.8653 10.8653 0 +5.58466 2.03379 3.58855 0 +0 10.8653 5.95964 4.39908 +1.3306 0.823123 0 2.50625 +>MA0645.1 ETV6 lnR0: 0.18 +0 -0.00444147 0.477104 2.21094 +4.12997 0.833718 0 3.76771 +2.61017 0 3.96353 4.84507 +10.1323 12.583 0 9.33283 +8.68713 12.583 0 8.62363 +0 12.063 9.09238 12.583 +0 8.29292 7.068 7.24343 +3.60992 6.91111 0 13.1029 +5.12531 2.45239 4.26969 0 +1.15879 3.19293 0 2.05854 +>MA0475.2 FLI1 lnR0: 0.18 +0 4.33096 2.53586 3.24892 +4.37821 0 4.50674 7.66615 +4.43801 0 8.81665 15.7807 +13.221 15.2607 0 14.2112 +15.7807 15.2607 0 9.90801 +0 10.325 10.4612 11.7109 +0 6.9659 10.1424 2.81723 +0.874544 5.3868 0 8.62709 +5.12311 1.00148 3.46857 0 +1.31447 1.25377 0 1.98223 +>MA0042.2 FOXI1 lnR0: -1.572 +3.55378 6.94701 0 12.7368 +6.049 5.82421 6.57758 0 +0 2.70629 6.50034 12.2168 +0 7.15681 11.6969 12.2168 +0 7.15681 6.83804 6.21014 +5.50451 0 6.6571 3.16784 +0 8.03268 7.04247 12.2168 +>MA0033.2 FOXL1 lnR0: -1.572 +0.865777 7.50592 0 4.72629 +8.67787 2.96479 11.5835 0 +0 2.37758 5.78285 12.1034 +0 6.34983 11.5835 8.14259 +0 5.27086 5.96659 12.1034 +12.2665 0 11.7465 2.31769 +0 5.85872 11.5835 7.97433 +>MA0157.2 FOXO3 lnR0: -0.988 +5.07349 8.96932 0 9.48927 +8.96932 8.44937 4.67928 0 +0 4.40192 5.88971 7.97911 +0 7.45916 8.44937 8.96932 +0 5.0238 8.44937 8.96932 +5.52843 0 8.96932 7.50885 +0 4.8995 8.44937 8.96932 +0 4.04734 2.5531 0.552533 +>MA0646.1 GCM1 lnR0: 0.764 +2.26417 0 0.723474 1.22799 +0 3.0098 1.87465 6.29238 +6.97917 6.52232 7.19191 0 +2.79143 6.2232 0 10.8063 +4.89461 0 5.17447 5.07989 +5.6406 6.32548 0 2.98574 +14.7671 11.948 0 9.6478 +14.7671 10.0408 0 11.3415 +7.11797 1.56179 6.58834 0 +0 2.33502 0.893368 3.37806 +4.56559 0 1.45911 2.97223 +>MA0647.1 GRHL1 lnR0: 1.348 +0 0.974045 1.89643 1.63681 +0 3.93771 2.05817 2.5471 +0 8.67226 3.89927 5.25387 +0 9.66247 7.68205 6.36221 +11.6926 0 11.1726 11.6926 +3.23702 0 5.528 3.97447 +3.39523 5.50078 0 4.11643 +11.6926 10.1824 0 11.6926 +4.96719 8.35348 9.08323 0 +4.24116 3.17967 6.98847 0 +1.69271 1.67002 2.79374 0 +0.32791 1.03795 -0.128159 0 +>MA0648.1 GSC lnR0: 0.18 +1.21967 0.0918245 0 1.71621 +2.09833 0 2.3578 1.28529 +12.4473 6.20256 11.9273 0 +0 5.8178 4.53282 6.01897 +0 11.9273 11.9273 12.4473 +12.4473 7.2729 4.8177 0 +4.34853 0 3.71028 3.43937 +4.74473 0 2.84696 2.96284 +2.02421 0 0.464569 1.61324 +1.51146 0 1.80798 0.538924 +>MA0649.1 HEY2 lnR0: 0.18 +4.5399 4.1299 0 4.62156 +0 0.560706 -0.45036 1.51992 +4.88202 0 4.37897 5.40361 +0 10.1888 3.24617 10.7087 +8.25803 0 10.7087 11.2287 +6.46837 4.57948 0 11.2287 +5.55026 3.33763 10.1888 0 +11.2287 5.62964 0 6.32297 +4.83826 0 2.99261 0.990303 +2.10924 0 1.17208 2.21818 +>MA0131.2 HINFP lnR0: 1.348 +4.31113 0 1.65579 2.25818 +0 0.584606 0.79404 2.38144 +0 2.04487 -0.177776 3.90521 +8.04914 0 1.96945 6.06872 +9.35445 4.96586 0 5.92888 +8.79265 8.2727 8.2727 0 +9.09693 0 4.8069 9.09693 +9.12833 0 8.60838 7.14791 +9.31866 3.84766 0 4.90288 +8.07462 0 4.58404 5.40061 +1.64481 1.73771 0 1.45821 +1.50097 0.858248 0 1.03608 +>MA0046.2 HNF1A(MA0046.2) lnR0: 3.1 +0 0.562567 0.0520375 0.783771 +0.557709 4.06691 0 3.97817 +5.17889 3.18077 3.40954 0 +2.25692 2.15794 4.13246 0 +0 11.1532 5.26302 9.78489 +0 3.91637 9.99469 5.2251 +3.43824 4.4911 10.1629 0 +0.958346 0.273035 0 1.36179 +0 9.84417 4.80651 4.39632 +4.27056 9.3635 3.50426 0 +8.28039 5.37112 10.8344 0 +0 5.31605 2.84939 3.07947 +0 3.78308 3.1344 6.27526 +3.73654 0 4.38758 4.43216 +0.170298 -0.138875 0.446207 0 +>MA0153.2 HNF1B lnR0: 1.932 +4.81166 4.85469 0 4.72116 +5.77329 3.0394 3.8624 0 +2.40418 2.60223 4.73513 0 +0 10.4765 5.69092 9.17792 +0 4.16141 7.17692 5.59743 +3.94793 4.67938 8.23987 0 +1.08039 0.0590778 0 1.32621 +0 8.09791 5.10573 4.83133 +4.49736 5.62788 3.71588 0 +8.48874 4.95902 13.2564 0 +0 4.70609 2.00348 3.27283 +0 3.82507 3.40178 6.18251 +3.7445 0 4.51452 0.835288 +>MA0486.2 HSF1 lnR0: 1.932 +4.44152 5.67863 5.23055 0 +6.85506 7.58578 5.75587 0 +7.63547 0 7.11552 8.36522 +8.10573 1.46834 2.06146 0 +0 1.23913 1.38034 8.42451 +10.9249 10.4049 0 10.9249 +0 6.74608 8.31553 7.4343 +0 7.58578 7.58578 5.64463 +3.81738 0 2.13673 0.983917 +0.789594 1.61846 0 2.19175 +5.7505 7.32532 9.88498 0 +7.62505 8.31553 7.58578 0 +8.94446 0 8.42451 8.62568 +>MA0652.1 IRF8 lnR0: 2.516 +0.606598 -0.515665 1.27042 0 +6.97746 0 8.11916 3.22503 +10.9383 12.3988 0 11.3493 +0 10.3094 11.8788 12.3988 +0 11.8788 11.8788 7.36112 +0 11.8788 11.8788 10.4184 +7.19396 0 3.30627 10.1389 +10.1389 0 12.3988 2.75593 +12.9187 12.3988 0 12.9187 +0 11.8788 9.8984 12.3988 +0 11.8788 10.3094 6.35005 +0 9.31917 11.8788 12.3988 +9.36886 0 2.44462 8.95788 +4.14941 1.47488 8.73993 0 +>MA0653.1 IRF9 lnR0: 3.1 +0 5.45297 5.71883 4.91686 +0 1.71962 2.99047 1.14053 +6.57611 0 6.6071 5.33739 +6.75873 9.66434 0 9.60506 +0 8.56515 10.1346 11.6448 +0 11.1248 11.1248 9.66434 +0 9.55537 11.1248 10.6546 +6.75873 0 4.09009 8.87531 +8.11726 0 11.6448 2.55924 +10.5953 11.6448 0 11.1745 +0 9.55537 11.1248 11.6448 +0 10.1346 11.1248 7.22899 +0 11.1248 11.1248 9.66434 +9.86552 0 3.81528 10.5953 +4.5033 0.519344 7.59153 0 +>MA0654.1 ISX lnR0: -0.988 +1.94335 0 1.23096 1.24255 +6.52859 -0.439719 9.43421 0 +0 4.82512 7.82521 6.30642 +0 6.33742 10.3849 7.47925 +10.9048 10.3849 10.3849 0 +10.9048 10.3849 5.78647 0 +0 10.3849 10.3849 5.31621 +0 0.79089 -0.392107 1.42673 +>MA0655.1 JDP2(MA0655.1) lnR0: -0.404 +0 5.771 2.98096 7.43168 +8.01091 7.27075 9.06041 0 +11.0905 8.59015 0 6.61124 +0 9.06041 8.48117 5.91615 +6.78118 0 1.45081 6.87974 +7.7907 10.0506 7.27075 0 +6.61124 0 8.59015 7.80111 +0 10.0506 10.0506 7.59994 +6.09129 1.47364 7.49096 0 +>MA0656.1 JDP2(MA0656.1) lnR0: 1.348 +1.87959 0.999169 0 2.11091 +0 3.64736 3.55922 10.303 +12.4517 10.6228 11.9318 0 +11.4022 14.4321 0 4.13718 +0 10.9416 11.1323 11.6523 +12.3924 0 11.6523 6.62924 +5.84249 11.8725 0 13.3827 +10.4713 9.3138 10.9416 0 +4.26175 0 12.1329 13.9619 +0 10.4866 10.6228 14.4321 +7.92122 -0.50075 3.31923 0 +1.97242 0 1.53947 2.18457 +>MA0657.1 KLF13 lnR0: 4.852 +0 2.05398 0.193172 1.33912 +1.25504 4.66132 0.617455 0 +1.79872 12.0579 0 6.72878 +1.40584 0 3.93025 3.65421 +4.09004 0 8.1874 4.38089 +0 10.59 7.04012 11.1099 +10.8211 0 7.33054 8.8407 +7.37297 9.88197 0 8.68195 +11.0569 0 10.537 8.08629 +8.63935 0 10.4186 10.9385 +10.2064 0 10.6766 7.14913 +2.29513 0 10.6815 7.77587 +8.37255 0.604587 7.8526 0 +3.66421 1.99492 4.64271 0 +3.5465 3.0974 2.89985 0 +1.59509 1.47838 0.88293 0 +2.02641 2.68894 1.25189 0 +2.60043 2.44236 0 1.63796 +>MA0658.1 LHX6 lnR0: 0.18 +0 0.738429 -0.260106 2.78218 +3.00396 0 1.91018 1.59304 +11.9974 3.56698 6.66703 0 +0 5.03337 2.63415 11.9974 +0 7.60881 11.4775 11.9974 +11.9974 4.913 7.51661 0 +11.9974 1.98819 4.77553 0 +0 11.4775 3.62436 10.428 +1.2437 2.09752 0 4.31081 +2.09632 0 1.17126 0.652832 +>MA0660.1 MEF2B lnR0: 1.348 +0.866895 4.55226 0 2.30638 +7.82143 0 11.5078 8.36356 +11.5078 6.33345 10.9879 0 +0 10.9879 10.9879 7.54698 +0.145157 8.4994 10.0688 0 +0 10.9879 7.32366 2.12686 +0 9.00745 9.41842 4.40809 +0 10.9879 10.9879 6.03833 +11.5078 10.9879 10.9879 0 +0 9.00745 9.41842 9.5274 +5.46332 7.2282 0 10.0474 +1.58629 0 4.37561 2.5765 +>MA0661.1 MEOX1 lnR0: 0.18 +0.640704 0.480675 0 1.78897 +3.9256 0 0.261506 4.30229 +5.47473 2.33417 5.21964 0 +0 1.28382 3.74122 6.16832 +0 10.9182 9.34875 9.45772 +8.29925 6.05934 10.9182 0 +7.5695 3.07096 2.63811 0 +0 10.9182 2.59534 8.65827 +0 -0.451146 0.557986 0.479779 +1.70123 0 1.08023 1.87605 +>MA0662.1 MIXL1 lnR0: 0.18 +0.161522 -0.193905 -0.331181 0 +1.68978 0 0.718354 0.594634 +2.52195 -0.119694 3.07246 0 +0 3.26473 2.33675 4.65596 +0 4.77778 5.02665 5.14657 +14.5788 5.14978 6.62459 0 +4.24429 2.11659 3.17777 0 +0 3.27072 7.26804 3.19157 +0 0.455445 -0.337948 1.28835 +0.590537 0 0.460727 1.45503 +>MA0663.1 MLX lnR0: 0.18 +0 4.5834 0.154697 2.06302 +8.25379 3.60474 1.83793 0 +6.43871 0 5.91876 6.11994 +0 7.27946 4.49959 7.79941 +8.45275 0 7.9328 8.45275 +8.5671 9.03736 0 8.5671 +6.65304 6.71233 6.71233 0 +7.98017 9.02967 0 6.98996 +0 4.02607 2.19616 3.78798 +3.2654 0.938879 4.50565 0 +>MA0664.1 MLXIPL lnR0: 0.18 +0 2.88105 0.120444 1.58606 +1.86631 3.4562 1.26971 0 +9.24427 0 5.17445 9.24427 +0 8.08151 6.51207 6.04181 +7.68749 0 5.07278 9.25694 +5.60096 7.86088 0 9.95028 +9.04754 8.52759 6.54717 0 +9.93467 9.41472 0 9.93467 +0 1.14891 1.48062 1.63077 +1.65585 0.750854 2.4866 0 +>MA0665.1 MSC lnR0: 0.18 +0 5.54933 1.34299 3.09865 +0 1.88512 3.56891 6.06928 +6.58923 0 4.08886 5.59902 +0 5.54933 5.54933 6.06928 +6.58923 2.40507 0 6.58923 +6.58923 0 4.08886 6.58923 +6.06928 5.54933 5.54933 0 +6.58923 6.06928 0 4.29003 +4.08886 2.12376 3.25013 0 +6.06928 2.25992 3.25013 0 +>MA0667.1 MYF6 lnR0: 0.18 +0 4.52737 2.10204 5.7409 +0 3.98524 3.59319 7.72132 +9.23149 0 8.71153 9.23149 +0 6.21116 5.22095 8.71153 +1.19695 3.02156 0 4.78299 +5.24045 0 3.2654 3.12887 +5.16167 8.19158 8.19158 0 +9.23149 7.14209 0 9.23149 +7.14209 3.71231 8.19158 0 +8.71153 0.941336 5.22095 0 +>MA0668.1 NEUROD2(MA0668.1) lnR0: 0.18 +0.864468 2.65557 0 3.4943 +1.24319 0 1.84367 10.199 +11.0489 0 4.0084 11.0489 +0 10.009 1.81846 4.85706 +10.5289 2.78574 10.009 0 +0 3.15782 4.77529 8.2297 +10.5289 1.72887 10.009 0 +11.0489 10.5289 0 4.29544 +9.89083 0.907656 0 0.87926 +1.6911 -0.311832 2.20277 0 +>MA0669.1 NEUROG2(MA0669.1) lnR0: 0.18 +0 5.78116 -0.0758201 7.87055 +0 0.965055 2.14738 8.65255 +8.18229 0 8.65255 6.61284 +0 8.1326 6.15218 8.65255 +6.35335 5.57294 3.78328 0 +0 4.99371 5.57294 8.65255 +6.09289 6.15218 8.1326 0 +9.1725 8.65255 0 9.1725 +6.67213 0.787364 0.993723 0 +8.70581 0 8.18586 1.86653 +>MA0670.1 NFIA lnR0: 0.18 +0.601654 0.120921 0 0.645032 +1.27344 1.28487 0 1.12217 +16.3812 15.8613 15.8613 0 +16.9418 16.4219 0 16.9418 +16.8725 0 16.3525 16.8725 +16.8694 0 16.3494 16.8694 +0 15.7618 15.7618 16.2817 +0 15.7673 15.7673 16.2873 +0.82581 0.424961 0 1.26953 +0.207996 0.619176 0.428145 0 +>MA0671.1 NFIX(MA0671.1) lnR0: -0.404 +0.66649 0 0.0138484 0.773326 +0.986197 0.815297 0 0.948224 +1.52768 1.2239 1.93066 0 +8.39111 7.38436 0 4.17744 +13.3969 0 3.30185 10.5185 +15.3773 0 14.8574 15.3773 +0 3.32285 6.911 8.12948 +0 4.0331 0.839582 3.73849 +0.665332 0.0150907 0 1.01951 +>MA0048.2 NHLH1 lnR0: 0.18 +1.96328 0 3.5387 4.75224 +2.72786 3.55449 0 4.40317 +9.51253 0 10.973 11.4929 +0 8.47263 9.46284 10.973 +11.4929 2.81525 0 4.71447 +4.95765 0 4.07541 11.4929 +10.973 8.15385 8.15385 0 +9.9235 8.6738 0 10.5027 +3.35905 0 4.35196 3.1204 +3.30246 1.54073 0 1.05505 +>MA0672.1 NKX2-3 lnR0: 0.18 +0 0.183914 0.316151 1.20603 +2.69379 0 1.03382 6.50102 +8.33702 0 13.0507 6.58446 +0 5.96632 8.48333 5.15722 +10.4318 0 13.0507 13.5707 +13.0507 12.5308 8.32444 0 +13.0507 2.75095 12.5308 0 +0.765628 1.77724 0 4.35441 +0 2.78478 1.79769 1.90939 +0 -0.319051 -0.336574 2.4592 +>MA0673.1 NKX2-8 lnR0: -0.404 +1.3729 0 0.308695 4.30223 +7.36642 0 12.936 2.49023 +0 3.28714 12.4161 4.01023 +9.58732 0 12.936 6.72806 +12.936 5.95636 12.4161 0 +8.39593 0.887085 12.4161 0 +1.80892 0.909555 0 4.45929 +0 2.68414 3.06351 1.96829 +0 0.174471 -0.222256 1.95692 +>MA0674.1 NKX6-1 lnR0: -0.988 +1.37489 0.0778869 0 1.45488 +10.5758 0.980666 10.0559 0 +0 0.276966 9.83709 2.81687 +0 2.90691 6.81884 5.6979 +11.003 10.4831 10.4831 0 +5.17795 5.01357 10.4831 0 +0 5.72276 3.49684 6.8739 +0 1.75581 2.79028 2.12428 +>MA0675.1 NKX6-2 lnR0: -0.988 +1.2041 0 0.213761 1.16182 +3.21119 -0.0211255 3.21142 0 +0 0.0570225 2.87586 2.1153 +0 5.35009 6.03908 5.06339 +4.96744 13.5498 13.5498 0 +2.91036 2.53329 4.53044 0 +0 5.09808 4.04386 4.75457 +0 0.993036 2.04057 1.3607 +>MA0678.1 OLIG2(MA0678.1) lnR0: 0.18 +0 3.58452 1.95864 3.84663 +0.965125 0 2.67477 6.23705 +4.90067 0 8.24936 11.0685 +0 8.45916 4.33006 6.06928 +10.5486 10.0286 10.0286 0 +0 5.54933 5.82226 8.24936 +6.13278 2.77836 10.0286 0 +7.64294 8.56814 0 4.25324 +7.88509 1.11586 0 0.7366 +3.41937 0.690475 4.22797 0 +>MA0068.2 PAX4 lnR0: -0.988 +3.62503 0 2.77134 2.15952 +2.47658 2.87598 0.93055 0 +0 6.21223 7.78168 6.32121 +0 7.78168 7.78168 8.30163 +8.30163 7.78168 5.22202 0 +4.09529 4.23181 4.35611 0 +0 1.35338 4.23181 4.63742 +1.65404 1.81121 0 3.48205 +>MA0680.1 PAX7 lnR0: 0.18 +2.42346 5.17207 4.65633 0 +0 7.01445 7.17334 8.96087 +0 9.24037 11.2208 11.7407 +8.96087 6.80501 9.24037 0 +8.50076 0 6.80798 2.42224 +1.68845 6.45859 0 11.7388 +0 11.2208 7.79522 8.31517 +8.07653 11.2208 11.2208 0 +7.32496 6.56637 7.93138 0 +0 5.09156 5.6905 3.85294 +>MA0683.1 POU4F2 lnR0: 3.684 +0 1.09922 0.420361 1.53256 +4.58962 3.93468 5.09902 0 +4.62804 6.55453 0 5.85823 +1.59959 0 9.59167 9.12141 +0 8.17544 8.65612 7.9254 +10.3641 10.8344 10.8344 0 +0 7.62402 7.04478 3.49505 +0 4.4127 5.02678 1.81107 +5.10064 5.06136 5.9757 0 +3.09932 7.46183 7.61235 0 +0 6.25576 3.16469 5.68342 +0 8.70535 7.71514 11.5245 +7.03997 5.89394 4.73036 0 +4.54607 3.66226 0 1.54176 +0 3.16765 2.9571 3.66329 +2.44777 2.05494 0 3.80586 +>MA0686.1 SPDEF lnR0: 0.764 +0 4.93023 4.14283 2.31909 +1.0487 0 2.32712 5.6032 +6.90539 0 5.58214 12.5772 +4.7597 0 11.0671 11.587 +11.0078 10.4878 0 12.5772 +9.79736 12.0573 0 9.43834 +0 11.5373 8.75746 10.4878 +3.08796 5.46805 7.98746 0 +2.06735 2.91406 0 6.57053 +6.23223 1.24463 6.72691 0 +0 1.21151 -0.0121217 1.2252 +>MA0687.1 SPIC lnR0: 2.516 +0 0.259931 0.540946 0.980392 +0 1.80578 0.667293 1.97168 +0 2.29864 3.18298 3.26667 +0 3.7235 7.01291 5.23366 +0 6.83361 6.83361 1.1668 +3.04855 1.24753 0 4.18416 +0 0.0433235 0.332644 6.41234 +8.21209 4.55324 0 6.23167 +4.53707 7.7872 0 3.59881 +0 4.11372 7.08435 3.55685 +0 2.04713 3.2281 4.37924 +4.53092 7.78105 0 8.301 +2.06337 2.41451 2.8838 0 +0 1.11244 2.98149 2.51123 +>MA0083.3 SRF lnR0: 3.684 +2.37048 2.61389 3.24508 0 +4.39485 2.87532 0 2.12221 +0 -0.483082 1.57406 1.88368 +11.2055 0 6.72468 11.2055 +9.23789 0 7.14849 6.93869 +0 5.76286 5.3266 4.15699 +4.78967 9.99448 7.21461 0 +0 9.56522 7.99577 10.0852 +9.55923 7.46984 6.8906 0 +0 9.56399 9.56399 6.03649 +1.27614 5.78737 9.45159 0 +8.16396 7.49349 0 11.3028 +8.14577 9.19526 0 8.31403 +1.37169 2.1499 -0.486286 0 +2.10342 0 2.78266 4.29283 +0 3.27855 2.65535 1.85768 +>MA0009.2 TBXT lnR0: 3.684 +6.953 4.88169 7.62562 0 +1.60118 0 1.83584 4.7067 +0 5.51129 0.896662 4.08961 +12.7606 0 12.2407 11.1912 +0 11.3668 4.287 11.8867 +5.01838 0 5.4564 4.15426 +1.46654 0 1.39184 2.94371 +3.34544 2.8669 4.36132 0 +0 4.52252 2.53044 3.28324 +2.94345 1.52237 0 1.50428 +3.94141 5.69094 0 4.79274 +12.6021 4.57886 8.31202 0 +9.62675 12.771 0 13.291 +3.52993 0.811564 5.83292 0 +4.71681 2.48687 0 2.58951 +0 7.72462 4.64812 7.77968 +>MA0688.1 TBX2 lnR0: 0.764 +0 1.10739 0.28234 0.638901 +0 5.15279 1.60889 2.81671 +2.89616 2.58777 0 3.65705 +8.75235 6.36335 0 8.17311 +11.5218 2.71744 6.58608 0 +7.33342 11.5218 0 8.37754 +3.33595 2.46784 6.24156 0 +3.84205 1.28981 0 1.68269 +0 6.29352 4.09288 4.67068 +0 1.81707 1.71619 1.92387 +0 1.18846 0.78952 1.13451 +>MA0689.1 TBX20 lnR0: 0.764 +0.338837 5.07436 0.510666 0 +0 4.01267 2.82798 4.4743 +3.97575 3.99363 0 4.88431 +9.59264 9.07269 0 4.28754 +9.07269 8.55274 5.12718 0 +9.59264 8.08248 0 7.29345 +5.9338 7.56253 5.00288 0 +4.0329 5.64713 0 3.28001 +0 7.56253 5.77287 5.64713 +0 4.5053 2.85419 1.72746 +1.46807 2.28034 0 2.8239 +>MA0691.1 TFAP4(MA0691.1) lnR0: 0.18 +0 2.2257 2.78793 3.86406 +0 1.44207 4.52966 0.764337 +12.1465 0 11.6265 12.1465 +0 9.53712 11.1066 11.6265 +10.577 5.26317 0 8.27783 +7.7307 0 6.03792 9.3666 +10.6363 10.1164 11.1066 0 +12.1465 10.6363 0 12.1465 +0 3.4182 1.89504 0.164519 +3.47826 1.78301 2.43079 0 +>MA0692.1 TFEB lnR0: 0.18 +0 1.14031 -0.117767 3.81447 +1.75805 0.292053 1.13737 0 +9.35216 0 12.9613 11.5008 +0 4.35638 6.52259 4.93735 +13.4813 0 6.63157 3.40594 +2.16116 4.86641 0 10.9216 +4.21803 5.1045 5.27381 0 +10.1919 9.53574 0 9.93139 +0 1.3568 2.76716 3.39765 +4.85143 0 3.36409 1.56858 +>MA0694.1 ZBTB7B lnR0: 1.348 +1.09024 2.29204 0 1.6299 +4.1597 0 3.01209 5.54456 +2.72806 6.46976 0 5.02726 +0 2.4059 10.2294 8.76895 +8.70967 0 9.75916 11.2693 +11.2693 0 9.17993 11.2693 +0 0.642961 8.65998 8.76895 +8.70967 0 10.7494 10.2791 +11.2693 0 10.7494 8.29869 +1.71275 1.94464 0 3.09277 +0 2.10034 2.51131 2.31704 +0 1.14888 1.47922 1.70145 +>MA0695.1 ZBTB7C lnR0: 1.348 +1.27768 1.94394 0 1.99701 +2.96515 0 2.21614 3.68716 +2.03844 2.95252 0 3.37613 +0 1.63154 6.23627 5.29672 +5.14523 0 9.89511 10.4151 +10.4151 0 7.33545 6.54642 +0 1.37741 6.23627 6.46955 +6.20872 0 6.92448 6.28596 +3.97098 0 4.17035 3.97098 +1.56532 1.9066 0 2.88277 +0 0.663625 1.47598 1.26617 +0 -0.440809 0.234246 0.923364 +>MA0696.1 ZIC1 lnR0: 2.516 +5.00374 2.681 0 2.02527 +0 2.54387 1.08102 9.79011 +5.5821 0 8.85113 8.28716 +5.00525 0 7.08504 7.14943 +3.77934 0 6.22074 5.25495 +15.2182 0 12.399 12.2475 +7.75926 0 11.2791 11.356 +10.0704 0 14.0297 1.34789 +4.37265 9.34961 0 11.4704 +10.5788 0 5.90358 2.52575 +4.43345 3.38691 1.74924 0 +9.30422 10.3345 0 14.4627 +2.3514 0.542928 2.70739 0 +10.3246 5.98713 0 4.14302 +>MA0697.1 ZIC3 lnR0: 3.1 +3.45616 1.66863 0 1.7362 +0 1.77056 1.35959 7.28552 +5.14663 0 7.59731 5.81807 +5.15362 0 5.62388 5.15362 +3.52888 0 7.48821 3.72854 +8.15868 0 7.63873 8.15868 +8.13812 0 7.61817 8.13812 +7.60973 0 7.08978 1.71382 +3.73281 5.13248 0 6.64264 +5.6313 0 4.63068 3.07165 +3.07918 2.05723 1.06702 0 +6.28315 7.74362 0 6.28315 +2.34986 0 2.65822 0.78041 +6.21187 6.10289 0 3.65221 +1.0042 0 2.48996 1.08144 +>MA0698.1 ZBTB18 lnR0: 1.932 +0.751579 0 0.737388 0.808026 +0 2.6765 0.943714 1.07884 +3.50208 2.27094 0.857366 0 +2.41863 0 2.81918 8.25161 +9.70851 0 11.6239 10.9854 +0 10.5247 8.04672 5.98616 +12.1439 5.73957 0 11.3444 +0 3.14782 5.03979 5.46563 +9.73569 9.12354 6.57884 0 +12.1439 12.6141 0 13.1341 +8.04459 4.86642 7.92593 0 +5.2183 4.94131 0.0322557 0 +1.73592 0 0.0598933 0.525261 +>MA0699.1 LBX2 lnR0: 0.18 +0.55995 0.169119 0 0.948757 +2.47087 0 1.57343 1.51613 +3.85824 0 3.8556 0.779886 +0 2.59343 2.64929 5.63561 +0 2.81154 3.95172 5.00794 +11.4362 6.05743 4.08897 0 +4.2687 2.97796 2.79689 0 +0 5.83722 4.24082 4.28774 +0.715028 1.37132 0 1.87819 +0.951523 0 0.402237 1.31393 +>MA0706.1 MEOX2 lnR0: 0.18 +0 0.553035 -0.277159 0.639483 +2.69795 0.737684 0 2.93971 +3.98559 1.70091 4.64689 0 +0 0.878868 2.43849 4.68489 +0 4.35457 5.8707 5.54632 +8.19875 8.65058 6.54738 0 +4.33258 1.44686 1.72398 0 +0 5.47552 2.00032 4.48958 +0 0.976093 0.70518 0.49133 +0.799033 0 0.330688 1.00927 +>MA0122.2 NKX3-2 lnR0: -0.404 +0 0.561982 -0.0737442 1.33055 +2.23816 0 1.00201 3.70174 +8.46203 0 8.15152 4.03157 +0 5.17585 6.2493 4.34433 +5.53257 0 7.64952 8.11751 +9.7982 6.67945 7.18348 0 +7.64952 4.28324 11.8379 0 +0 3.43714 4.46783 2.87793 +0 1.55158 0.685483 1.5901 +>MA0710.1 NOTO lnR0: 0.18 +0.731297 0.198468 0 1.38498 +4.65284 0 4.45628 1.42559 +1.57694 1.87559 4.64976 0 +0 0.726052 13.2261 6.68658 +0 13.7249 13.7249 14.2449 +14.2449 13.7249 13.7249 0 +5.77786 7.80618 5.08584 0 +0 13.7249 2.82567 3.45598 +0.644455 0.9839 0 1.94464 +1.42984 0 0.484459 1.41382 +>MA0711.1 OTX1 lnR0: -0.988 +0.74728 -0.114314 0.9043 0 +4.92508 7.41066 13.8547 0 +0 13.8547 5.93865 5.37357 +0 13.8547 13.8547 14.3747 +6.52159 13.8547 2.34239 0 +5.64623 0 5.10006 6.41245 +5.36317 0 1.4221 3.29338 +2.99535 0.770072 0 1.6553 +>MA0132.2 PDX1 lnR0: -0.988 +1.23149 0.144547 0 1.7954 +3.9529 0.387516 11.5475 0 +0 0.547892 4.13565 5.87889 +0 6.68514 12.1546 12.6746 +12.6746 12.1546 12.1546 0 +12.6746 12.1546 12.1546 0 +0 12.1546 12.1546 12.6746 +0.91744 1.23157 0 2.25921 +>MA0713.1 PHOX2A lnR0: 0.764 +2.37751 2.65257 3.95696 0 +0 5.08562 2.34419 3.47812 +0 12.8292 7.75017 10.7895 +3.03856 0.836347 3.62107 0 +3.22806 -0.313225 0.88007 0 +2.41662 0.0560593 2.53656 0 +0 3.43428 2.04634 4.66031 +0 5.26022 4.63414 6.36298 +13.3492 9.40368 11.2598 0 +3.29881 3.3178 6.53393 0 +0 5.06056 3.24976 2.75867 +>MA0714.1 PITX3 lnR0: -0.404 +0.760219 0 0.233262 1.3589 +1.05511 -0.311749 1.5156 0 +3.62634 6.32252 8.67775 0 +0 6.97215 4.01784 5.24582 +0 11.9672 8.00632 12.4871 +4.52689 4.91791 1.96018 0 +4.77107 0 5.17569 5.19555 +5.25085 0 4.65763 3.18382 +1.87994 0 1.58796 1.81018 +>MA0715.1 PROP1 lnR0: 0.764 +3.13889 4.89599 5.13464 0 +0 8.5602 8.5602 5.53029 +0 8.5602 6.99076 9.08015 +3.74063 3.29038 4.35386 0 +3.6297 0.281443 3.57085 0 +0.488418 1.61774 1.17631 0 +0 3.32654 8.5602 4.0425 +0 6.57978 3.05999 6.30028 +7.51071 8.5602 8.5602 0 +5.31007 4.35386 5.78033 0 +0 8.5602 4.59936 3.54987 +>MA0716.1 PRRX1 lnR0: -0.988 +1.64182 0 1.05205 1.02495 +2.40427 -0.322017 2.95499 0 +0 3.89224 3.19272 4.83326 +0 4.99287 6.29197 6.76349 +14.4022 11.9018 13.8823 0 +4.19818 2.82231 4.00692 0 +0 4.64048 6.85372 4.23826 +0 0.622296 0.0515611 1.32168 +>MA0717.1 RAX2 lnR0: -0.988 +2.07197 0 1.15383 1.08217 +2.96051 0 3.50534 0.551566 +0 3.11041 2.56279 3.96485 +0 4.1067 5.10443 5.18495 +7.09375 5.14069 7.66786 0 +4.12312 2.64731 3.39164 0 +0 3.31908 6.16415 3.15851 +0 0.31269 -0.403605 1.24718 +>MA0718.1 RAX lnR0: 0.18 +0.766226 1.30049 0 1.91187 +2.00576 0 1.18394 0.98644 +3.07072 0 5.56869 0.697715 +0 6.47756 8.62624 5.82151 +0 5.373 6.94244 6.52821 +4.24049 10.6067 10.6067 0 +5.01709 4.49714 5.01805 0 +0 10.6067 6.25734 4.20634 +0 1.34571 0.057928 1.4698 +1.14944 0 1.11653 0.877999 +>MA0719.1 RHOXF1 lnR0: -0.988 +0 -0.236719 0.269348 0.0137984 +1.9246 12.763 3.9463 0 +0 11.795 -0.475459 1.99909 +0 12.763 12.763 13.283 +12.723 12.2031 0.528561 0 +13.8029 0 13.283 13.8029 +13.8029 0 13.283 2.75981 +0.618394 0 0.698658 1.21457 +>MA0721.1 UNCX lnR0: -0.988 +1.92986 0 1.21428 0.573536 +2.31684 -0.261917 2.71767 0 +0 3.30346 2.46089 3.77423 +0 4.25758 5.87157 5.32051 +6.19822 4.94201 7.68864 0 +3.53382 2.66998 3.80954 0 +0 3.50154 5.08136 3.21652 +0 0.291601 -0.125702 1.50662 +>MA0722.1 VAX1 lnR0: -0.988 +3.12563 0 2.58039 0.681026 +2.92093 1.85576 5.11115 0 +0 2.05887 4.22251 4.07573 +0 4.52261 6.21805 5.24129 +4.0995 5.33839 4.05258 0 +3.33471 3.4689 0.894528 0 +0 5.32206 1.43942 3.68255 +1.47766 0 1.02347 0.930925 +>MA0724.1 VENTX lnR0: -0.404 +0 3.57924 2.61319 2.22146 +0.997371 0 0.996268 1.74541 +5.87618 0 14.4038 3.08763 +1.55853 1.49827 0 5.15913 +0 6.2865 13.8838 8.23593 +14.4038 13.8838 13.8838 0 +14.4038 13.8838 13.8838 0 +0 13.8838 13.8838 14.4038 +1.28827 4.37383 0 3.2786 +>MA0725.1 VSX1 lnR0: -0.988 +3.96714 0 3.8727 1.23636 +2.85707 1.57492 4.00141 0 +0 3.87275 4.04958 4.56696 +0 5.86921 5.71226 7.14997 +6.23221 5.50508 6.43926 0 +3.87794 3.59418 3.22747 0 +0 4.14833 1.48392 3.27298 +0.501957 -0.450556 -0.491347 0 +>MA0726.1 VSX2 lnR0: -0.988 +4.95666 0 4.37786 1.67529 +3.63929 1.79799 4.67433 0 +0 4.54676 4.75506 5.04887 +0 6.20124 6.21272 7.67752 +6.79146 5.62582 6.62369 0 +4.41743 4.03866 4.3777 0 +0 4.84947 2.16391 3.72929 +1.08296 0.398924 0 0.856827 +>MA0112.3 ESR1 lnR0: 4.268 +0 1.28203 0.660143 1.37486 +0 5.27009 0.431789 8.56991 +9.71445 9.1945 0 4.63538 +8.17894 9.22843 0 9.74839 +9.01417 8.49422 6.5138 0 +8.26673 0 8.73699 7.68749 +0 8.27573 3.37004 8.79568 +2.14088 0 2.62431 4.30273 +1.91974 0.600338 0 2.86599 +0.789461 1.66265 0 4.82485 +8.9091 3.84907 7.39894 0 +8.16546 9.21496 0 9.73491 +0 7.34481 7.34481 8.85497 +9.28195 0 7.19255 9.28195 +5.30553 0 8.74642 9.26637 +8.88656 1.26687 5.39598 0 +3.03936 1.59 0 0.554376 +>MA0141.3 ESRRB lnR0: 0.764 +3.9633 1.68205 3.95851 0 +7.89577 0 2.74354 8.21454 +0 9.15506 10.1453 8.36602 +0 9.15506 8.16485 10.6652 +9.20475 9.09578 0 10.195 +10.195 8.36602 0 9.20475 +7.88535 6.5954 7.00638 0 +9.61573 0 9.67501 7.22433 +0 10.1453 4.36948 8.6848 +0.567674 1.48527 4.03938 0 +0 0.544296 1.32863 0.361673 +>MA0017.2 NR2F1(MA0017.2) lnR0: 1.932 +1.76065 0 1.78686 2.0288 +0 1.56125 2.10878 1.88004 +0 3.4696 -0.144468 3.71565 +0 12.405 0.632649 12.925 +13.9452 8.51952 0 13.9452 +13.9452 13.4252 0 13.9452 +13.4252 12.9053 12.9053 0 +13.9452 0 13.4252 13.9452 +0 12.9053 6.44557 13.4252 +0 0.216423 1.12399 1.1605 +0.960255 0.561634 0 2.08485 +0.763821 0.647164 0 1.19219 +3.19128 3.62579 0 3.89702 +>MA0113.3 NR3C1 lnR0: 4.268 +1.00696 1.99137 0 1.42636 +1.03787 6.81806 0 6.28315 +9.80918 11.6237 0 9.88062 +0.223934 3.56195 1.33353 0 +0 10.3549 10.2044 10.5882 +14.9567 0 10.5681 14.9567 +0 9.30414 4.15384 7.92091 +2.09535 -0.358906 2.21064 0 +0 0.550579 -0.0556152 0.369664 +0 3.00929 0.0126204 2.62051 +8.09815 4.81838 8.25662 0 +15.105 11.0352 0 12.5453 +11.2951 10.6246 8.29712 0 +0.230001 1.18304 3.43979 0 +9.91309 0 11.8711 9.1257 +6.42524 0 6.21649 1.09267 +1.03387 0 1.50781 1.32422 +>MA0727.1 NR3C2 lnR0: 4.268 +1.77184 1.57846 0 1.17588 +1.35281 6.82303 0 6.11557 +10.3312 12.473 0 10.2591 +0 3.11282 0.864055 0.356379 +0 10.2483 10.4391 11.4397 +15.9755 0 12.8959 15.9755 +0 9.55502 4.42209 7.16729 +1.82145 0 2.51381 0.666701 +0 1.35795 0.545137 0.695141 +0 3.01214 0.181985 2.4854 +6.6904 4.87288 10.2575 0 +16.2105 12.4012 0 16.2105 +12.9916 10.2308 12.7904 0 +0.423455 0.799123 3.22645 0 +11.7035 0 11.9416 9.42117 +5.9825 0 5.4076 1.1515 +1.44971 0 1.15063 1.49481 +>MA0729.1 RARA(MA0729.1) lnR0: 4.852 +1.54391 7.92725 0 7.13822 +0 7.39053 3.26142 8.90069 +9.96956 9.44961 0 9.96956 +8.98126 9.45152 0 5.69185 +9.03991 5.9603 7.52975 0 +8.32542 0 4.66658 9.89487 +0 8.4386 6.13941 8.95855 +0 8.43319 3.62277 1.67636 +0 8.43319 6.45277 3.75659 +0 5.86265 6.12311 8.94226 +9.99612 9.47617 0 9.00591 +9.98669 9.46674 0 3.37959 +7.02593 8.4864 8.4864 0 +9.89083 0 9.37088 8.32138 +0 8.47065 7.48044 8.9906 +0 3.30955 3.56231 1.55366 +6.71064 7.76013 -0.00232804 0 +8.26988 0.959085 0 0.61089 +>MA0730.1 RARA(MA0730.1) lnR0: 4.268 +0 4.87299 1.25796 9.99133 +10.9569 10.4369 0 9.38745 +10.9209 8.83155 0 4.81142 +7.28054 5.99059 5.41136 0 +7.93918 0 7.55539 6.94897 +0 5.77331 6.27089 8.77126 +0.937205 0.022933 2.22836 0 +1.95657 0.42982 0 1.89133 +2.69414 0 2.08079 0.946461 +0 2.48185 1.74731 2.06666 +0 5.24184 1.00656 6.92027 +0 5.47162 1.52132 9.04881 +9.35543 10.4049 0 8.62568 +9.91987 7.4195 0 5.79077 +6.90645 5.97553 5.75531 0 +9.02384 0 6.09475 6.84376 +0 7.93465 5.26065 7.00946 +>MA0731.1 BCL6B lnR0: 4.268 +7.62505 2.82549 7.1051 0 +6.01254 7.47301 0 7.00275 +8.96007 0 8.44012 7.39062 +7.65899 7.13904 7.13904 0 +7.66568 7.14573 7.14573 0 +7.65899 7.13904 5.56959 0 +9.02458 0 8.50463 9.02458 +7.67234 3.48818 2.07332 0 +0 7.53484 7.53484 8.05479 +7.89003 7.37008 0 7.89003 +7.87351 7.35356 0 7.87351 +0 7.57988 6.01043 8.09983 +0 7.5848 7.5848 8.10475 +7.67897 5.58957 7.15902 0 +7.65227 3.08487 7.13232 0 +1.60705 0 4.56369 8.37305 +0 -0.199232 3.95933 7.44991 +>MA0472.2 EGR2 lnR0: 0.764 +0 0.240559 3.0523 2.98801 +11.0161 0 5.68572 4.86743 +4.14044 11.7496 0 4.54499 +8.24265 0 5.84815 6.16367 +6.42046 0 6.53806 7.24877 +10.9376 0 5.18397 2.89812 +0 3.71257 5.73213 9.39097 +11.0362 0 8.9468 6.49612 +5.70557 11.8611 0 5.02747 +8.74785 0 6.17778 4.25621 +0 2.90067 1.13708 1.98703 +>MA0732.1 EGR3 lnR0: 3.1 +1.44531 0 1.19941 0.971295 +0.279064 -0.366792 0.959941 0 +0 0.0305074 5.9677 5.5639 +9.70219 0 10.7517 7.50155 +5.48096 5.9727 0 6.32921 +11.2724 0 9.18301 11.2724 +11.2739 0 10.754 7.84838 +11.2468 0 7.75621 4.969 +0 0.813882 6.01043 7.78105 +11.2869 0 7.79637 9.7175 +6.21386 6.15332 0 6.77535 +9.73566 0 9.79495 6.88933 +0 3.95707 2.3534 3.92399 +1.07678 0 2.41295 0.646631 +0.777174 0.449525 1.03082 0 +>MA0733.1 EGR4 lnR0: 3.684 +0.735122 -0.103605 0.429894 0 +0.889328 -0.166757 1.47393 0 +0 -0.0124943 3.61436 4.06999 +5.91924 0 4.83885 4.28588 +4.14679 3.85133 0 3.8041 +8.97038 0 6.05904 6.10791 +5.66944 0 5.31186 6.31514 +12.506 0 5.2582 5.53062 +0 1.55121 3.13288 3.59272 +7.06763 0 5.2073 4.64096 +5.34649 1.91671 0 5.22933 +9.0645 0 4.52021 4.78488 +0 1.912 1.92911 3.21954 +0.0465214 -0.177695 1.57669 0 +0.887966 1.21543 1.53421 0 +1.01339 0.583722 0.83883 0 +>MA0735.1 GLIS1 lnR0: 3.684 +0 0.284696 4.43331 1.84134 +11.4847 7.50707 0 3.5728 +0 11.981 9.20115 9.36208 +12.6314 0 10.542 12.6314 +10.3209 0 10.5307 10.6397 +12.6282 0 8.55834 12.6282 +10.654 0 9.55479 11.065 +12.5999 0 12.0799 9.62926 +9.75889 0 9.45915 10.9693 +0 10.1025 4.8238 9.82302 +12.5526 0 12.0327 12.5526 +10.7186 13.1693 0 8.04461 +0 9.55041 6.8546 1.49338 +0 0.55555 10.8429 0.0304287 +10.6446 10.5356 0 9.01684 +2.33414 0 1.17198 2.07312 +>MA0736.1 GLIS2 lnR0: 2.516 +4.11666 2.34604 0 1.58911 +0 2.54874 2.08971 8.58402 +8.50841 0 7.98846 7.92917 +8.19229 0 9.97154 9.50128 +7.52086 0 9.97154 6.62284 +8.93921 0 9.98871 10.5087 +4.69832 0 9.95416 8.17491 +4.79552 0 8.9572 3.88855 +1.65791 6.07867 0 4.64594 +8.51902 0 5.16907 4.43016 +1.49455 4.57504 0 4.29003 +0 4.2671 0.51514 1.07204 +0 0.0911507 1.31416 1.03286 +6.49975 2.46001 0 4.51933 +>MA0737.1 GLIS3 lnR0: 2.516 +6.68779 3.9672 0 1.88836 +0 6.54971 4.34907 8.6391 +8.61978 0 7.10962 7.62957 +8.57474 0 8.05479 8.57474 +7.14561 0 8.1951 5.42565 +8.61485 0 8.0949 7.62464 +5.7969 0 7.57615 8.0961 +8.17222 0 7.65227 3.8229 +0 8.18676 3.1491 6.40751 +7.13404 0 4.46541 3.99515 +2.02064 5.12152 0 3.5285 +0 6.87186 3.49025 2.56506 +0 1.40294 4.87953 2.50212 +9.67969 5.11229 0 7.38049 +>MA0738.1 HIC2 lnR0: -0.404 +0 2.17586 -0.332241 2.79696 +12.1362 4.80101 11.6163 0 +3.79252 3.74748 0 5.4792 +8.1161 0 8.26758 12.6562 +3.97383 0 12.1362 6.80711 +1.73163 0 11.6274 12.1473 +0 1.27286 0.420722 2.61454 +2.01849 0 0.822021 2.18745 +1.69563 0 0.782651 0.825802 +>MA0741.1 KLF16 lnR0: 0.764 +1.78147 1.57388 0 3.23574 +1.35029 0 4.32735 4.26806 +5.1524 0 7.77134 5.60168 +0 0.78408 4.55416 10.0691 +5.06446 0 6.42211 6.79155 +2.19888 3.18114 0 2.49772 +7.93227 0 10.5512 11.0712 +9.50172 0 7.41232 11.0712 +7.02372 0 8.5708 4.52121 +1.93089 0 5.8202 5.31467 +6.07616 0 6.01114 2.61945 +>MA0747.1 SP8 lnR0: 1.348 +1.09017 1.48178 0 3.33645 +1.56119 0 6.766 4.98675 +3.18548 0 7.31995 4.06982 +0 1.43931 5.48675 5.42747 +4.86927 0 6.32974 5.28024 +3.18548 2.1234 0 2.57007 +5.28024 0 4.54008 6.27045 +6.27045 0 5.33953 7.8399 +7.8399 0 5.02075 3.87906 +0 -0.299735 3.14426 4.46366 +4.06982 0 2.90417 2.57007 +1.36158 0.120833 4.80247 0 +>MA0749.1 ZBED1 lnR0: 1.932 +1.68802 0 2.12161 2.37789 +3.55471 7.25735 5.96084 0 +0 7.31028 0.366305 8.65218 +9.52656 8.64759 11.7865 0 +12.7904 0 9.4906 8.58408 +6.01159 10.4427 0 11.3736 +10.487 0 12.2662 6.05826 +10.652 10.132 0 12.9512 +0 8.44856 8.07376 12.2579 +9.7023 0 11.9622 2.81948 +0 8.17463 8.29893 5.13483 +5.35601 3.64462 2.44167 0 +0 2.97255 0.20782 2.33579 +>MA0751.1 ZIC4 lnR0: 3.1 +3.32567 2.12109 0 1.63714 +0 1.3519 0.426386 7.02854 +3.67234 0 5.70303 5.33037 +4.26602 0 4.52191 4.76587 +2.66372 0 3.57389 3.80832 +8.81873 0 11.4377 10.9674 +5.17246 0 11.431 8.40107 +6.931 0 8.22958 1.55255 +2.62869 6.05919 0 6.55858 +6.96717 0 3.14077 1.67186 +1.71139 1.47074 0.345275 0 +4.77369 7.98572 0 6.68414 +1.03509 -0.0471091 0.745523 0 +6.3763 3.2872 0 2.46759 +0.69464 0 1.73363 0.933649 +>MA0088.2 ZNF143 lnR0: 3.684 +3.83136 0.801308 2.51196 0 +0 9.275 5.50491 0.53555 +6.63577 0 9.54139 10.0613 +9.49906 0 10.5486 11.0685 +11.0685 0 10.5486 11.0685 +0 10.0286 7.72941 8.56814 +10.2659 0 3.85009 0.934041 +0 2.61894 1.51897 10.2386 +0 9.99539 3.96752 9.52513 +7.76868 10.0286 9.0384 0 +5.16887 5.33953 0 7.72853 +11.0685 0 10.5486 11.0685 +0 2.73567 7.95089 5.69097 +1.62743 -0.502667 5.4987 0 +3.50764 -0.445421 5.83865 0 +2.4882 6.04966 0 4.13426 +>MA0752.1 ZNF410 lnR0: 4.268 +1.3287 0.726978 0.291255 0 +0.645015 0 2.20547 9.71521 +11.2444 0 11.7147 3.78293 +0 9.75424 10.3335 9.54444 +6.16896 6.22825 4.36831 0 +6.28134 0 10.8405 10.0514 +8.69973 0 11.844 12.3639 +12.3639 0 10.8538 12.3639 +0 8.76403 10.3335 10.2742 +11.8444 8.03499 11.3244 0 +0 8.18551 11.3244 11.8444 +0 9.75352 9.34255 10.8527 +9.54408 8.54345 11.3233 0 +0 7.17473 5.89785 7.22539 +0.782633 0 1.04225 0.856612 +3.68063 0.939551 0.992862 0 +2.22138 0 4.75866 2.83225 +>MA0755.1 CUX2 lnR0: 0.18 +2.46558 2.76414 2.86977 0 +0 2.61763 0.423994 1.88353 +0 6.91084 5.81374 6.97224 +6.5046 4.06347 5.9669 0 +9.6764 0 8.81875 6.41197 +1.71601 7.17859 0 6.78557 +0 8.73506 7.51882 7.81359 +6.77581 6.75975 8.79764 0 +0 1.41864 2.04102 1.89458 +0 0.524646 1.43064 0.818252 +>MA0757.1 ONECUT3 lnR0: 2.516 +0 0.938713 0.501792 1.7539 +0 2.78887 1.21692 2.41583 +0 3.90313 3.05193 2.76306 +0 4.55701 5.17367 2.2924 +0 7.11666 5.30604 6.72227 +0 9.36743 6.58756 8.89717 +7.45202 5.29224 8.05844 0 +8.42691 0 10.4666 10.4073 +0 6.96177 0.362017 8.28117 +0 9.14721 8.63768 7.96776 +7.04105 9.14721 8.95645 0 +0 5.26503 4.44645 4.09498 +0 1.53041 2.56437 1.59814 +0.310934 0.336122 1.33083 0 +>MA0758.1 E2F7 lnR0: 2.516 +1.36057 2.43593 1.12303 0 +4.47129 6.21437 4.97866 0 +9.81584 7.31547 9.29589 0 +9.80693 8.29676 9.28697 0 +10.3313 0 8.24195 10.3313 +10.3328 0 6.38731 10.3328 +10.3388 0 9.81881 10.3388 +8.813 8.87229 0 10.3824 +10.3695 0 9.84953 10.3695 +10.3564 0 5.70734 9.36618 +0 9.21824 9.21824 7.17854 +0 8.25592 7.26571 6.98621 +0 7.56336 9.13281 4.24678 +0 7.07034 7.07034 1.04521 +>MA0760.1 ERF lnR0: 0.18 +0 4.7921 2.05364 5.63083 +5.16057 0 4.47236 3.05213 +3.47678 0 4.83138 8.1312 +8.1312 7.61125 0 8.1312 +8.1312 5.63083 0 8.1312 +0 5.11088 5.11088 6.04181 +0 7.0913 7.0913 2.70556 +1.81857 3.48215 0 8.1312 +7.61125 1.75177 3.54143 0 +1.07633 1.66472 0 2.51582 +>MA0474.2 ERG lnR0: 0.18 +0 3.52562 1.8837 2.275 +3.31176 0 3.48236 6.00801 +3.33626 0 7.55874 9.7781 +11.5678 12.038 0 12.558 +12.558 11.0478 0 7.69911 +0 7.16875 11.5181 9.06739 +0 4.67879 8.54744 1.8556 +0.888506 4.62752 0 6.93007 +4.99908 0.990065 3.12531 0 +1.24173 0.594294 0 1.58303 +>MA0098.3 ETS1 lnR0: 0.18 +0 3.1132 1.52581 3.43732 +4.37219 0 3.13996 7.31934 +3.14941 0 8.30803 11.7986 +11.7986 6.86289 0 11.7986 +11.7986 11.2787 0 8.1344 +0 10.7587 10.7587 11.2787 +0 7.4693 5.80766 1.54517 +1.03427 6.10681 0 7.37833 +4.40927 0.932642 3.42002 0 +0.946828 1.41709 0 1.95492 +>MA0762.1 ETV2 lnR0: 0.764 +0 1.69158 1.0351 1.66285 +0 6.1652 5.05068 7.55106 +4.83003 0 3.39574 10.6307 +3.82756 0 8.13029 10.6307 +10.6307 10.1107 0 10.6307 +10.6307 10.1107 0 10.6307 +0 9.59076 9.59076 10.1107 +0 8.60055 9.59076 3.01098 +0 7.5416 0.792413 9.631 +5.90437 0.892125 3.58406 0 +0 1.65591 0.22203 1.6628 +>MA0763.1 ETV3 lnR0: 0.18 +0 2.39873 1.92536 3.08058 +3.99258 0 3.81033 3.24787 +4.90951 0 7.67897 4.42884 +8.19892 7.67897 0 4.33028 +8.19892 7.67897 0 4.15147 +0 4.02013 7.15902 5.37977 +0 7.15902 7.15902 1.56945 +2.37387 3.81033 0 8.19892 +7.67897 2.16401 4.18839 0 +1.41256 1.22493 0 2.42998 +>MA0767.1 GCM2 lnR0: 0.18 +1.23738 -0.195321 -0.334902 0 +0 3.5221 1.59771 4.79643 +5.72584 4.40644 5.14758 0 +2.82023 5.27091 0 10.7859 +4.43923 0 3.21667 3.8544 +5.14124 9.27571 0 4.77917 +10.7859 10.2659 0 7.01579 +9.79566 10.2659 0 10.7859 +3.79078 0.773976 3.28627 0 +0 1.54886 0.283076 1.30305 +>MA0768.1 LEF1 lnR0: 3.1 +0 1.56379 0.944305 2.09398 +0 4.03766 1.12094 3.32468 +0 5.86402 3.75558 5.48596 +7.90365 2.09612 0 8.48288 +0 8.83874 6.53954 5.39785 +6.42671 7.21575 9.19617 0 +6.42504 0 4.18513 7.73403 +0 8.86302 8.86302 7.08377 +0 8.859 6.5598 9.37895 +0 8.86502 5.09494 7.08578 +5.44583 5.36515 0 10.4835 +2.60469 2.18176 0 3.26177 +1.36476 1.7457 0 2.69697 +0.0192793 1.99819 1.52711 0 +0.202872 1.59866 1.89528 0 +>MA0770.1 HSF2 lnR0: 1.932 +4.15442 5.808 4.54485 0 +6.98442 9.4351 5.47426 0 +7.997 0 9.95505 12.0444 +10.5343 1.62359 2.88515 0 +0 1.94941 1.46766 11.5245 +10.475 11.5245 0 11.0542 +0 5.41594 8.70535 6.71408 +0 10.0143 6.46447 4.82257 +3.53074 0 1.14558 1.0337 +0.792265 1.35396 0 1.74859 +4.43472 4.95582 4.59221 0 +6.05501 4.57625 5.59856 0 +5.61615 0 4.70923 3.61602 +>MA0771.1 HSF4 lnR0: 1.932 +2.36794 2.74108 2.62107 0 +3.75063 6.18766 2.79928 0 +7.18172 0 6.4266 7.59772 +7.24855 0.68547 1.09403 0 +0 0.794082 0.540939 8.12965 +11.7068 9.5031 0 10.5484 +0 3.04017 7.05876 3.55157 +0 4.03553 4.1995 2.57937 +1.94786 0 0.747425 0.891815 +0.870102 0.576875 0 1.30413 +2.90464 4.57238 4.14273 0 +4.92239 6.36958 5.61882 0 +7.1228 0 6.57428 6.02158 +>MA0772.1 IRF7 lnR0: 2.516 +0 -0.314933 1.83375 0.952515 +3.77692 0 4.19003 4.82667 +5.16842 3.77906 0 3.88279 +0 7.30655 8.29676 9.80693 +0 9.28697 9.28697 8.81672 +0 7.71753 8.29676 8.81672 +1.3653 1.67184 0 5.2859 +6.47847 0 7.52796 1.14652 +5.42118 7.8265 0 7.35625 +0 5.23953 6.98778 7.24727 +0 7.30655 7.30655 8.81672 +0 5.86141 6.31634 4.4674 +0.580147 0.363983 0 2.53311 +2.2992 1.84275 4.08734 0 +>MA0773.1 MEF2D lnR0: 1.348 +0 3.70742 -0.388097 0.364805 +8.08996 0 12.3804 7.20183 +10.4 7.3812 11.8605 0 +0 8.72159 10.291 9.60056 +0.117699 10.9282 9.35871 0 +0 9.56128 11.8605 2.86899 +0 11.8605 10.291 4.6883 +0 10.291 10.8703 6.31115 +12.3804 11.8605 11.8605 0 +0 11.8605 9.56128 12.3804 +4.57332 8.25133 0 10.3407 +0 -0.219652 4.92349 2.42824 +>MA0498.2 MEIS1(MA0498.2) lnR0: -1.572 +0.0701359 -0.117093 0.825878 0 +3.11942 3.23349 4.03801 0 +16.5966 5.88963 0 16.5966 +0 4.16547 6.25418 16.0766 +16.5966 0 16.0766 6.52126 +0 15.5567 2.50826 4.27814 +1.31095 1.00151 0 1.49839 +>MA0774.1 MEIS2(MA0774.1) lnR0: -0.988 +1.70804 1.80806 1.56115 0 +5.34801 7.79869 4.474 0 +10.819 10.2991 0 10.819 +0 7.79869 5.12468 4.38029 +7.5296 0 10.2991 8.25935 +0 6.80848 7.47991 10.2991 +4.48927 3.7346 0 4.79114 +2.65043 0 0.107748 3.47037 +>MA0775.1 MEIS3 lnR0: -0.988 +0.87803 5.24553 0.419045 0 +3.90417 3.66071 4.21231 0 +13.2015 9.9017 0 13.2015 +0 7.81231 3.41521 6.98303 +7.50298 0 9.54268 5.94238 +0 9.02273 3.37505 5.56214 +2.58285 1.90396 0 2.2768 +2.09237 0.299255 0 2.07024 +>MA0776.1 MYBL1 lnR0: 1.348 +0 5.35812 1.48217 2.94926 +3.16073 0 4.12652 4.76761 +3.58269 0 3.01928 11.521 +5.93241 8.03044 0 9.22182 +7.71166 5.77278 10.4811 0 +7.5755 7.34223 10.4811 0 +0 10.4811 6.8169 7.13243 +0 6.27478 5.88272 11.0011 +7.65238 0 10.0109 7.85681 +4.22681 0.346517 0 1.7321 +2.66025 2.58049 0 1.82088 +1.67153 -0.0384769 4.14382 0 +>MA0777.1 MYBL2 lnR0: 3.1 +0 3.9252 0.28314 4.1847 +0 2.77294 0.242616 1.3931 +4.29119 0 3.80408 5.41756 +3.99863 0 2.66419 5.78169 +8.12773 10.1674 0 9.69718 +6.87803 6.86761 5.04909 0 +10.1674 6.35808 9.64749 0 +0 3.47965 3.42362 1.12243 +0 4.69643 5.60004 7.86824 +0 4.41383 4.83706 3.9074 +6.81874 0 7.38756 8.38819 +3.50284 0.157996 0 1.20365 +4.37476 3.28132 0 4.16689 +1.72681 0.188846 2.44882 0 +4.48079 0 5.0596 0.700789 +>MA0105.4 NFKB1 lnR0: 1.932 +0 1.52733 2.54042 3.3327 +11.3087 14.0782 0 12.0385 +14.6078 12.1075 0 13.0384 +12.3079 14.0871 0 6.3711 +6.85993 12.1282 0 9.86832 +0 6.97997 3.31053 8.65839 +0 7.92262 7.13395 0.0538285 +9.19659 2.89976 6.35281 0 +9.48643 0 10.7964 6.65097 +4.73757 0 12.0997 11.6294 +11.3189 0 12.1079 12.0486 +10.8458 0 11.5363 10.4868 +2.90098 2.31089 0.952427 0 +>MA0778.1 NFKB2 lnR0: 1.932 +0 0.506995 0.596985 1.33457 +7.76775 7.30495 0 12.0757 +13.3625 12.8426 0 12.3723 +11.2151 11.2744 0 5.29887 +2.79862 9.99678 0 4.21563 +0 2.54892 2.7376 3.68136 +0.202186 6.02833 6.25637 0 +3.19341 2.42604 2.79533 0 +4.17421 0 9.01573 3.0544 +6.08885 0 12.5059 8.57802 +12.4508 0 12.5101 12.4508 +10.9012 0 11.5398 9.50006 +1.95066 0.319983 0.921083 0 +>MA0779.1 PAX1 lnR0: 4.268 +3.81298 0 1.13781 3.75521 +10.7813 12.2417 0 6.50165 +4.18442 5.18609 11.4639 0 +10.5536 0 11.0238 3.72625 +0 3.50254 9.59878 11.6882 +10.9642 0 12.0137 3.27647 +10.7915 10.6826 0 10.7915 +12.5064 0 2.09271 12.5064 +0 4.18968 5.07901 0.529194 +8.3991 2.77981 9.85957 0 +11.5944 1.38076 0 6.85986 +0 9.60077 2.0413 11.6902 +1.49274 0 0.401076 1.63845 +5.74573 2.22453 6.39861 0 +2.83253 8.39876 0 2.78136 +1.32919 0 1.14681 11.7322 +0 -0.215822 1.22215 1.02411 +>MA0780.1 PAX3(MA0780.1) lnR0: 0.18 +1.97432 4.45613 3.76796 0 +0 7.31422 5.77393 7.87813 +0 7.71083 8.64501 9.0591 +9.53977 5.70212 8.18012 0 +9.09775 0 6.32324 1.48596 +1.48114 6.68064 0 9.7897 +0 7.82995 6.50859 7.87813 +12.8292 8.44058 8.44058 0 +7.00412 5.75927 6.93608 0 +0 4.51591 4.75456 2.87502 +>MA0781.1 PAX9 lnR0: 4.268 +4.44048 0 1.02439 3.78643 +12.2998 11.7799 0 8.87426 +5.46032 7.19816 8.18837 0 +12.2863 0 11.7663 4.9327 +0 4.91902 9.4591 10.5583 +12.3181 0 11.7981 4.33094 +12.3492 11.8292 0 12.3492 +12.2557 0 2.32101 12.2557 +0 3.8904 6.45006 0.682183 +10.5347 4.95627 11.005 0 +10.2189 1.31725 0 10.2189 +0 10.9572 2.17059 11.4771 +1.70092 0 0.558817 2.18159 +8.71977 3.35463 10.9797 0 +5.13187 8.5628 0 4.32246 +1.44648 0 2.31784 11.6335 +0 0.183885 1.22308 1.34373 +>MA0783.1 PKNOX2 lnR0: 1.348 +4.92377 9.60037 6.31097 0 +9.8684 7.55878 0 10.8586 +0 7.53611 5.74645 7.25661 +10.7081 0 10.1881 7.41868 +0 9.57256 8.58235 7.79332 +7.79125 10.2419 0 3.93456 +4.61492 1.19292 0 9.88475 +10.1346 7.31547 9.61467 0 +8.85852 9.32878 0 10.8389 +6.6645 4.71126 7.01046 0 +7.17525 0 7.4253 8.7447 +0 8.60777 5.1822 6.82852 +>MA0785.1 POU2F1 lnR0: 1.348 +0 0.855118 1.22661 1.27754 +0 1.81082 0.787569 0.0323953 +3.76806 2.4238 3.91389 0 +0 9.05441 7.85977 7.83259 +6.04293 3.83491 5.05295 0 +6.28552 6.92595 0 3.48613 +5.60551 0 2.93952 2.15218 +0 7.07675 6.61419 0.91574 +0 6.0167 3.03302 3.71072 +0 7.52208 7.07399 5.99729 +2.8664 3.96596 3.25 0 +1.0977 0.67957 0.239599 0 +>MA0786.1 POU3F1 lnR0: 1.348 +0.469788 2.94694 1.61342 0 +2.26607 3.16816 3.69858 0 +0 7.67054 5.93283 6.74534 +5.72303 4.94262 6.22539 0 +6.48452 7.39104 0 3.89387 +4.33584 0 2.55274 1.65095 +0 8.86302 5.43745 0.436618 +0 4.00632 3.6766 3.08613 +0 6.29185 5.98674 5.21986 +3.21729 4.12067 3.69858 0 +1.59288 1.40764 0.382502 0 +0 1.12123 1.20096 0.645018 +>MA0787.1 POU3F2 lnR0: 1.348 +0.24143 2.94487 1.48721 0 +2.94979 3.73014 4.41026 0 +0 5.66792 5.06094 10.2353 +5.42489 4.80967 6.05115 0 +6.47565 6.94591 0 4.88259 +4.70654 0 3.03967 2.29587 +0 6.51691 7.8259 0.185733 +0 5.66792 4.72035 4.76583 +0 6.93549 9.71536 6.46523 +4.29405 5.43575 4.90494 0 +2.58191 1.79805 0.363906 0 +0 1.75514 1.76059 1.18777 +>MA0788.1 POU3F3 lnR0: 1.932 +0 2.37592 1.52375 0.977884 +0.527562 3.36672 1.73082 0 +3.02322 3.65626 3.49348 0 +0 5.90703 5.79268 5.07115 +5.32242 4.41923 3.86829 0 +6.01752 6.55128 0 4.11692 +5.68637 0 3.14952 2.15302 +0.174821 6.25355 7.56253 0 +0 5.90703 3.23302 3.7168 +0 6.67702 5.49605 6.1082 +4.27829 5.10757 5.79268 0 +2.14142 2.37714 1.63936 0 +0.0158732 2.11257 1.68508 0 +>MA0789.1 POU3F4 lnR0: -0.404 +3.52616 4.4206 5.76053 0 +0 8.249 6.74036 8.60069 +7.45997 6.94002 8.19068 0 +8.13043 9.02941 0 5.96422 +6.80044 0 4.16343 2.61455 +0 8.58524 6.23501 0.460567 +0 4.49173 4.56659 3.61372 +0 7.25879 6.37674 5.9806 +3.93815 4.91275 4.67455 0 +>MA0790.1 POU4F1 lnR0: 2.516 +0 0.69146 0.624125 1.33521 +4.48411 3.34829 4.25083 0 +2.40235 3.32237 0 2.85781 +0 -0.470117 5.265 4.43836 +0 5.3639 6.23977 4.35465 +5.20307 7.18198 7.18198 0 +0 4.20422 3.70583 1.08363 +0 3.97956 3.76753 2.16866 +2.75335 4.33534 4.05719 0 +3.0116 4.88914 3.05815 0 +0 1.53838 1.47981 1.32602 +0 5.8434 5.2771 7.56097 +3.45158 2.55722 3.25428 0 +2.21464 2.38 0 1.64038 +>MA0791.1 POU4F3 lnR0: 3.684 +0 0.854022 0.409746 1.11576 +3.78153 3.12675 3.20893 0 +2.64405 3.61926 0 2.64405 +0.627401 0 6.27071 5.31978 +0 5.6655 5.88019 4.57238 +5.31513 6.9147 6.67605 0 +0 4.01731 3.94066 0.935843 +0 4.10489 4.04751 2.21527 +3.10184 4.65057 3.94625 0 +2.92873 5.22177 3.69561 0 +0 1.70781 1.43355 1.81734 +0 6.83693 6.46213 7.15722 +4.10695 2.85323 3.81956 0 +2.50849 2.22346 0 1.71858 +0 0.632587 1.23447 1.62508 +1.2691 1.03722 0 1.82481 +>MA0792.1 POU5F1B lnR0: -0.404 +2.81496 1.87625 3.00198 0 +0 8.15163 6.53954 6.74071 +5.73379 4.13898 4.94924 0 +5.35352 6.58182 0 2.90655 +5.05165 0 2.85094 1.82108 +0 6.33299 5.99241 0.958368 +0 5.45779 2.91964 3.37442 +0 6.58219 6.01745 5.49004 +2.58387 3.58475 3.10826 0 +>MA0793.1 POU6F2 lnR0: 0.18 +0 1.97698 1.12893 1.73993 +2.07063 0.83256 0 3.47782 +4.26343 0 3.86778 4.16011 +5.3862 5.0896 4.27453 0 +1.33184 0 5.31531 5.15685 +0 4.86625 11.053 7.15718 +11.573 8.75381 11.053 0 +11.573 7.3888 5.71348 0 +0 6.29272 6.57373 5.87441 +0.0112133 0.693457 2.08856 0 +>MA0794.1 PROX1 lnR0: 1.348 +3.59295 0 1.45276 0.905818 +0 6.95391 4.57747 6.10275 +0 3.31433 5.52327 2.97063 +6.18165 11.603 0 11.1327 +0 6.66724 4.73637 10.0335 +7.17186 0 11.603 6.96446 +8.16207 10.0335 0 3.97465 +7.59045 0 7.48148 0.534368 +10.1425 0 7.93875 7.91657 +9.30377 9.10259 4.14042 0 +7.47386 3.72945 5.81319 0 +0 1.4066 1.27373 4.78324 +>MA0600.2 RFX2 lnR0: 3.684 +2.53257 0 0.479109 1.78209 +6.1494 9.96826 0 11.0135 +8.81115 7.86796 9.23298 0 +2.62487 3.25677 9.08827 0 +1.53331 5.02614 0 3.2638 +10.4098 0 7.06361 3.66513 +12.407 0 10.8968 2.36545 +0 7.37136 6.6198 5.66732 +5.90526 6.65194 8.20543 0 +2.45191 10.461 0 12.3821 +3.19658 6.59817 0 12.0803 +3.10374 0 4.50253 1.45993 +0 7.82059 2.72051 2.92616 +0 8.75136 7.96557 9.0925 +11.1945 0 12.655 5.97007 +1.68262 0.571266 0 2.41988 +>MA0795.1 SMAD3 lnR0: 0.18 +2.22438 0 4.33533 0.656654 +7.82525 7.60717 0 7.96822 +5.01977 6.27581 4.80493 0 +8.88516 0 8.10475 9.39469 +11.6546 5.63445 6.18361 0 +0 6.22897 6.65539 11.6546 +12.1746 8.22905 0 10.1941 +0 3.56564 8.57501 5.87883 +7.82525 0 8.22905 7.82525 +0 2.4556 2.90766 2.18033 +>MA0796.1 TGIF1 lnR0: 1.348 +8.2868 8.75706 12.0465 0 +10.8169 10.4475 0 11.8071 +0 10.4793 8.11044 12.9797 +13.0953 0 11.0059 11.1149 +0 9.90543 7.98581 10.6858 +10.1475 9.14684 0 4.20026 +5.01884 0 2.04672 10.0916 +12.5174 7.06889 9.84876 0 +10.531 9.79086 0 10.7915 +8.02475 8.37589 10.9939 0 +8.94636 0 9.81479 9.97572 +0 8.36361 7.4977 7.975 +>MA0797.1 TGIF2 lnR0: 1.348 +4.58059 4.23865 5.67872 0 +7.36432 7.83458 0 8.24243 +0 7.7953 4.32589 6.18024 +6.9828 0 7.74969 6.69106 +0 8.21995 4.87134 8.05479 +5.65166 5.4341 0 2.63189 +2.8096 0 0.773172 6.79927 +7.2848 4.27638 7.07374 0 +6.74673 7.17045 0 7.58453 +4.2511 3.68446 5.98825 0 +7.82473 0 6.36578 7.14827 +0 5.51252 4.32949 4.76199 +>MA0510.2 RFX5 lnR0: 3.684 +2.45336 0 0.439583 1.64075 +5.42514 11.3493 0 8.57982 +9.09152 5.83311 6.90992 0 +5.83059 4.27647 7.41536 0 +1.5377 4.31064 0 4.03612 +9.64587 0 5.87268 5.55701 +10.4707 0 7.97037 2.05016 +0 5.06666 4.90951 3.47154 +4.26625 5.08014 6.37665 0 +2.07935 7.48758 0 8.4185 +4.68873 5.70877 0 11.7885 +4.01256 0 4.65619 1.38159 +0 7.02748 3.87423 5.47279 +0 6.0634 6.43173 7.70972 +6.91855 0 7.44272 5.59902 +1.47897 0.0238498 0 2.16217 +>MA0511.2 RUNX2 lnR0: -0.404 +0 1.28734 3.01123 0.489703 +0 3.0166 1.90124 3.47138 +0 3.78184 12.0488 12.5688 +13.0887 0 12.5688 13.0887 +13.0887 0 12.5688 13.0887 +1.80502 6.923 0 5.75028 +13.0887 0 12.5688 13.0887 +0 3.2381 3.29305 5.05808 +0 2.08634 1.35029 2.76197 +>MA0800.1 EOMES lnR0: 1.932 +0 1.76887 0.46302 1.08176 +0 5.37233 2.41524 3.87199 +2.96478 3.25822 0 3.40391 +9.11344 6.65843 0 7.14798 +8.85395 3.47277 6.99673 0 +10.3641 9.99468 0 11.6731 +4.26703 2.12764 6.04916 0 +6.00801 4.11681 0 3.8127 +0 7.8032 6.03481 8.53518 +0 1.78624 2.71291 1.53741 +0 0.649093 1.20384 1.36499 +0 0.991765 0.987401 0.429125 +0.161266 -0.401433 -0.00625582 0 +>MA0801.1 MGA lnR0: -0.988 +0 4.15991 1.2433 2.8452 +3.31456 2.99835 0 4.46263 +11.2227 5.84392 0 8.62166 +11.086 2.55817 7.69497 0 +11.4015 13.76 0 11.7203 +4.82185 2.75037 5.73681 0 +5.93204 4.07929 0 2.73544 +0 7.50237 4.47961 6.72626 +>MA0802.1 TBR1 lnR0: 0.18 +0 5.99848 2.82044 4.54397 +2.8235 3.3725 0 3.43624 +9.35756 7.01106 0 7.78142 +9.65732 3.73139 7.99486 0 +15.4471 12.1473 0 13.1479 +3.81602 2.31516 7.17492 0 +5.34728 3.72053 0 2.7986 +0 7.96311 5.3049 7.3159 +0 2.77554 3.55859 2.47434 +0 1.18272 1.48822 1.64611 +>MA0803.1 TBX15 lnR0: -0.988 +0 6.53995 3.42238 6.47433 +4.9919 6.62063 0 7.11284 +9.46807 10.2571 0 13.7477 +7.33183 5.32138 4.84303 0 +13.7477 10.0888 0 13.7477 +6.15808 4.02544 4.44518 0 +8.3096 4.48446 0 3.9709 +0 6.59826 4.52658 6.69244 +>MA0804.1 TBX19 lnR0: 6.02 +0.568789 0.965424 0.41049 0 +1.50591 1.78338 0.901227 0 +6.93982 4.83391 7.04553 0 +1.34832 0 1.41736 3.85499 +0 5.09658 0.42423 3.58846 +9.11084 0 8.26102 7.55381 +0 8.6442 3.47594 10.0208 +3.95495 0 4.25434 2.97761 +1.48066 0 1.06107 2.33526 +2.85026 2.66383 3.26707 0 +0 3.58499 2.25473 2.83548 +2.38311 1.48431 0 1.649 +2.93113 4.62063 0 3.97215 +8.94525 3.3079 6.76151 0 +7.89625 11.0716 0 8.99825 +3.21199 0.592872 4.66525 0 +4.45561 2.67339 0 2.10703 +0 7.54096 4.63057 6.99615 +0 1.46924 1.59706 1.85471 +0 0.893788 0.902682 0.95337 +>MA0805.1 TBX1 lnR0: -0.988 +0 6.12402 3.01041 4.35736 +3.42552 4.027 0 4.63381 +13.9299 13.41 0 13.9299 +8.59955 5.21768 5.81027 0 +13.9299 10.8503 0 13.9299 +6.32019 3.7186 6.17505 0 +6.85017 4.00906 0 4.00567 +0 7.85236 8.68368 13.41 +>MA0806.1 TBX4 lnR0: -0.988 +0 4.83894 2.43658 3.82244 +3.09107 2.97178 0 4.48378 +9.33406 6.55202 0 9.53006 +14.0478 2.94854 6.01711 0 +14.5677 14.0478 0 14.5677 +3.55163 2.15843 5.35595 0 +4.26444 1.7712 0 1.66172 +0 4.41578 2.87327 4.22897 +>MA0807.1 TBX5 lnR0: -0.988 +0 3.76363 1.59742 3.08683 +3.42636 3.20863 0 4.23492 +11.2318 10.7119 0 6.42141 +5.24239 3.2165 2.88051 0 +6.47154 10.7119 0 11.2318 +3.43509 2.44831 2.60869 0 +4.31156 1.5335 0 1.48895 +0 3.98649 1.84816 2.64192 +>MA0808.1 TEAD3 lnR0: -0.988 +0 6.95329 -0.0334041 3.46264 +3.39714 0 5.36674 14.5886 +0 13.7275 13.7275 14.2475 +14.2475 13.7275 13.7275 0 +1.86745 8.84544 3.56081 0 +14.7674 0 14.2475 14.7674 +14.7674 0 14.2475 12.4682 +0 3.80329 0.77627 0.643896 +>MA0810.1 TFAP2A(MA0810.1) lnR0: 1.348 +1.52312 0.208835 2.94826 0 +2.75365 1.06073 0 5.23222 +8.41025 0 4.08246 12.3711 +12.3711 0 8.42558 7.33343 +8.44011 0 3.62761 2.04983 +3.55236 0 0.981599 0.836785 +0.638851 0 0.444432 3.41334 +0.660842 2.17795 0 6.475 +4.86038 6.77207 0 12.3711 +9.81143 2.32147 0 8.94553 +5.76399 0 3.06456 4.62116 +0 1.60333 0.443034 1.50198 +>MA0811.1 TFAP2B(MA0811.1) lnR0: 1.348 +1.07435 0.4637 2.52094 0 +2.73837 1.64272 0 5.41982 +7.50078 0 3.56613 7.50078 +11.0506 0 11.5209 6.96179 +7.86727 0 3.71085 1.60129 +3.00991 0 0.811406 0.653372 +0 0.143143 0.020739 2.82232 +0.925874 2.95553 0 11.1412 +5.71112 7.39181 0 12.0409 +6.84431 2.89879 0 8.37665 +5.56572 0 2.68641 4.21138 +0 2.72594 0.923451 1.92195 +>MA0812.1 TFAP2B(MA0812.1) lnR0: 0.764 +0 -0.186089 2.38881 0.663294 +7.18891 2.66533 0 7.44167 +12.5526 0 9.73349 12.5526 +12.5526 0 11.0425 5.31135 +7.24867 0.641548 1.60708 0 +2.3837 0 0.499878 3.10194 +0 1.97042 2.41222 7.78146 +4.74717 9.73349 0 10.9832 +9.77277 8.60712 0 11.5624 +6.92525 0 3.78732 7.80111 +0 1.75054 0.138223 0.587882 +>MA0813.1 TFAP2B(MA0813.1) lnR0: 1.932 +1.27984 1.74545 2.4206 0 +10.4768 1.67243 0 10.4768 +10.2768 0 9.75685 10.2768 +10.1925 0 9.67256 10.1925 +7.46438 0 5.02481 2.9955 +4.07519 -0.23937 1.56403 0 +1.91509 0.181958 0 0.549331 +0 1.00376 0.13979 3.76033 +2.02116 3.91719 0 6.58582 +10.692 10.1721 0 10.692 +10.8137 10.2938 0 10.8137 +10.2345 0 2.42901 10.2345 +0 2.05959 1.31655 1.50509 +>MA0524.2 TFAP2C(MA0524.2) lnR0: 1.348 +1.11271 0.447572 2.63427 0 +3.22401 1.76683 0 5.8485 +6.81845 0 3.19813 7.26336 +8.3096 0 9.09863 6.04511 +7.01954 0 3.19151 1.49161 +2.53921 0 0.671568 0.704098 +0 0.202496 -0.0262731 3.083 +1.07164 3.22184 0 7.94813 +5.62247 8.72383 0 8.86055 +6.16728 2.94419 0 7.71144 +4.9919 0 2.29187 3.76952 +0 2.60914 1.21346 1.89377 +>MA0815.1 TFAP2C(MA0815.1) lnR0: 1.932 +1.44636 1.52318 2.21676 0 +11.6269 1.83231 0 11.6269 +11.6954 0 11.1755 11.6954 +11.6442 0 11.1242 11.6442 +7.30118 0 4.38984 3.14154 +3.72165 -0.241076 1.05302 0 +1.84447 0.0170902 0 1.6276 +0 0.947557 -0.478498 3.73942 +3.12512 4.36698 0 7.26551 +11.9966 11.4767 0 11.9966 +12.0219 11.5019 0 12.0219 +11.4677 0 2.01368 11.4677 +0 2.32601 1.3605 1.54188 +>MA0464.2 BHLHE40 lnR0: 0.18 +0 -0.185212 -0.137693 1.38768 +2.1393 3.13443 -0.207645 0 +7.99334 0 13.3225 9.97377 +0 5.83794 6.56044 7.09859 +9.30233 0 11.753 8.8474 +7.8357 8.41676 0 13.8424 +6.00251 4.92043 6.40631 0 +11.5432 9.65824 0 7.71318 +0 -0.3589 4.93706 3.52977 +2.38662 0 2.02182 1.64968 +>MA0817.1 BHLHE23 lnR0: 1.348 +0 1.3542 1.03501 1.46786 +0 5.89868 1.94583 6.73104 +0 0.580245 1.03977 8.18997 +8.27331 0 12.1691 12.6891 +0 11.6492 5.62131 8.04003 +12.1691 9.34998 10.659 0 +0 9.08953 9.66876 12.1691 +6.63884 4.85834 9.08953 0 +12.6891 9.86994 0 9.71845 +7.10186 0.218554 -0.333531 0 +4.31603 1.23156 5.17404 0 +0.075758 0.289313 0.208616 0 +>MA0820.1 FIGLA lnR0: 0.18 +0 1.17394 1.79057 0.969425 +0.526139 0 2.08724 2.04881 +11.2127 0 10.6928 6.35385 +0 4.6726 10.1728 6.82411 +11.2127 0 1.73691 11.2127 +7.9233 0 2.48847 11.2127 +4.91697 10.1728 6.0437 0 +6.05425 5.6551 0 5.22749 +2.4023 1.34362 0.0220456 0 +0.718428 0.874933 0.845066 0 +>MA0822.1 HES7 lnR0: 1.348 +2.33096 -0.393844 3.73345 0 +6.68015 6.47898 0 9.29812 +4.0194 5.89974 0 9.7091 +10.2883 0 10.7586 9.29812 +0 8.25822 7.26801 10.7586 +11.2785 0 10.7586 11.2785 +8.97935 9.76838 0 10.2883 +8.77817 8.25822 9.24843 0 +9.7091 9.76838 0 11.2785 +8.13965 0 8.19894 4.78812 +11.2785 0 7.46919 7.98914 +0 3.74019 -0.15791 2.75149 +>MA0823.1 HEY1 lnR0: 0.18 +2.53023 1.21924 0 2.83844 +0 0.534046 -0.326515 3.59422 +11.1203 0 9.61019 8.14972 +0 6.16496 4.18454 7.17483 +12.1106 0 11.5906 12.1106 +12.1106 7.38427 0 12.1106 +11.5906 2.26592 7.64509 0 +7.11555 7.31099 0 7.63128 +2.89657 0 2.18853 1.53881 +2.68916 0 2.51373 3.26091 +>MA0058.3 MAX lnR0: 0.18 +0 0.556596 0.818708 2.17835 +1.06701 0 0.882527 2.63795 +7.87289 0 12.6228 13.1427 +0 12.1028 5.70662 7.38911 +13.1427 0 9.65214 5.37403 +4.8583 7.35294 0 8.8631 +6.55349 4.85257 7.7535 0 +13.1427 7.86248 0 7.98426 +1.38043 0 0.574871 1.27281 +1.16819 -0.329191 0.832654 0 +>MA0825.1 MNT lnR0: 0.18 +0 0.58716 0.410311 1.09608 +0.801779 0 0.165146 2.34115 +5.08113 0 9.32147 7.28177 +0 8.80152 8.80152 4.9057 +9.84142 0 6.35084 5.79397 +5.88058 9.32147 0 9.84142 +9.32147 8.80152 4.84068 0 +9.84142 9.32147 0 5.187 +1.41228 0 1.08444 1.72869 +1.03839 0 1.58192 0.583453 +>MA0826.1 OLIG1 lnR0: 0.18 +0 4.98843 2.35092 5.73256 +0 -0.00717731 1.62464 12.4116 +8.19191 0 13.3438 13.8638 +0 11.8336 5.76437 7.06602 +9.6796 8.86302 6.05786 0 +0 6.54607 8.69476 9.91824 +5.80365 5.43745 12.8239 0 +13.8638 13.3438 0 7.69592 +8.4242 0.651946 -0.470176 0 +4.49175 1.47813 4.89106 0 +>MA0827.1 OLIG3 lnR0: 0.18 +0 2.67289 1.62129 3.81092 +0.993729 0 2.3931 7.76509 +3.59256 0 10.7971 9.33667 +0 6.85162 3.69837 6.31786 +10.7971 5.56885 4.14796 0 +0 3.64234 6.72732 10.7971 +5.02135 2.5399 8.70774 0 +9.01789 8.49794 0 3.28794 +5.07343 0.0827926 -0.361722 0 +2.82071 0.459859 2.88269 0 +>MA0834.1 ATF7 lnR0: 2.516 +1.26463 0 0.660191 1.02421 +1.02363 1.56495 0 1.2232 +0 5.13522 1.81403 8.75963 +10.5493 11.28 8.17323 0 +9.91077 11.1285 0 3.9433 +0 10.4403 7.75416 10.4349 +10.2698 0 9.0615 8.57039 +8.35907 10.8098 0 12.3199 +9.44474 9.53176 7.35534 0 +3.33249 0 8.45453 10.1398 +0 12.0098 7.99061 10.5493 +7.78653 0.869996 4.88058 0 +1.04285 0 1.9112 1.73932 +0.57229 0.257505 0 1.56275 +>MA0838.1 CEBPG(MA0838.1) lnR0: 0.18 +0 1.8432 0.749753 5.43184 +6.75004 7.10118 6.01432 0 +8.69974 9.47366 3.95438 0 +1.01291 11.8657 0 5.84055 +7.94142 0 9.29425 5.9924 +4.38022 6.7423 0 6.22644 +5.74523 0 8.76186 4.67708 +0 13.68 8.21051 10.1525 +0 13.68 9.13992 8.69974 +6.15059 -0.108173 4.5206 0 +>MA0839.1 CREB3L1 lnR0: 2.516 +0 0.256643 -0.077919 1.2833 +4.06671 1.53017 3.92157 0 +5.471 7.31995 0 5.61398 +3.92441 0 9.30037 8.25087 +7.8399 0 9.30037 7.26066 +0 8.78042 6.8 9.30037 +9.82032 0 7.31995 9.82032 +5.40454 7.31995 0 9.82032 +6.32974 8.78042 6.8 0 +2.95743 0 3.99527 6.39475 +0 3.74276 2.65119 4.03054 +2.28034 0.160052 0.72409 0 +3.61488 0 3.33696 3.56028 +0 2.7952 1.46047 2.3689 +>MA0841.1 NFE2 lnR0: 0.764 +0.883309 0 0.438384 3.78753 +0 10.2525 3.29123 11.5022 +12.4924 10.403 13.5419 0 +14.5818 14.0619 0 13.0124 +0 9.99206 13.5419 11.7627 +8.99807 0 1.66637 10.0655 +14.0619 9.19261 11.5615 0 +13.5916 0 14.0619 12.6014 +0 9.77184 10.403 11.5022 +14.0619 2.26007 10.1164 0 +4.81428 0 0.950916 2.03357 +>MA0843.1 TEF lnR0: 1.348 +1.08084 -0.389225 -0.0886299 0 +0 1.85894 -0.248729 7.6994 +5.25484 6.97263 8.61931 0 +5.01016 11.179 6.22792 0 +0 11.179 4.47704 11.6989 +8.08977 0 11.6989 3.50093 +1.29407 11.0444 0 11.5643 +11.6989 4.18206 5.77299 0 +0 4.97353 7.6291 4.43093 +0 11.179 6.89935 8.27336 +11.4623 0 2.9446 1.03209 +0 -0.245384 0.785428 1.39022 +>MA0844.1 XBP1 lnR0: 2.516 +0 2.42652 1.91086 0.825021 +0 1.14756 -0.0859354 0.868458 +1.83778 1.20957 0.0575007 0 +3.72159 4.59357 0 2.48195 +0.561802 0 5.93006 4.42274 +5.88237 0 4.95784 4.49722 +0 8.16112 4.25591 5.98285 +9.9497 0 11.1497 9.81354 +8.18714 13.339 0 10.4334 +13.0242 8.45676 9.36531 0 +4.73141 0 7.17089 8.10181 +0 6.76005 4.94972 6.3646 +4.74296 0.956041 0.4869 0 +3.16684 0 2.3508 2.83256 +>MA0845.1 FOXB1 lnR0: 0.764 +0.885305 3.46714 3.97742 0 +0 3.77688 1.29602 3.21747 +1.2796 3.90793 3.01209 0 +3.05518 6.89072 0 6.23784 +5.18905 4.2601 5.32953 0 +0 0.793277 5.42951 5.98756 +0 4.42985 12.0955 4.12202 +0 6.56524 6.56524 4.92991 +7.23477 0.496646 4.87673 0 +0 12.0955 4.86325 5.4766 +1.2214 2.25672 2.29967 0 +>MA0032.2 FOXC1 lnR0: 0.764 +0.890866 3.40237 4.7309 0 +0 3.73446 1.24441 3.33552 +0.420669 1.85567 1.588 0 +1.99365 5.28585 0 8.47557 +2.8602 2.92953 4.98902 0 +0 0.755191 8.60962 8.07586 +0 6.81382 13.5157 8.23506 +0 7.73996 6.43599 7.28228 +6.24089 -0.376757 5.29265 0 +0 8.75545 4.83996 6.57804 +0.806467 2.3701 2.85794 0 +>MA0846.1 FOXC2 lnR0: 1.348 +0.361965 2.61869 4.09629 0 +0 3.07395 1.46614 3.26497 +0 1.16406 1.31426 0.300815 +1.63792 4.94364 0 7.13368 +3.3174 1.89461 5.4108 0 +0 1.06191 7.26397 7.30557 +0 5.31224 7.36485 7.49136 +0 6.99811 5.61046 6.33288 +9.25101 0 7.63339 1.76896 +0 7.05306 5.38008 6.50115 +0 2.12481 2.40928 0.884127 +0 1.29759 1.51287 0.21464 +>MA0848.1 FOXO4 lnR0: -1.572 +2.19092 8.50171 0 12.7917 +3.91974 5.68257 4.86573 0 +0 1.55346 6.75684 7.92248 +0 4.62266 7.47223 7.92248 +0 11.7518 5.30776 8.84623 +6.96669 0 7.23414 2.98333 +0 8.32628 8.32628 6.96669 +>MA0849.1 FOXO6 lnR0: -1.572 +2.77826 12.6534 0 13.1733 +5.4485 12.1334 7.13843 0 +0 2.06804 9.16281 12.6534 +0 4.59328 12.1334 7.94505 +0 12.1334 12.1334 12.6534 +13.1733 0 7.70234 4.665 +0 12.1334 8.36336 12.6534 +>MA0850.1 FOXP3 lnR0: -1.572 +1.39104 7.03893 0 7.55888 +3.30295 1.46047 7.13232 0 +0 7.13232 7.13232 2.70121 +0 7.13232 3.84291 4.51337 +0 3.17147 1.54371 7.65227 +8.17222 0 2.65726 2.90239 +0 7.13232 2.92597 7.65227 +>MA0855.1 RXRB(MA0855.1) lnR0: 2.516 +1.65031 3.17092 0 4.2932 +1.67957 8.61297 0 10.2914 +8.48415 10.8426 0 8.92723 +11.2448 11.7151 0 3.37717 +12.0112 9.92178 7.94136 0 +7.98247 0 5.90566 4.80647 +0 11.8654 8.20118 11.3951 +0 9.305 5.02539 7.43356 +0 10.8519 4.12404 12.3621 +11.3304 11.8007 0 9.35002 +10.7054 11.7549 0 4.06601 +11.0049 9.90576 7.19558 0 +9.13157 0 6.03803 5.72137 +0 8.07431 3.69613 10.3839 +>MA0856.1 RXRG(MA0856.1) lnR0: 2.516 +1.95899 2.47055 0 3.9909 +1.06897 8.26713 0 10.379 +9.31291 12.0824 0 8.67764 +8.20309 11.0148 0 2.99454 +12.5468 9.46715 7.6662 0 +11.3531 0 6.21515 4.33534 +0 14.5419 8.33649 12.7627 +0 10.5369 4.57932 5.84778 +0 14.3435 3.77289 12.3037 +11.9352 13.7145 0 10.8753 +11.4793 13.6334 0 3.32597 +13.4787 10.399 7.52061 0 +9.73368 0 5.68206 4.53808 +0 9.08825 3.42132 10.2539 +>MA0525.2 TP63 lnR0: 4.852 +0 5.29971 0.142689 3.73716 +0 9.52413 3.04899 6.61852 +11.7165 0 11.1965 11.7165 +0 10.5048 4.2994 8.72559 +1.74692 5.53364 10.5713 0 +12.3764 11.8565 0 12.3764 +7.58135 4.56669 10.93 0 +4.28107 0.406187 5.60274 0 +2.1754 2.09155 0 7.65814 +4.3562 1.26819 0 1.50758 +1.61073 9.9602 0 5.94007 +0 10.4701 4.91034 5.52055 +11.8534 0 11.3335 11.8534 +0 10.4431 9.45291 3.44495 +5.16454 1.65065 7.69246 0 +12.1912 11.6713 0 12.1912 +5.90829 3.38665 9.98674 0 +2.08532 0 3.36627 2.29304 +>MA0106.3 TP53 lnR0: 4.852 +0 2.31375 -0.320972 1.71649 +0 5.90631 1.57043 3.79904 +9.17599 0 10.3554 5.02973 +0 5.28572 3.62844 3.9719 +3.43109 5.07958 6.50769 0 +11.5568 12.6063 0 14.6957 +6.08088 0 6.7049 1.27006 +4.29674 0 5.31747 3.20287 +3.8603 0 2.44017 2.15726 +1.87635 2.72774 0 2.73014 +2.81292 4.51461 0 4.01355 +0.829165 8.27024 0 5.99528 +14.6207 0 11.8015 13.6305 +0 5.11083 5.77205 3.44896 +3.25817 6.6393 7.03832 0 +6.43081 9.14894 0 8.65782 +4.30057 1.87561 6.66311 0 +3.13447 0 3.44089 0.529784 +>MA0861.1 TP73 lnR0: 4.852 +0.624239 3.59612 0 0.596089 +0 3.29383 0.380394 4.84443 +13.7915 0 13.2715 13.7915 +0 5.55112 3.41392 5.4068 +1.56535 4.71558 3.27309 0 +10.7737 8.5822 0 12.9224 +6.44073 1.65651 6.42564 0 +3.06117 0 3.34691 2.07408 +0.959895 0.00365076 0.398365 0 +0.548328 0.551608 0 1.04871 +1.47756 4.10045 0 3.44977 +0 5.46586 2.22118 4.40015 +13.9024 0 13.3824 13.9024 +0 5.55583 4.60587 2.11556 +4.99434 -0.0181221 5.43707 0 +10.0079 6.19017 0 8.78552 +2.78765 -0.509498 4.69303 0 +0.87107 0 3.26893 1.70706 +>MA0862.1 GMEB2 lnR0: -0.988 +2.75042 1.12277 0.594562 0 +3.17506 3.88397 0.929665 0 +0 7.30953 4.74988 7.82948 +6.05024 0 7.82948 8.34943 +8.34943 5.53029 0 8.34943 +7.82948 2.89376 7.30953 0 +0 1.30283 3.64532 4.54008 +0 0.962889 2.71114 5.26983 +>MA0863.1 MTF1 lnR0: 2.516 +4.62668 5.09694 2.79775 0 +3.32468 2.2255 1.35959 0 +4.70834 4.18839 5.1786 0 +4.95721 5.01649 0 6.52665 +5.63926 0 6.10952 6.62947 +0 5.1786 4.18839 4.70834 +5.01978 0 4.49983 6.58923 +0 3.17147 4.16168 4.68164 +6.54782 0 6.02787 6.54782 +5.61928 6.08954 0 5.61928 +2.60369 3.8037 0 2.46753 +6.46121 0 5.94126 3.32232 +0 1.5547 2.00963 3.93076 +4.86927 0 4.92855 4.45829 +>MA0024.3 E2F1 lnR0: 1.348 +1.13904 1.74434 2.10688 0 +1.3871 3.20827 2.11546 0 +1.57172 3.52522 1.56424 0 +4.49533 3.59062 0 9.22988 +10.3164 4.80144 0 10.3164 +9.65842 0 9.13847 8.08898 +10.4024 8.89223 0 10.4024 +8.06254 0 4.98293 9.63199 +9.60506 0 3.58489 3.98816 +0 1.0742 4.07844 2.10844 +0 2.11136 2.5641 1.46698 +0 2.49175 1.5874 1.15558 +>MA0866.1 SOX21 lnR0: 3.1 +0 6.96204 5.72275 7.13626 +0 5.39827 2.42693 6.02453 +10.3708 0 9.0013 9.73328 +0 10.3211 8.8125 12.8215 +0 9.52169 7.51599 13.8117 +11.0319 11.3114 8.38608 0 +5.25859 9.14219 0 1.23861 +2.54854 2.60932 0 1.25429 +5.96341 -0.306647 6.23738 0 +0 8.94246 7.98667 12.8215 +7.81536 9.96941 0 1.59036 +7.46508 9.33093 7.06791 0 +10.9061 11.5125 0 11.1928 +8.77407 9.16267 8.09522 0 +5.76203 3.75849 4.45728 0 +>MA0872.1 TFAP2A(MA0872.1) lnR0: 1.932 +1.65552 1.8909 2.08825 0 +10.8274 1.90672 0 10.8274 +10.8369 0 10.3169 10.8369 +10.8421 0 10.3221 10.8421 +4.98522 0 3.50451 3.56953 +3.50451 -0.212649 1.07607 0 +2.0381 0.108483 0 1.62712 +0 0.774999 -0.473022 2.84547 +3.37199 4.36346 0 5.19157 +11.3141 10.7942 0 11.3141 +11.3081 10.7882 0 11.3081 +10.5243 0 1.56815 10.5243 +0 2.2619 1.32108 1.45358 +>MA0028.2 ELK1 lnR0: 0.18 +0 3.4979 1.28375 2.97238 +5.70173 0 4.90442 8.04017 +7.44296 0 9.48267 11.4359 +15.8517 10.916 0 11.1433 +13.5525 9.99221 0 6.46471 +0 7.01847 8.89302 10.6773 +0 6.51015 8.93911 4.3594 +4.40594 4.23564 0 7.72743 +5.5873 2.31194 4.77657 0 +0.896122 1.35855 0 1.51829 +>MA0873.1 HOXD12 lnR0: 0.764 +0 1.47414 -0.26221 3.38312 +1.99837 1.80014 0 7.1716 +9.32565 4.20731 6.65702 0 +8.85539 0 7.75621 10.8358 +3.21076 8.74642 0 10.8358 +9.32565 6.37035 9.79591 0 +0 9.79591 8.22647 2.59133 +0 9.79591 7.81549 10.3159 +0 9.79591 7.01604 4.87778 +0 2.33056 4.23617 2.08436 +0 -0.363238 2.24149 0.977019 +>MA0875.1 BARX1 lnR0: -0.988 +0.773657 0.293144 0 1.85601 +3.60966 0 4.33604 2.12743 +0 0.217663 0.735518 5.19484 +0 4.46294 4.56986 12.6079 +12.6079 12.088 12.088 0 +12.6079 12.088 12.088 0 +0 12.088 12.088 12.6079 +0.852662 0.790627 0 1.67577 +>MA0876.1 BSX lnR0: -0.988 +1.94434 0 0.77093 2.25698 +3.50963 0 5.6909 1.29456 +0 0.173809 0.348555 5.05869 +0 4.92755 2.48356 6.97365 +12.9804 12.4604 12.4604 0 +6.44506 12.4604 12.4604 0 +0 12.4604 12.4604 12.9804 +0 -0.296639 -0.325283 1.10671 +>MA0882.1 DLX6 lnR0: -0.988 +1.13275 0 0.439017 1.66308 +3.84109 0 5.9443 0.735953 +0 2.70766 3.62668 3.78871 +0 3.82882 10.7264 5.47058 +7.58215 10.7264 10.7264 0 +5.68662 3.65676 4.67769 0 +0 5.82072 6.67897 3.72085 +0.744797 0 0.789947 0.914835 +>MA0886.1 EMX2 lnR0: 0.18 +0.805966 0.599859 0 1.70893 +1.7332 0 0.330526 1.31598 +5.09255 1.3875 14.1832 0 +0 2.36696 5.20167 4.86473 +0 14.5168 14.5168 15.0368 +15.0368 14.5168 14.5168 0 +15.0368 14.5168 2.65895 0 +0 14.5168 14.5168 15.0368 +1.46192 1.29775 0 2.90476 +1.63746 0 0.353108 1.21173 +>MA0887.1 EVX1 lnR0: 0.18 +1.17166 0.767819 0 2.07973 +0.878661 0.0684243 0 2.3806 +2.69487 1.21486 4.30228 0 +0 0.622404 0.517933 3.40773 +0 7.44117 4.48851 12.82 +12.82 6.27216 4.3129 0 +5.03278 3.52876 4.94646 0 +0 8.43138 2.88924 5.45813 +1.53826 0.370769 0 1.15541 +1.7198 0 0.753185 1.98886 +>MA0888.1 EVX2 lnR0: 0.18 +1.33669 0.605804 0 1.84872 +0.968609 0.157474 0 2.36905 +2.97652 1.31051 3.83287 0 +0 0.480329 0.62299 3.71017 +0 6.43437 3.96873 14.1775 +11.6179 6.34616 4.29278 0 +6.01035 3.99819 4.94284 0 +0 13.6576 3.15409 5.45959 +1.44002 0.674297 0 1.59011 +1.53972 0 0.620369 1.48338 +>MA0889.1 GBX1 lnR0: 0.18 +0 0.0464882 -0.171845 1.83162 +3.64972 0 1.09393 2.50831 +5.76434 -0.493511 9.13665 0 +0 4.96003 4.6002 7.36216 +0 6.71264 9.21563 10.0544 +9.12495 7.1319 13.0843 0 +6.38558 5.38234 6.20393 0 +0 8.45759 10.9356 6.34508 +1.60227 0.927013 0 2.50553 +2.23521 0 1.09568 1.32796 +>MA0890.1 GBX2 lnR0: 0.18 +0 0.475661 -0.179937 1.45169 +1.98872 0 0.31613 1.68322 +4.94608 0 7.10934 0.903922 +0 5.0082 4.05345 6.83964 +0 6.18239 7.29742 9.94142 +14.5958 8.17999 8.09068 0 +6.35986 5.0082 4.77128 0 +0 7.92723 9.1702 5.34083 +0.885508 1.22826 0 1.92029 +1.27752 0 0.368768 1.18665 +>MA0891.1 GSC2 lnR0: 0.18 +1.08676 0 0.626806 1.19597 +1.74233 0 2.1159 0.928659 +4.06742 10.3506 10.3506 0 +0 3.95438 4.57479 3.28728 +0 6.80071 10.3506 3.88431 +10.8705 5.01105 3.23114 0 +3.46879 0 3.45201 3.78617 +3.94835 0 2.23142 2.69508 +2.26534 0.0626667 0 1.16506 +1.18963 0 2.24756 1.1455 +>MA0892.1 GSX1 lnR0: 0.18 +0.757275 0 0.891649 1.14548 +2.20308 0 1.03901 1.74736 +2.52885 0.175823 3.34675 0 +0 0.427075 3.12431 2.11439 +0 2.91409 2.70344 4.49261 +3.66542 3.32952 7.60913 0 +3.43404 2.91409 9.58955 0 +0 9.58955 6.30015 3.47466 +0 0.316567 -0.00905068 1.35424 +0 -0.323949 0.180261 0.150063 +>MA0894.1 HESX1 lnR0: 0.18 +1.57724 1.19792 0 1.73503 +1.21653 0 1.66105 0.643799 +4.39385 11.3545 6.27546 0 +0 11.3545 5.65598 6.92343 +0 8.3839 8.06512 11.8745 +11.8745 11.3545 7.39369 0 +11.8745 7.39369 11.3545 0 +0.722266 5.74854 0 4.9522 +0.948586 1.11066 0 2.66778 +1.50838 0 1.77635 0.920854 +>MA0895.1 HMBOX1 lnR0: 0.18 +0 -0.404139 0.790501 2.2362 +2.97106 0 1.85264 0.83664 +3.97952 4.9919 3.70507 0 +0 9.64633 1.20621 4.72819 +9.11678 4.52164 0 8.12657 +5.45794 8.65612 7.08667 0 +2.34875 4.02943 6.50743 0 +0 7.34713 5.51722 3.54524 +0 0.128181 1.98033 2.39519 +1.92553 0 0.544153 2.70056 +>MA0899.1 HOXA10 lnR0: 0.764 +0.886763 1.06163 0 1.36941 +2.29115 2.2313 0 3.13699 +4.82633 -0.29868 5.65296 0 +0 0.363247 2.48483 3.09856 +0 3.63912 2.98859 4.91836 +4.46537 8.83567 12.3855 0 +0 5.55197 5.03572 1.28605 +0 7.22708 6.1801 4.40085 +0 3.32285 5.47656 4.61244 +0 1.46902 1.88114 2.00552 +0 0.00494988 0.761146 0.555297 +>MA0903.1 HOXB3 lnR0: 0.18 +0 0.304716 -0.0110042 0.717951 +1.21151 0 0.0490725 1.42847 +2.16109 0.143032 3.1544 0 +0 0.0839667 2.66419 3.44699 +0 3.99771 3.76855 5.67417 +13.5214 5.83391 13.0015 0 +4.81953 3.38231 13.0015 0 +0 6.16218 13.0015 4.44373 +0.578481 1.14735 0 2.15486 +0.837298 0 0.418142 1.06684 +>MA0905.1 HOXC10 lnR0: 0.18 +1.61152 1.60411 0 8.09432 +6.82687 3.1505 11.0153 0 +3.83267 0 7.871 4.86882 +0.800656 8.75534 0 7.45677 +6.77492 11.0153 11.0153 0 +0 7.89273 8.15319 1.03714 +0 9.03484 8.45561 4.91417 +0 4.80983 4.63539 4.05458 +0 1.99591 2.04595 1.57034 +0.142839 0.158033 0.73517 0 +>MA0906.1 HOXC12 lnR0: 0.764 +1.09689 3.03312 0 2.87478 +2.27173 2.57436 0 11.481 +8.40143 5.38262 9.8619 0 +4.90222 0 8.28708 5.18572 +3.99661 10.3818 0 12.4712 +11.9513 9.8619 10.4411 0 +0 7.5627 8.87169 2.92677 +0 11.4313 9.8619 7.29687 +0 7.66126 11.4313 7.09244 +0 2.20739 3.4336 3.02828 +0 -0.183242 1.41277 0.100472 +>MA0907.1 HOXC13 lnR0: 0.764 +2.08365 0.771642 0 1.19138 +5.27797 0 4.37106 6.94598 +7.89692 5.26039 7.11651 0 +6.00772 0 6.77055 3.72985 +2.81688 7.89692 0 8.41687 +10.1961 9.67616 7.11651 0 +0 8.68595 8.10672 2.89327 +0 7.37696 8.10672 7.05722 +0 9.67616 9.67616 9.2059 +0 2.30608 3.24786 2.58486 +0 -0.40163 0.864242 0.102491 +>MA0908.1 HOXD11 lnR0: 0.18 +1.35224 2.05012 0 8.29483 +7.77488 7.25493 7.25493 0 +4.24739 0 7.77488 3.75476 +2.24611 7.77488 0 8.29483 +4.63599 7.25493 7.25493 0 +0 6.86646 6.86646 1.61062 +0 7.25493 7.25493 5.79446 +0 4.95573 7.25493 4.80425 +0 2.39608 2.44451 1.66536 +0 0.247753 1.35231 0.343059 +>MA0914.1 ISL2 lnR0: -0.988 +2.33031 1.09491 0 2.84914 +5.59826 0 5.41719 2.9609 +0 4.54072 4.80997 4.45538 +1.34461 0 4.98389 4.30175 +4.63878 4.85294 4.48065 0 +4.29287 2.42056 8.04742 0 +0 4.19934 5.96844 2.03523 +0 1.65123 0.261541 1.88145 +>MA0852.2 FOXK1 lnR0: 2.516 +0 0.306816 -0.173858 0.20443 +0 0.712338 0.0957172 1.07853 +0.668551 0.935149 0.0113958 0 +3.08785 4.85721 0 6.05848 +3.91926 6.71233 3.8339 0 +0 4.15742 5.92841 7.09405 +0 4.15172 5.7984 6.57881 +0 5.61067 5.95519 6.35084 +6.9028 0 6.1442 4.12293 +0 5.3235 5.70673 6.12082 +0 0.825704 0.790429 1.83493 +2.11728 1.47945 0 2.9616 +1.0933 0.42283 0 1.49062 +0.544883 0 0.0918684 0.935877 +>MA0036.3 GATA2 lnR0: 0.764 +0.513163 0.141136 0.0380099 0 +1.36413 -0.190621 0.27143 0 +3.98055 0 3.08498 3.3688 +4.86003 5.10778 5.88407 0 +4.98962 8.01271 8.67601 0 +0 9.25978 7.72243 7.82332 +6.51314 6.88876 7.55288 0 +7.60105 0 6.69613 6.5251 +2.18812 3.91363 4.33138 0 +0.428521 -0.438851 -0.416372 0 +0.558022 -0.200511 0.59719 0 +>MA1106.1 HIF1A lnR0: 0.18 +1.57711 0.843142 0 2.06212 +1.67756 -0.183363 -0.145977 0 +0 9.31503 7.74558 8.26553 +10.3593 0 9.83936 9.3691 +9.3691 9.83936 0 10.3593 +8.20276 4.2146 5.70239 0 +3.80093 4.2881 0 6.59771 +3.72335 0 5.26642 5.01638 +1.00653 0 0.171948 0.86849 +1.44823 0 0.2142 0.967557 +>MA0147.3 MYC lnR0: 1.348 +1.18069 0.290912 0 1.3685 +1.29763 0.444409 0 1.50854 +3.58311 0 2.95659 4.19028 +7.20311 0 7.1702 7.88091 +0 5.6796 4.18343 5.28262 +6.82032 0 5.93559 4.42568 +5.22486 4.80949 0 7.32806 +6.21745 4.26977 5.6053 0 +8.09432 6.33866 0 7.13419 +3.23114 0 1.21264 2.91237 +1.17814 0 0.550946 0.619851 +1.74808 0 0.400878 1.272 +>MA0100.3 MYB lnR0: 0.18 +0 -0.509855 -0.0237661 0.159486 +1.06464 0 0.10715 0.581184 +10.9807 0 7.90107 7.69127 +0 7.92695 4.63754 7.45669 +0 8.37698 9.94643 7.68651 +10.9938 0 10.4739 10.9938 +9.35767 3.95525 3.7792 0 +7.84462 8.48314 0 10.9835 +0.305926 -0.47626 1.21346 0 +0.839402 0 1.21493 1.09784 +>MA0104.4 MYCN lnR0: 1.348 +1.23427 0.369868 0 1.60457 +1.09781 0.738017 0 1.74621 +3.95922 0 2.81616 4.14955 +8.07462 0 8.76509 10.1831 +0 6.21763 3.91343 4.48941 +8.58685 0 5.67163 4.80792 +4.80792 5.67163 0 8.58685 +4.48941 3.91343 6.21763 0 +10.1831 8.76509 0 8.07462 +4.14955 2.81616 0 3.95922 +1.74621 0 0.738017 1.09781 +1.60457 0 0.369868 1.23427 +>MA1109.1 NEUROD1 lnR0: 1.932 +0.8877 0.750202 0 0.875047 +0.780095 1.47057 0 2.10523 +0 0.975057 0.848392 4.70171 +7.41182 0 7.25089 7.8767 +0 7.53102 6.45421 6.81526 +7.43624 6.36535 0 5.0396 +0 3.19572 4.1394 6.46744 +5.21655 4.80247 6.16748 0 +7.76509 8.04459 0 6.58412 +5.50264 4.34133 0 4.02328 +1.79336 0 1.1111 1.16408 +0 -0.166221 -0.314093 0.610497 +0.740544 0.0866066 0 0.775422 +>MA0161.2 NFIC(MA0161.2) lnR0: 0.764 +0.558702 0.0213822 0.115596 0 +0 0.337673 0.372163 0.157988 +5.14819 0 4.94875 5.49051 +6.0603 4.57806 4.29738 0 +4.87974 4.43883 5.33791 0 +5.62542 6.35155 0 7.52981 +6.07943 6.42752 0 5.70561 +5.80666 0 6.84541 4.81376 +0 4.10814 3.8435 4.10249 +0.796004 0.109424 0 0.682118 +0 -0.220791 -0.245845 0.258155 +>MA0060.3 NFYA lnR0: 0.764 +0 0.791296 -0.456859 2.38689 +0 1.7069 -0.470112 1.57316 +8.04608 0 6.98713 5.84544 +7.65217 0 7.27285 6.90468 +0 6.69535 7.4251 5.53885 +0 5.01815 4.62609 7.50356 +6.86597 4.55635 7.9927 0 +5.13231 0 3.68332 5.53475 +0 3.69445 2.51098 6.76077 +2.64773 1.2492 0 3.36277 +0 -0.0862178 0.533203 1.36271 +>MA1110.1 NR1H4 lnR0: 0.764 +1.56325 0.918996 0.43347 0 +2.30665 0 1.43923 1.62747 +0 4.81958 4.58093 4.28582 +0 3.27801 2.92998 3.79796 +6.84521 4.34484 5.52581 0 +4.68974 5.79755 0 5.62392 +0 3.74719 4.35782 4.87778 +4.59819 0 8.78658 5.75666 +5.66648 0 6.03087 5.78082 +1.56291 0.154107 0.876872 0 +0 -0.477303 -0.163928 0.010543 +>MA1111.1 NR2F2 lnR0: 0.764 +1.01805 0 0.718799 0.709238 +0 0.638174 1.14281 1.34131 +0 4.98266 2.80913 3.08099 +0 6.4371 4.08531 6.37781 +6.25764 6.88679 0 6.04821 +6.4327 7.28619 0 6.71007 +6.82331 5.95319 5.52677 0 +6.45761 0 6.13501 4.01807 +0 6.36887 5.01034 5.8572 +0 -0.192132 -0.30386 0.269501 +0 0.608103 0.0400422 1.06633 +>MA0014.3 PAX5 lnR0: 1.348 +0.616927 1.66907 0 2.81668 +0 1.53063 0.290382 1.11908 +6.47989 2.98931 0 7.02201 +6.53114 0 5.13846 4.39083 +3.95936 5.06081 0 6.16 +3.62433 3.19758 4.70422 0 +6.77578 5.10673 0 8.52403 +0 4.39035 3.57063 4.30745 +5.77455 0 4.44897 6.56322 +4.43148 0 3.15349 3.39114 +0.622035 0 0.371643 0.864468 +1.12776 0 0.16473 0.577678 +>MA1114.1 PBX3 lnR0: 4.268 +0.973908 0.353726 0 1.03985 +0.873287 0.164115 0 0.581039 +1.06083 0.0597373 0 0.522916 +3.22279 4.09053 2.94476 0 +5.27913 4.76543 0 5.78244 +0 5.09717 4.3338 4.59884 +4.35707 2.61761 0 2.84252 +4.61921 4.40656 3.8956 0 +5.94415 4.70616 0 6.7436 +0 5.24476 2.79636 5.3472 +5.90012 0 4.90898 6.01841 +0 4.97605 3.28047 3.97498 +4.42468 3.74767 0 3.85838 +2.70249 1.54996 0 3.07053 +1.59381 0 0.730648 1.31109 +0.664418 0.349485 0 1.01213 +1.08254 0.296727 0 1.07018 +>MA1115.1 POU5F1 lnR0: 0.764 +0 1.4095 0.786315 0.0395317 +0.415032 0.262849 0.802888 0 +0 6.10391 5.20977 7.40886 +7.18445 6.02967 6.96637 0 +4.4912 5.84808 0 4.66669 +4.74934 0 4.18981 3.07504 +0 5.8827 6.04159 3.37284 +0 3.37545 2.80937 3.61816 +0 4.92818 4.99841 5.2653 +1.30709 1.06502 1.08759 0 +0.0646632 0.0442466 -0.485774 0 +>MA1116.1 RBPJ lnR0: 0.18 +1.79213 0 0.473912 0.977429 +1.34499 0 0.146339 2.27805 +9.54169 6.92697 9.02174 0 +6.48458 6.42952 0 10.6137 +8.2973 6.71744 0 5.71403 +8.61361 7.9254 0 5.34217 +0 10.581 8.28177 6.24207 +0 6.62794 9.59858 8.80954 +0 -0.342043 -0.197805 0.835472 +0.847785 0.292928 0 0.893954 +>MA1117.1 RELB lnR0: 0.764 +1.49394 1.90624 0 2.14296 +0 0.601324 0.105838 0.797423 +0 3.90493 3.60412 3.98627 +3.70123 4.13803 3.57654 0 +5.01485 4.30414 5.24044 0 +4.81378 0 6.09835 4.51285 +5.52886 0 6.67363 5.87477 +4.83508 0 5.61927 5.81561 +5.71462 0 4.76595 5.90538 +0.822503 0.640729 0 0.676117 +1.00091 0.111722 0 1.10277 +>MA1118.1 SIX1 lnR0: 0.764 +3.63741 4.24678 0 3.44481 +0.430435 2.24942 2.0292 0 +0 5.21163 6.6381 4.81861 +0 6.31535 6.02868 6.10555 +4.92387 0 6.14569 3.82432 +3.4391 0 4.72151 3.68697 +4.19764 3.82211 4.41663 0 +4.8651 6.61548 0 5.7165 +0 6.47563 5.89639 5.61689 +1.73446 0.925194 0.243874 0 +0 0.0737221 2.33774 2.05273 +>MA1119.1 SIX2 lnR0: 3.684 +0 -0.0854577 0.02139 0.253309 +0 -0.152146 -0.133638 0.219475 +2.09875 0 1.79433 2.45165 +2.16874 3.59066 2.22463 0 +5.40326 6.41037 0 5.38615 +0 2.92936 3.15106 1.46443 +0 3.64348 5.60782 4.31095 +0 6.4544 5.55639 6.25896 +4.99107 0 4.62914 3.08157 +3.32087 0 4.36067 3.5415 +3.79951 3.41747 4.16015 0 +4.38889 5.33982 0 5.15004 +0 5.51756 5.34097 5.76457 +2.45676 1.78526 0.83981 0 +0 -0.109764 1.55836 1.84512 +2.05971 0 2.27897 1.20549 +>MA0442.2 SOX10 lnR0: 0.764 +0 0.253629 -0.150148 0.601336 +0 0.816931 -0.183304 0.59013 +0 1.0495 1.27739 2.14677 +0 8.05633 8.3751 6.22105 +9.3908 0 7.3014 5.69938 +0 7.38912 7.38912 7.21549 +0 5.50574 5.96685 5.56629 +0 5.76954 6.64541 4.93366 +7.96207 7.09761 0 7.03832 +0 -0.25219 -0.415564 1.59103 +0 -0.321185 -0.186568 0.827674 +>MA1120.1 SOX13 lnR0: 0.764 +0 0.681843 -0.379706 0.681114 +0 0.376373 0.246866 1.24559 +0 7.00236 6.17653 6.73176 +6.71374 0 6.07162 5.19625 +0 5.69144 5.82505 5.13457 +0 5.90218 5.52066 6.33724 +4.72609 5.20548 6.61892 0 +3.20479 5.98895 0 6.16087 +2.27809 2.02117 0 3.02444 +0.553268 0 0.224575 0.856438 +0 -0.396177 -0.290991 0.0911908 +>MA1121.1 TEAD2 lnR0: 1.932 +0.109561 -0.490894 -0.124867 0 +1.93113 0 1.52821 1.32539 +0 4.05282 2.09238 4.83323 +4.06684 0 4.94807 5.7868 +0 5.84893 4.85872 5.63913 +7.37827 5.0022 5.64789 0 +4.94826 5.25026 5.09974 0 +6.26192 0 5.4553 4.80242 +6.29852 0 6.93704 5.23107 +0 1.57301 1.6699 0.680118 +1.39159 0.884342 0 1.39159 +1.14108 0 0.22297 1.12838 +1.52309 0 0.902847 1.71756 +>MA1122.1 TFDP1 lnR0: 0.764 +1.4281 0.65464 0 1.74948 +2.33566 0.453606 0 3.45017 +5.71727 4.64754 0 6.56867 +6.48488 0 6.29607 5.18578 +7.46106 5.08499 0 8.35907 +6.12086 4.48158 0 6.57097 +6.55977 5.8051 0 6.46121 +0 5.63334 3.66728 5.84599 +0 2.71496 3.02126 4.82965 +0.993161 0.00220289 0 1.89424 +1.27711 0.100292 0 1.30353 +>MA0750.2 ZBTB7A lnR0: 1.932 +0.530615 0.244237 0 1.07455 +1.45497 0 0.281792 1.85368 +5.17919 0 3.02838 6.4239 +2.67936 0 4.13468 6.05201 +6.80148 6.0061 0 7.22897 +7.40406 6.37706 0 7.27356 +0 5.07952 4.79332 6.21288 +0 4.74572 5.13471 5.37346 +4.85658 4.16183 0 6.569 +2.85828 0.765548 1.83531 0 +2.886 1.86045 0 3.33879 +1.6224 0.414308 0 2.30123 +1.28102 0 0.0560884 1.60847 +>MA0103.3 ZEB1 lnR0: 0.764 +1.82341 0 0.607281 1.62406 +0.761949 0 0.0988186 0.752832 +7.8307 0 6.84793 5.32807 +0 13.6212 5.89024 13.1509 +9.66411 0 7.58922 7.78457 +7.08827 0 4.84101 9.70809 +11.7955 4.69106 5.18201 0 +5.92108 6.69245 0 7.66933 +2.76736 0 0.875978 1.99335 +1.14615 0.108768 0 1.57524 +1.50483 0 0.252513 1.3624 +>MA1124.1 ZNF24 lnR0: 1.932 +3.54252 0 3.62775 3.07651 +0 2.75833 2.64428 3.55789 +4.30369 2.66199 4.15409 0 +5.60292 4.75433 4.99036 0 +6.54151 0 7.46561 5.40604 +0 6.08703 4.90849 7.17328 +7.74652 4.07799 6.83393 0 +6.88101 5.51444 6.36106 0 +6.41968 0 7.79805 5.27695 +0 5.19641 4.65186 6.23657 +4.2221 2.68326 4.01528 0 +4.23749 2.6179 3.63315 0 +3.59069 0 4.32571 3.2137 +>MA1125.1 ZNF384 lnR0: 1.348 +0.132295 0.538914 0.348552 0 +0.00672197 -0.141053 0.307137 0 +0.420021 1.34765 0.91525 0 +0 0.243498 0.940567 1.40853 +0 11.2533 10.4538 8.89482 +0 9.09693 9.93662 7.24798 +0 9.79482 9.50226 6.51259 +0 10.449 10.2583 7.54343 +0 9.50842 10.3481 7.226 +0 11.4465 14.2264 10.3306 +0 2.25711 2.32809 2.17396 +0 1.71263 2.15961 2.00241 +>MA1154.1 ZNF282 lnR0: 4.268 +3.65161 0 1.93054 2.5979 +3.21237 3.54647 4.99161 0 +4.46827 7.99577 4.85688 0 +6.50929 6.40032 5.98934 0 +8.15868 0 6.06928 8.15868 +8.15186 0 7.63191 7.16165 +8.1312 0 5.63083 6.56176 +0 -0.0291081 6.54971 2.65388 +3.84195 0 5.41677 0.585896 +0 5.42688 2.21075 2.03135 +0 7.51951 7.51951 6.47001 +6.59602 0 5.34631 6.18504 +0 1.88919 5.75783 4.8766 +7.17525 0 6.07607 6.59602 +4.79001 8.1387 0 1.70503 +0 1.40723 0.839651 1.82629 +1.64632 0 0.0145034 1.43977 +>MA1155.1 ZSCAN4 lnR0: 3.1 +2.38932 1.30125 3.04875 0 +3.07305 9.0884 0 11.1778 +11.1268 0 9.61659 11.1268 +0 9.71536 9.71536 8.66587 +11.1174 0 10.5974 11.1174 +0 9.70316 8.13371 8.65366 +9.16831 0 10.6288 5.00007 +0 0.513411 0.735532 6.36151 +8.16292 0 10.6136 9.56411 +7.48737 6.55645 3.91955 0 +9.305 5.14858 0 3.58675 +0 2.82013 1.73401 1.60827 +0 1.58965 9.63935 7.37943 +0 9.68972 8.12028 9.21946 +0 1.77355 0.917366 2.10096 +>MA0037.3 GATA3 lnR0: -0.988 +0 0.616678 7.3764 0.878269 +10.3882 9.86822 0 10.3882 +0 9.34827 9.34827 9.86822 +9.86822 9.34827 9.34827 0 +0 7.65192 9.22137 3.41158 +0 5.17694 2.93235 4.12745 +2.55221 0.652985 0 2.61572 +0 0.634316 -0.126834 2.59375 +>MA0099.3 FOS::JUN(MA0099.3) lnR0: 0.18 +0 1.86104 0.668956 3.8166 +7.87489 6.7757 7.76591 0 +7.14272 8.60319 0 2.78493 +0 2.09108 6.76731 4.11697 +3.61394 1.90963 0 4.13125 +7.29709 7.76735 7.76735 0 +5.4301 0 7.83542 8.0366 +0 7.76879 7.76879 7.55899 +4.46429 0.329317 2.02224 0 +1.03257 0 1.25787 1.79524 +>MA1126.1 FOS::JUN(MA1126.1) lnR0: 3.684 +1.1671 2.68767 0 1.24404 +0 3.0428 0.0644241 4.12654 +4.0492 2.89169 3.14077 0 +4.41275 2.51253 0 2.27519 +0 3.98434 1.91731 3.07547 +3.85961 0 4.27792 4.79787 +2.94939 2.6264 0 4.84575 +4.4221 4.66717 4.21224 0 +4.4524 0 4.19291 4.35032 +0 4.612 4.05194 4.69269 +4.40526 0.991601 2.91833 0 +0.625479 0 0.99464 1.06208 +0 -0.47958 0.465844 0.649489 +0.952315 0.525061 -0.0191658 0 +1.68515 2.24643 0.609674 0 +0.546177 -0.486108 -0.00151412 0 +>MA1127.1 FOSB::JUN lnR0: 0.764 +2.07459 2.99061 0 2.32332 +0 2.33667 1.0473 3.69307 +6.15459 5.87329 5.63464 0 +6.06504 6.24863 0 3.60111 +0 6.1436 5.15339 5.45313 +4.65713 0 5.0425 4.84373 +4.04772 5.84589 0 6.36584 +5.0712 3.40504 5.33703 0 +1.99822 0 5.00528 4.7161 +0 5.22755 5.40635 5.37917 +2.64897 0.649385 2.90561 0 +>MA1128.1 FOSL1::JUN(MA1128.1) lnR0: 1.932 +0.487494 -0.271106 -0.311028 0 +1.64782 1.23947 0 0.909834 +0 2.19735 0.555682 4.43726 +8.87372 7.77453 8.35377 0 +8.34646 8.23748 0 5.09322 +0 7.77166 7.77166 7.88064 +5.40848 0 3.95223 3.56686 +4.55921 7.50747 2.00726 0 +2.88203 0 8.04288 7.83308 +0 7.02748 6.03727 7.54743 +3.28941 0.70533 1.73082 0 +0.576535 0 0.820409 0.979515 +0.580322 0 0.2823 1.07235 +>MA1129.1 FOSL1::JUN(MA1129.1) lnR0: 0.18 +0 2.64144 0.728934 4.52233 +4.93868 4.32346 4.63076 0 +4.78479 3.52671 0 1.98702 +0 4.36685 2.39972 4.18915 +5.66999 0 4.39565 3.62877 +3.66222 4.47423 0 5.55424 +4.25906 2.41658 4.31835 0 +1.99467 0 3.47319 4.69888 +0 4.74677 4.27499 4.8403 +4.63673 0.744133 2.60565 0 +>MA1130.1 FOSL2::JUN(MA1130.1) lnR0: 1.348 +1.15329 0.247009 0 0.656591 +1.17047 0.904348 0 0.845062 +0 1.61303 0.410996 3.24537 +8.87658 8.35663 8.35663 0 +9.15059 8.63063 0 2.8995 +0 2.22662 8.12253 4.77383 +3.24175 2.27689 0 4.05154 +8.87658 8.35663 8.35663 0 +6.00999 0 8.84915 9.3691 +0 9.34684 8.35663 8.87658 +4.83484 0.44625 2.10409 0 +0.857649 0 0.90902 1.21667 +>MA1131.1 FOSL2::JUN(MA1131.1) lnR0: 0.764 +1.55431 2.25336 0 1.54156 +0 3.79157 0.439057 5.25637 +7.05803 6.17906 6.17906 0 +7.29532 5.87735 0 4.34718 +0 6.51602 6.00649 5.27577 +6.69886 0 5.2495 4.35282 +3.67412 4.15983 0 6.02016 +5.86328 3.12243 5.92256 0 +1.34241 0 5.15162 6.58013 +0 5.86736 5.52285 5.85204 +3.85392 0.868951 1.2562 0 +>MA1132.1 JUN::JUNB(MA1132.1) lnR0: 0.18 +1.51366 1.64843 0 1.15619 +0 1.67614 1.18793 3.58674 +6.24056 5.84491 4.19141 0 +6.84659 5.33643 0 4.74187 +0 5.84189 4.45703 5.58107 +5.35652 0 2.80602 5.07916 +3.23008 3.93679 0.150474 0 +2.62688 0 5.94936 3.02032 +0 4.64927 5.04133 5.00733 +1.39266 0.47884 2.3975 0 +>MA1133.1 JUN::JUNB(MA1133.1) lnR0: 1.348 +3.02791 1.24651 -0.172027 0 +0.885692 2.13845 0 4.45463 +3.85404 3.75316 4.50472 0 +4.24214 4.5564 0 2.1881 +0 4.52863 3.06664 2.57423 +5.63761 0 4.12745 4.12896 +4.43544 4.50753 0 4.8128 +4.81835 4.4438 3.89899 0 +3.67087 0 4.4913 4.82546 +0 4.94954 4.10984 5.04077 +4.34732 1.95605 1.90046 0 +0.385599 -0.391453 -0.397044 0 +>MA1134.1 FOS::JUNB lnR0: 1.348 +1.60108 1.13097 0 0.894374 +0 1.94211 0.617039 3.96566 +8.87658 8.35663 8.35663 0 +9.19737 8.67742 0 3.21215 +0 4.39316 8.30864 7.51961 +4.14321 0.987904 0 5.04853 +8.87372 8.35377 7.36356 0 +5.58731 0 8.83744 9.35739 +0 8.35663 8.35663 8.87658 +6.30183 0.677527 3.10788 0 +0.915312 0 1.01395 1.4868 +0.621861 0 0.244622 1.46862 +>MA1135.1 FOSB::JUNB(MA1135.1) lnR0: 0.18 +2.34323 1.22043 0 1.17947 +0 2.72023 0.366778 4.78677 +8.87658 9.34684 8.35663 0 +9.37056 9.84082 0 6.08115 +0 8.3552 8.3552 8.87515 +4.57219 0 0.936207 3.75535 +8.23897 8.29826 4.01864 0 +2.57467 0 8.57522 9.09517 +0 9.34684 8.35663 8.87658 +3.89102 0.623794 1.64736 0 +>MA1136.1 FOSB::JUNB(MA1136.1) lnR0: 0.18 +0 2.67599 0.0810569 5.38079 +4.8403 4.06759 5.1786 0 +6.11059 3.86051 0 2.03345 +0 3.71124 3.27665 4.85885 +5.23849 0 4.86395 3.53709 +4.55626 4.58884 0 5.87878 +3.83825 2.8163 4.28366 0 +2.65764 0 4.34932 6.06688 +0 5.1879 4.32966 4.80425 +5.73554 0.816145 2.78024 0 +>MA1137.1 FOSL1::JUNB lnR0: 1.932 +0.335485 -0.364682 0.0929003 0 +1.30902 1.34545 0 1.02894 +0 1.94468 0.447762 3.52737 +5.24884 5.22152 5.22152 0 +5.04872 5.27145 0 4.26591 +0 4.87673 4.81027 4.37285 +3.78004 0 1.63949 2.9553 +3.70751 4.49654 2.24578 0 +1.83732 0 6.03625 4.64905 +0 4.7899 3.97201 4.52907 +3.32339 0.758368 1.15676 0 +0 -0.510427 0.0287642 0.591151 +0.796638 0 0.422092 0.898083 +>MA1138.1 FOSL2::JUNB(MA1138.1) lnR0: 0.18 +1.9305 1.29332 0 1.06802 +0 2.97142 0.452003 5.41983 +9.86822 9.34827 9.34827 0 +10.368 9.84808 0 6.49939 +0 9.34827 9.34827 9.86822 +3.85788 0 0.948154 3.21928 +8.84038 9.31064 4.6023 0 +2.797 0 9.60547 10.1254 +0 9.34827 9.34827 9.86822 +4.02628 0.726461 1.87223 0 +>MA1139.1 FOSL2::JUNB(MA1139.1) lnR0: 1.348 +1.17246 1.24118 0 0.963029 +0 2.72326 0.71604 4.36958 +6.68582 5.17566 6.52489 0 +6.37084 5.09933 0 2.55443 +0 6.74951 5.53909 6.40356 +6.81209 0 5.5886 4.06982 +4.0714 5.67185 0 6.81368 +6.40356 5.64496 6.5293 0 +2.55838 0 4.97137 6.26131 +0 6.74363 5.02367 6.68434 +4.42025 0.728934 2.68285 0 +0.959055 0 1.22777 1.16224 +>MA1141.1 FOS::JUND lnR0: 1.932 +1.29253 0.363549 0 0.804114 +1.60089 1.20312 0 1.07738 +0 1.95565 0.622379 3.89045 +9.86822 8.35806 9.34827 0 +10.1925 9.67256 0 3.23889 +0 2.7301 9.1898 5.74891 +3.99918 4.36089 0 5.90632 +9.86822 9.34827 9.34827 0 +5.48728 0 9.82618 10.3461 +0 9.34827 9.34827 9.86822 +4.75332 0.544395 2.42527 0 +1.07816 0 0.911553 1.50632 +0.66344 0.14349 0 1.20806 +>MA1142.1 FOSL1::JUND(MA1142.1) lnR0: 0.18 +0.593227 0.331589 0 0.764176 +0 1.56793 0.43448 3.71425 +4.83406 4.67973 4.14074 0 +5.55028 3.6137 0 2.9599 +0 5.47688 2.82846 4.32151 +4.0263 0 1.58425 2.18848 +2.73165 3.30667 1.29553 0 +1.75205 0 4.5807 3.79167 +0 3.91314 5.08914 4.78714 +1.41439 0.613715 1.16308 0 +>MA1143.1 FOSL1::JUND(MA1143.1) lnR0: 0.18 +0 2.33829 0.262445 3.7399 +4.51246 3.53407 3.71288 0 +4.75973 2.90251 0 3.71693 +0 3.68148 3.81144 4.23283 +5.13727 0 3.64892 4.08355 +2.96966 3.40375 0 2.37827 +2.28215 0.61724 3.30763 0 +0 0.197664 2.15667 3.66683 +0 2.71735 2.13102 1.75579 +2.20019 0 2.25373 0.545045 +>MA1144.1 FOSL2::JUND(MA1144.1) lnR0: 0.18 +2.19896 1.61821 0 1.20875 +0 2.82684 0.589865 5.35082 +9.86822 9.34827 9.34827 0 +10.3753 9.85531 0 6.94969 +0 8.35663 9.34684 9.86679 +4.17007 0 1.03579 3.84522 +6.99234 9.25226 3.37958 0 +3.10471 0 9.65442 10.1744 +0 9.34827 9.34827 9.86822 +3.8662 0.598124 1.81391 0 +>MA1145.1 FOSL2::JUND(MA1145.1) lnR0: 3.1 +0.765201 0.404567 -0.27786 0 +1.14603 0.835512 0 0.946369 +0 3.05047 0.188698 3.23928 +5.06845 4.49654 5.83127 0 +6.86449 3.81496 0 1.84268 +0 6.48607 4.31489 5.43658 +6.59237 0 4.61732 4.91705 +3.09354 5.63083 0 5.3012 +4.98603 5.61228 5.85093 0 +5.26667 0 5.82354 6.75446 +0 6.5293 5.7593 6.27925 +4.54503 0.2131 2.81465 0 +1.50688 0 2.03055 1.33426 +1.86186 0.894164 0 1.5625 +0.73277 0 0.253556 0.883923 +>MA1146.1 NR1H4::RXRA lnR0: 3.1 +1.52286 1.37199 0 2.04889 +0 2.99113 0.686839 5.71172 +5.43788 5.81594 0 6.01712 +5.28688 5.9568 0 1.50355 +4.99847 3.48831 2.46981 0 +6.64918 0 5.90901 3.60602 +0 5.11088 0.993161 5.27181 +2.16717 1.89395 2.57008 0 +5.07737 2.62235 3.53775 0 +3.28287 2.8438 0 4.78825 +0 2.21031 2.72165 3.92392 +3.01466 0 6.21284 3.69246 +3.30161 0 4.314 4.42298 +4.2851 -0.0813433 2.31005 0 +1.96922 -0.243656 0.310774 0 +>MA1147.1 NR4A2::RXRA lnR0: 3.1 +0.880618 0.796574 0 2.01095 +0 1.45761 -0.00918743 4.0163 +5.92748 6.20698 0 4.77659 +4.43366 6.58772 0 3.01881 +3.84205 1.81478 1.87973 0 +7.14272 0 4.64235 3.06411 +0 3.3681 0.257982 4.36141 +1.26825 2.7577 2.23418 0 +8.1874 3.16762 6.67724 0 +4.04444 3.3014 0 6.46977 +0 3.51522 5.11088 7.77951 +2.89143 0 8.03431 6.57384 +4.99163 0 7.47759 5.94742 +6.93763 0 4.43726 0.808401 +2.67316 0 1.3753 1.46273 +>MA1148.1 PPARA::RXRA lnR0: 4.852 +0 1.42196 1.78969 1.40727 +0.0197047 2.02027 2.29626 0 +0.94097 0.64508 0 1.17179 +3.26383 2.13425 0.81627 0 +0 1.81742 -0.113798 3.48473 +4.09716 5.34631 0 4.03636 +3.88993 5.68693 0 4.57911 +3.65909 1.28001 0.647526 0 +2.25926 0 1.1315 1.50377 +0 5.13113 3.15071 4.79284 +0 4.17777 1.14425 2.7173 +0 4.38929 1.94398 4.90924 +3.43697 5.61029 0 6.62782 +5.83601 5.65376 0 2.5847 +5.45387 3.47442 2.27218 0 +3.21195 0 2.0069 2.34462 +0 3.62163 1.0433 3.93215 +0.41896 -0.193989 -0.229557 0 +>MA1149.1 RARA::RXRG lnR0: 4.852 +0.776275 1.84238 0 2.17471 +0 3.1158 -0.412533 6.08954 +6.55231 7.82202 0 5.4167 +6.5704 7.61989 0 2.87897 +7.17384 5.2527 3.10402 0 +5.91908 0 3.78042 3.635 +0 6.59786 2.4168 6.2519 +0.29237 -0.043534 0.581057 0 +1.0859 0.357115 0 1.0859 +0.524284 -0.0023892 -0.356932 0 +0 0.258945 0.0469167 0.591713 +0.707636 1.55516 0 2.20914 +0 1.9025 -0.180139 4.21211 +5.57309 7.46228 0 4.87544 +6.43347 7.01808 0 2.76083 +3.27055 1.86986 0.873346 0 +3.72384 0 2.8026 2.85442 +0 3.1463 1.22668 4.05969 +>MA1150.1 RORB lnR0: 0.764 +0 5.13563 4.14542 2.16238 +0 3.72485 3.8348 0.303945 +0.780134 0.776713 0.47026 0 +3.31042 1.18617 0.68354 0 +0 4.757 0.220899 4.43726 +6.20285 5.07593 0 4.57845 +5.28795 5.99293 0 5.52267 +4.69735 1.85863 3.37093 0 +4.5066 0 5.38783 2.82281 +0 5.23215 3.25172 5.0046 +1.18007 0 1.15193 0.528715 +>MA1151.1 RORC lnR0: 1.348 +0 0.242751 -0.288054 0.259529 +0.334277 1.32027 1.01899 0 +0 5.25751 5.57628 2.79497 +0 5.01034 3.44089 0.286672 +0.815788 0.151657 0 0.671608 +4.05886 2.5487 2.14179 0 +0 4.07616 0.330776 5.64463 +7.7094 8.17966 0 4.10122 +5.16095 7.81903 0 7.18051 +3.42989 2.00559 1.43057 0 +7.33002 0 5.31032 2.91424 +0 5.34006 1.73628 4.15108 +>MA1152.1 SOX15 lnR0: 0.18 +4.55204 0 1.88822 1.55992 +2.96495 -0.241161 3.65543 0 +0 6.71233 6.13309 0.792124 +7.872 7.35205 6.5526 0 +7.88064 7.77166 7.77166 0 +3.89356 5.28757 0 7.66364 +5.22926 7.73825 7.32728 0 +1.47145 0.889712 1.46895 0 +0.946561 0.195102 1.3271 0 +0.746185 0.579364 0.764734 0 +>MA0693.2 VDR lnR0: -0.988 +1.02189 0.171675 2.82048 0 +1.18336 3.59069 0 4.58511 +0 3.91132 -0.00231682 3.9506 +5.67066 5.09468 0 5.27404 +5.57425 4.64332 3.09386 0 +3.70268 4.12759 2.76601 0 +4.21522 0 4.63535 2.58746 +0 4.89735 2.97153 5.4173 +>MA1418.1 IRF3 lnR0: 6.604 +1.28257 0.354057 0 1.43873 +1.87257 0.378384 0 2.1548 +1.31776 4.35445 0 3.307 +0 8.87102 -0.0145892 4.3119 +0 7.17219 1.85018 3.05747 +0 5.8941 6.04093 5.60797 +0.558627 0 1.37517 1.59782 +6.99382 1.85311 0 3.62322 +7.94357 10.7599 0 10.8688 +0 9.6225 7.83284 10.6777 +0 9.61992 7.7317 8.37595 +0 9.10723 8.18052 5.84385 +5.9034 0 3.9568 4.88483 +5.15925 0 2.40705 3.45401 +6.607 11.4894 0 12.0094 +0 6.53976 7.24896 9.39031 +0 7.93878 8.42496 5.26299 +0 7.23854 7.8094 4.57728 +5.43282 0 2.41511 5.57224 +2.15239 0.14914 1.53543 0 +0.874629 2.33217 0 2.64884 +>MA1419.1 IRF4 lnR0: 3.1 +1.36486 0 3.13308 0.956967 +7.40834 0 8.92062 3.42372 +7.46421 9.31011 0 10.8857 +0 7.89927 8.33716 8.5634 +0 11.658 10.1424 6.60528 +0 12.017 12.4977 12.1779 +8.35613 0 6.1927 6.96448 +11.0765 0 13.0176 4.06064 +10.0361 12.5369 0 13.8563 +0 9.29665 11.8262 12.7572 +0 11.247 10.2568 5.44431 +0 10.836 12.4977 11.5467 +6.23473 0 3.38089 9.55898 +4.28907 0.130982 6.18491 0 +0 1.89724 1.61747 1.34257 +>MA1420.1 IRF5 lnR0: 2.516 +2.73749 0 2.85758 2.48366 +4.49693 0 3.27345 2.68884 +4.95987 6.42034 0 4.50494 +0 5.64153 4.4311 4.76029 +0 4.65768 4.91814 2.2992 +0 7.22367 4.66401 6.75341 +6.95616 0 7.42642 5.64718 +7.96207 0 7.44212 2.76552 +2.29023 3.52664 0 5.81339 +0 3.66747 4.2467 6.74708 +0 4.31835 2.4438 2.31307 +0 0.864328 3.54676 3.77008 +3.01466 0 2.69914 3.39424 +2.753 0.434544 2.17225 0 +>MA1421.1 TCF7L1 lnR0: 1.348 +0 1.8457 3.41515 2.11658 +0 3.75967 1.8246 4.27962 +0 6.7303 6.7303 4.69059 +7.44022 1.88261 0 4.66035 +0 3.44089 2.96022 3.04391 +7.25025 3.95043 3.44089 0 +5.21054 0 7.25025 7.7702 +0 5.16085 5.74009 7.25025 +0 6.7303 6.7303 7.25025 +0 6.7303 5.16085 7.25025 +7.7702 3.96084 0 5.21054 +2.47553 3.47659 0 3.99654 +>MA1463.1 ARGFX lnR0: 0.18 +0.727548 1.34938 0.0111632 0 +3.19021 0 3.21394 2.40817 +5.87777 3.31676 6.82554 0 +0 7.86063 13.3608 11.5816 +0 13.3608 13.3608 13.8808 +13.8808 13.3608 13.3608 0 +13.8808 7.92275 13.3608 0 +0 4.48283 2.92007 3.94423 +0 3.6355 0.199385 3.48624 +0 0.241305 1.03484 1.13338 +>MA1464.1 ARNT2 lnR0: 0.18 +1.79889 2.73022 0 4.36706 +2.06484 2.50104 1.55192 0 +6.78503 0 8.36928 15.6801 +0 7.76563 5.67086 6.39813 +15.6801 0 15.1601 8.53158 +9.33343 15.1601 0 15.6801 +5.90292 4.87103 7.89946 0 +11.8114 15.1601 0 5.85243 +0.767006 0 2.47092 2.12772 +1.1709 0 0.0486722 1.10736 +>MA1466.1 ATF6 lnR0: 2.516 +3.01065 1.08749 2.10842 0 +3.45047 2.27961 0 2.55951 +0 1.40769 0.310558 7.14658 +10.079 7.98962 9.55907 0 +8.61855 8.0986 0 8.29977 +0 8.56886 6.0092 8.50957 +10.599 0 10.079 9.60876 +9.02952 10.079 0 10.599 +10.079 7.57865 9.55907 0 +5.94455 10.079 0 6.63813 +7.62834 9.08881 0 3.05153 +5.69327 0 10.079 6.93476 +0 3.78328 1.53511 4.27839 +1.0407 0.198425 0 0.86784 +>MA1467.1 ATOH1(MA1467.1) lnR0: 0.18 +0 2.44339 1.01649 10.3169 +0 1.94256 1.91895 9.88102 +10.8369 0 10.3169 10.8369 +0 9.79696 9.79696 4.11147 +10.8369 10.3169 0 3.40256 +3.23256 0 10.3169 10.8369 +10.3169 9.79696 9.79696 0 +10.8369 10.3169 0 10.8369 +3.29699 1.13355 4.14814 0 +10.3058 0 9.78589 1.6533 +>MA1468.1 ATOH7 lnR0: 0.18 +0 2.31507 1.77524 3.46621 +0 -0.00974121 0.437632 2.69299 +9.90492 0 9.38497 9.90492 +0 8.86502 2.24398 3.55992 +5.42413 2.18955 3.01596 0 +0 1.4386 2.62295 9.38497 +9.38497 4.2106 4.2106 0 +9.90492 9.38497 0 9.90492 +5.54999 0.375618 -0.36508 0 +4.95365 0 6.99336 0.873891 +>MA1101.2 BACH2(MA1101.2) lnR0: 5.436 +0 0.60099 0.433613 0.770033 +0 1.5782 1.4569 0.641047 +0 2.86812 2.25682 1.9257 +1.28943 0.00262327 0 1.18006 +3.20972 0 3.16296 3.4148 +0 7.31758 1.50128 15.7868 +14.9115 12.4111 14.3915 0 +13.6412 15.9011 0 10.6963 +0 5.3829 11.6028 13.113 +9.94658 0 0.279504 11.3571 +13.9152 11.0263 5.72787 0 +9.62973 0 15.9006 14.4402 +0 13.8122 11.8318 15.9016 +10.2735 1.90991 4.40488 0 +3.45205 0 0.205641 3.23233 +0 -0.369201 -0.483504 0.730551 +1.55326 1.48664 2.29139 0 +0.718856 1.32759 1.70445 0 +0.767567 0.214128 0.680917 0 +>MA1470.1 BACH2(MA1470.1) lnR0: 6.02 +0 1.89559 1.27371 1.51464 +0 3.52048 2.36201 1.14621 +0 3.82369 2.61326 2.39329 +0.873527 0.127068 0 0 +4.10654 0 0.768959 8.06738 +0 7.74266 7.74266 6.28219 +5.9323 7.71155 7.71155 0 +2.25602 8.27137 0 8.79132 +0 7.73825 6.74804 8.25821 +8.78256 0 8.26261 8.78256 +8.79568 8.27573 0 8.79568 +8.25821 7.73825 7.73825 0 +8.76487 0 1.44181 8.76487 +0 3.773 7.73384 8.25379 +7.94383 1.48262 7.42388 0 +6.44625 0.902719 0 3.06465 +0 -0.350019 0.106796 0.950708 +1.82629 2.63714 6.30135 0 +1.47725 3.92793 5.23692 0 +1.10598 1.75381 1.29126 0 +>MA1471.1 BARX2 lnR0: 1.348 +0 -0.101713 -0.160506 0.413611 +0 1.68893 1.68144 0.564365 +0 7.44863 7.98762 0.89863 +0 9.22258 7.54946 1.90005 +0 2.53339 2.72873 3.28484 +3.08341 0 3.62068 1.07858 +1.3607 0 2.44247 3.52961 +0 8.53967 0.969217 14.6482 +11.6776 14.1283 8.78875 0 +10.3686 3.23317 14.1283 0 +0 5.86128 5.51301 2.70962 +1.04527 0 0.319277 1.33103 +>MA1472.1 BHLHA15(MA1472.1) lnR0: 0.18 +0 0.774781 0.433887 2.00937 +0 0.0371854 0.0752829 3.41922 +5.44188 0 7.67234 5.9345 +0 4.8946 4.8946 3.41328 +7.4223 5.54652 0 2.18864 +2.25742 0 4.32298 7.4223 +4.72745 7.63306 9.93226 0 +10.9722 10.4522 0 10.9722 +4.16614 0.206523 0.521797 0 +1.49481 -0.0328353 0.338152 0 +>MA1473.1 CDX4 lnR0: 0.764 +2.21394 2.42272 0 1.71406 +3.69362 4.41199 0 8.32567 +14.2263 0 13.7064 1.26975 +0 -0.346623 8.28975 13.4641 +0 13.8502 13.8502 14.3702 +14.3702 13.8502 13.8502 0 +0 13.8502 13.8502 14.3702 +0 13.8502 13.8502 14.3702 +0 8.04959 13.8502 14.3702 +0 1.30932 2.87591 2.25276 +2.57604 0 1.59182 1.58321 +>MA1474.1 CREB3L4(MA1474.1) lnR0: 1.348 +1.24127 -0.30825 0.592141 0 +2.72918 3.93321 0 1.97652 +2.30065 0 4.5067 4.45894 +4.38018 0 5.05613 4.61138 +0 5.6727 3.65768 8.67065 +8.55941 0 7.46022 5.36492 +4.14828 5.82432 0 12.3295 +6.11099 3.13184 5.34833 0 +3.44863 0 2.46934 4.27979 +0 2.36658 1.79475 3.7804 +3.66994 0 1.80634 1.49204 +1.89485 0 1.13064 1.82361 +>MA1475.1 CREB3L4(MA1475.1) lnR0: 1.348 +1.81896 1.33041 0 1.58462 +1.16101 1.81517 0 3.86647 +10.2364 2.66722 4.15673 0 +5.63706 2.26 0 2.81804 +0 4.95618 3.38673 4.96659 +10.7564 0 7.45655 5.35038 +4.46106 8.256 0 10.7564 +6.18897 3.12344 4.55801 0 +3.36187 0 2.48021 4.90731 +0 4.59716 2.52082 4.93132 +3.17219 0 1.39042 0.968937 +1.81795 0 1.12099 1.95837 +>MA1476.1 DLX5 lnR0: -0.988 +1.88533 0.663719 0 2.08034 +6.37937 0 12.7684 1.03607 +0 6.95494 7.47338 13.5236 +0 13.0037 13.0037 13.5236 +13.5236 13.0037 13.0037 0 +13.5236 13.0037 13.0037 0 +0 13.0037 13.0037 13.5236 +1.25045 0 0.296743 0.551782 +>MA1478.1 DMRTA2 lnR0: 1.348 +0 0.722537 0.933142 1.12301 +0 1.64929 0.984663 1.07427 +1.04554 1.43975 1.62581 0 +2.37287 0.61328 1.08073 0 +11.1554 9.64527 0 8.37556 +0.430464 0.369377 5.89966 0 +1.5479 2.97665 5.25667 0 +0 6.82612 4.006 6.86539 +11.1554 0 10.6355 9.17501 +0 5.57545 3.87346 2.6807 +0.867858 1.63333 0.834418 0 +2.23471 1.55629 1.44304 0 +>MA1479.1 DMRTC2 lnR0: 1.348 +0 2.12277 2.41408 1.55858 +0 2.84694 2.03086 1.46469 +2.21048 2.91381 3.99742 0 +4.11609 2.71179 2.14834 0 +10.1958 6.01162 0 10.1958 +0 0.25182 7.24873 1.62002 +3.0828 2.87809 6.18525 0 +0 6.37601 9.15588 7.11617 +10.1958 0 8.10638 10.1958 +0 9.15588 3.85078 3.52716 +1.8286 1.85304 2.87809 0 +1.59911 1.08918 0.973287 0 +>MA1480.1 DPRX lnR0: 0.18 +0 1.19707 1.10121 2.2892 +3.6807 3.05075 0 4.76707 +0 0.540403 5.13209 3.92822 +12.936 12.4161 12.4161 0 +0 1.76398 2.38339 2.96846 +0 12.4161 12.4161 12.936 +12.936 12.4161 4.85419 0 +3.56647 0 5.21148 5.08341 +5.28878 0 3.46927 1.91188 +1.47548 0 0.384455 1.23345 +>MA1481.1 DRGX lnR0: -0.988 +3.29459 0 1.58737 0.807807 +3.00832 0.0391372 2.44666 0 +0 4.32057 2.31897 13.7242 +0 13.2043 13.2043 13.7242 +13.7242 13.2043 13.2043 0 +13.7242 3.63006 5.56556 0 +0 9.07518 3.38993 6.61462 +1.09153 0 0.217148 1.09704 +>MA1484.1 ETS2 lnR0: 0.18 +0.634924 1.00052 0 1.46358 +0 4.57793 1.87216 4.47885 +5.17395 0 3.64287 14.4135 +4.19264 0 13.8936 14.4135 +11.4429 13.8936 0 11.8539 +12.1143 10.9229 0 14.4135 +0 9.60353 10.403 13.8936 +0 5.24331 12.8476 1.21335 +2.66879 13.6106 0 14.1305 +12.8726 -0.510501 3.73734 0 +>MA1485.1 FERD3L lnR0: 2.516 +4.26042 8.65947 0 7.48452 +5.94069 0 5.78702 1.57831 +0 2.01226 -0.342423 7.50922 +0 0.189921 1.74949 3.13815 +10.0697 0 14.7082 15.2281 +0 7.26797 7.36092 7.59857 +15.2281 5.08565 0 3.15155 +3.51031 0 5.9125 15.2281 +8.41288 7.23462 6.54273 0 +15.2281 14.7082 0 15.2281 +4.01347 1.89731 2.08728 0 +7.09438 0.25635 0.800331 0 +0 4.62105 1.05714 4.89977 +15.2281 0 14.7082 9.6684 +>MA1489.1 FOXN3 lnR0: -0.988 +7.05819 6.53824 0 7.05819 +6.53824 6.01829 6.01829 0 +0 6.01829 6.01829 6.53824 +0 6.01829 6.01829 6.53824 +0 6.01829 6.01829 6.53824 +7.05819 0 6.53824 7.05819 +0 6.01829 6.01829 6.53824 +0 6.01829 6.01829 6.53824 +>MA1493.1 HES6 lnR0: 0.18 +5.55113 3.42556 0 3.80936 +5.1679 3.57608 0 5.44526 +5.08624 0 4.41577 5.2545 +0 8.17544 4.88603 5.14553 +7.6459 0 5.40599 5.1679 +5.78978 5.03118 0 9.21534 +8.69539 5.20481 3.31659 0 +9.21534 8.69539 0 9.21534 +3.65773 3.75967 8.17544 0 +1.37869 -0.0675654 7.11877 0 +>MA1494.1 HNF4A(MA1494.1) lnR0: 3.1 +1.12796 2.17745 0 3.38096 +0.734749 5.40192 0 5.92187 +7.79674 7.68776 0 6.80653 +7.68776 7.74705 4.60815 0 +3.18413 0 3.91768 3.12864 +6.80653 0 6.95801 5.81632 +0 8.73726 5.76663 9.25721 +0 7.74705 7.16781 7.27679 +0 8.73726 6.1776 9.25721 +9.77716 9.25721 0 8.78695 +7.79674 9.25721 0 3.81375 +9.25721 6.43806 4.13886 0 +8.20771 0 6.28658 4.65784 +0 5.6978 0.784445 5.488 +0.833821 0 1.08503 0.961838 +>MA1495.1 HOXA1 lnR0: -0.988 +1.7 0.246605 0 1.51553 +12.7288 1.71735 12.2089 0 +0 1.29167 2.02761 12.7288 +0 12.2089 12.2089 12.7288 +12.7288 12.2089 12.2089 0 +12.7288 1.95381 1.17206 0 +0 12.2089 1.68991 12.7288 +1.76535 0 0.326162 1.75687 +>MA1496.1 HOXA4 lnR0: -0.988 +0.842392 1.7617 0 4.32819 +11.1513 0.809549 10.6313 0 +1.31712 0 3.11082 11.0253 +0 10.6313 1.30357 11.1513 +11.1513 10.6313 5.36148 0 +11.1513 3.26123 3.27775 0 +0 3.50212 2.68199 11.1513 +0.916839 0.496732 0 1.63246 +>MA1497.1 HOXA6 lnR0: 0.18 +1.60596 0.766335 0 1.27914 +2.9245 2.04079 0 2.66368 +5.534 -0.0121005 4.81722 0 +0 0.40512 2.55988 2.25756 +0 2.71918 2.43686 9.13887 +12.6887 12.1688 12.1688 0 +1.89458 4.37547 3.14426 0 +0 5.66325 3.28223 3.40547 +0 0.441462 0.198911 0.846907 +1.5032 0 0.279651 1.23505 +>MA1499.1 HOXB4 lnR0: -0.988 +0 1.22793 -0.429947 2.17484 +13.0199 1.56911 12.5 0 +1.10627 0 12.2931 12.8131 +0 12.5 4.52354 13.0199 +13.0199 12.5 12.5 0 +13.0199 12.5 4.49167 0 +0 12.5 6.74946 13.0199 +0.609954 1.71509 0 2.25648 +>MA1500.1 HOXB6 lnR0: -0.988 +1.44151 0.0675547 0.11043 0 +12.4731 2.5722 11.9532 0 +0 2.70474 11.9532 3.4205 +0 11.9532 11.9532 12.4731 +12.4731 3.26754 2.53844 0 +3.89966 2.19322 0.0553692 0 +0 10.9779 -0.490428 11.4978 +3.30718 0 2.26556 2.3792 +>MA1501.1 HOXB7 lnR0: 0.18 +1.52145 1.38009 0 2.20656 +10.1203 9.60031 0 3.72407 +9.60031 0.671644 3.43573 0 +0 1.35583 9.08036 9.60031 +0 4.22151 9.08036 9.60031 +9.60031 9.08036 4.12931 0 +3.34028 7.09994 9.08036 0 +0 9.08036 1.90339 9.60031 +0 0.439817 -0.249788 2.15308 +1.92248 0 0.495236 2.43355 +>MA1502.1 HOXB8 lnR0: -0.988 +2.90656 2.34887 0 2.62262 +11.7316 0 11.2116 0.935208 +0 -0.116935 5.0607 12.0089 +0 11.489 11.489 12.0089 +12.0089 11.489 11.489 0 +3.93396 11.489 2.49312 0 +0 11.489 11.489 12.0089 +1.0518 0 1.0267 1.66114 +>MA1503.1 HOXB9 lnR0: 0.18 +2.06938 2.68685 0 9.69215 +10.7416 4.81571 10.2217 0 +11.2616 0 10.7416 11.2616 +2.01981 7.96177 0 11.2616 +10.7416 10.2217 9.23148 0 +0 6.55748 8.24127 1.97346 +0 10.2217 10.2217 10.7416 +0 4.84855 10.2217 6.61254 +0 2.09261 2.63845 1.90127 +0.750785 0.0971644 0.898173 0 +>MA1504.1 HOXC4 lnR0: -0.988 +0.560166 0.583309 0 1.56298 +5.48029 0.958521 12.4486 0 +1.02913 0 12.2105 12.7304 +0 12.4486 3.34869 12.9685 +12.9685 12.4486 12.4486 0 +12.9685 12.4486 12.4486 0 +0 12.4486 2.85342 12.9685 +0 0.198017 -0.487168 0.793932 +>MA1505.1 HOXC8 lnR0: -0.988 +1.58536 1.24983 0 1.25226 +13.05 0.495435 12.53 0 +0 1.22812 8.25039 3.20478 +0 8.18069 12.53 13.05 +13.05 12.53 4.87774 0 +3.23708 5.95119 1.26579 0 +0 12.53 0.569437 13.05 +1.27792 0 1.37619 1.69859 +>MA1506.1 HOXD10 lnR0: 0.764 +1.44219 2.16093 0 2.88054 +2.5742 3.45759 0 12.5825 +12.0625 6.23746 9.97312 0 +7.58746 0 12.0625 12.5825 +2.3683 11.0723 0 12.5825 +12.0625 11.5426 4.36559 0 +0 11.5426 7.33623 3.6108 +0 11.5426 11.5426 12.0625 +0 6.38411 11.5426 9.09189 +0 2.7713 3.58235 2.64584 +0.658374 0 1.56846 0.57413 +>MA1507.1 HOXD4 lnR0: -0.988 +0 0.222291 -0.482146 1.7044 +11.619 0.988329 11.099 0 +0.789178 0 10.7571 11.277 +0 11.099 3.70454 11.619 +11.619 11.099 11.099 0 +11.619 11.099 11.099 0 +0 11.099 3.56618 11.619 +0.577076 1.11496 0 1.37265 +>MA1508.1 IKZF1 lnR0: 1.348 +0.750776 0.905036 0 1.69997 +0 0.340567 0.0204205 1.39982 +0 2.26168 2.46109 3.64795 +0 3.70718 2.70347 4.64818 +4.17057 0 2.74219 5.3461 +0 5.00628 4.76043 5.2359 +6.8478 6.56135 0 6.92945 +5.07838 5.77341 0 6.66497 +0 4.8069 4.54453 7.55855 +0 5.89518 4.71887 5.09377 +1.09007 1.53843 0 2.76083 +0.60346 -0.341539 0.0230854 0 +>MA1509.1 IRF6 lnR0: -0.404 +0 3.44791 1.4915 4.83377 +5.75415 0 5.3433 2.73701 +11.782 0 6.78279 7.5024 +6.22227 8.70241 0 8.49261 +0 10.7421 10.7421 6.55373 +0 10.5474 7.25802 2.74452 +0 10.7421 6.61301 9.69262 +11.782 0 7.59785 11.782 +4.48429 2.0848 7.55816 0 +>MA1512.1 KLF11 lnR0: 0.764 +1.57142 0.926597 0 2.10071 +1.96169 0 3.75014 2.71613 +4.21753 0 5.72939 4.57467 +0 2.19949 5.64065 8.19115 +13.5496 0 13.0296 8.31593 +2.27514 7.21822 0 5.04154 +10.0027 0 8.82626 9.01247 +12.5631 0 8.68406 10.5827 +13.5178 0 10.6987 3.82252 +0 -0.371465 5.48675 2.59606 +4.33423 0 4.50449 3.20607 +>MA1513.1 KLF15 lnR0: 0.764 +2.72291 0.922464 0 2.17004 +3.28693 0 1.60344 2.34788 +8.53883 0 6.94412 10.5545 +7.31563 0 4.98447 11.8256 +13.8609 0 12.3507 13.8609 +13.861 13.341 0 13.861 +10.3081 0 11.7686 10.3081 +8.05738 0 4.87921 12.8177 +10.1823 0 6.7335 11.8661 +2.50037 0 1.67907 2.46792 +2.72916 0 0.675428 1.71902 +>MA1514.1 KLF17 lnR0: 3.1 +1.19288 0 2.09324 2.50505 +0 0.440586 2.6288 3.12851 +7.53756 0 7.86117 8.47719 +8.14699 0 8.07461 8.86042 +0 6.60023 7.80825 3.49993 +8.88881 0 9.03366 6.60968 +2.25667 1.79268 0 4.77221 +3.16908 0 8.0377 6.74294 +0 3.59113 1.34821 1.18115 +5.62694 0 4.3455 7.51387 +8.27035 0 7.15338 9.45593 +7.53841 0 8.45878 7.4632 +0.790621 0 1.92764 2.65812 +2.57371 1.73271 2.76335 0 +1.98808 0.370426 2.1088 0 +>MA1515.1 KLF2 lnR0: 0.764 +0.900474 0 0.0593117 1.17099 +0 0.653965 -0.273419 2.5077 +3.13345 0 3.18889 4.2192 +4.00193 0 4.58242 4.36652 +0 0.49866 1.58267 4.38309 +12.5754 0 12.0554 6.33331 +1.29071 3.37559 0 4.59955 +12.5754 0 6.46682 8.0961 +5.63279 0 4.51526 9.28597 +6.52665 0 5.39337 3.86384 +0 0.159429 1.69552 0.546976 +>MA1516.1 KLF3 lnR0: 0.764 +2.28594 3.28989 0 2.57142 +0 4.75751 -0.102116 6.82847 +5.37781 0 4.42405 6.39905 +7.62644 0 7.3679 7.45977 +0 4.66883 0.170379 5.93476 +4.73563 0 10.8342 5.41086 +3.83602 6.94408 0 5.62585 +8.17963 0 10.2989 15.7699 +9.44019 0 10.3911 15.7699 +9.54606 0 9.69023 5.6188 +0 0.226394 2.93657 0.218175 +>MA1517.1 KLF6 lnR0: 0.764 +1.01298 0.00456413 0 0.843291 +0.678989 1.22572 0 3.56919 +2.44479 0 2.69269 3.80481 +2.8375 0 2.84655 4.44033 +0 2.3951 4.59741 5.11736 +11.51 0 10.99 6.91159 +1.60649 10.99 0 11.51 +11.51 0 10.99 11.51 +6.85556 0 5.11736 11.51 +5.40046 0 7.32582 5.54658 +0 -0.00356734 3.61214 0.867154 +>MA1518.1 LHX1 lnR0: -0.988 +1.47379 0.342509 0 1.35442 +3.76832 0 3.97062 1.20241 +0 1.0802 1.35118 2.81468 +0 5.2096 7.94279 4.66738 +13.7326 13.2126 13.2126 0 +3.7256 0.93156 1.72765 0 +0 4.34609 4.03192 2.80036 +1.24913 0 0.362468 1.26672 +>MA1519.1 LHX5 lnR0: -0.988 +3.72442 0.120469 0 2.11809 +12.1816 0.737638 11.6617 0 +0 4.6764 12.157 12.677 +0 12.157 12.157 12.677 +12.677 12.157 12.157 0 +12.677 5.04741 7.34661 0 +0 12.157 4.89788 12.677 +0 0.274445 0.361278 1.03346 +>MA1520.1 MAF lnR0: 3.1 +0 0.377509 0.193675 0.0694791 +3.45202 1.67197 4.95312 0 +5.65049 5.93883 0 8.78938 +3.44989 0 5.65982 4.17313 +2.674 2.99635 4.04634 0 +3.60111 3.84281 0 2.50455 +0 2.43029 3.97096 2.62153 +2.38541 0.162537 0 2.55321 +2.33434 4.34734 2.19866 0 +2.68519 0 4.10412 3.68952 +0 4.2369 2.65379 2.98298 +4.18467 5.70565 0 3.58582 +6.38111 0 5.64512 5.93415 +0 4.44207 1.52375 3.44573 +0 0.236338 0.476115 0.0325025 +>MA1521.1 MAFA lnR0: 3.1 +0.121577 0.136332 -0.320262 0 +3.18797 1.21941 3.74563 0 +5.24707 5.28083 0 6.57967 +3.52187 0 5.36275 4.35745 +3.03287 2.49398 3.60968 0 +4.07 4.03628 0 3.12976 +0 1.67264 3.99501 2.58019 +3.2319 0.0139096 0 3.1072 +2.5283 4.39603 1.5379 0 +3.22168 0 4.19725 3.96533 +0 3.60162 2.64001 2.82649 +4.54956 6.18282 0 3.5207 +8.7154 0 5.18567 5.48541 +0 4.20833 1.11187 2.90441 +0 -0.308686 0.159151 0.0743132 +>MA1522.1 MAZ lnR0: 0.764 +1.57681 0 0.278544 1.25447 +2.00977 0.0265256 0 1.28916 +10.1226 0 7.54495 9.54332 +8.63263 0 5.19665 14.2212 +9.07261 0 5.60636 11.4512 +8.95589 0 5.34548 13.2355 +10.9501 13.21 6.24547 0 +7.80911 0 10.5943 11.954 +9.71149 0 7.19632 14.2516 +3.56777 0 2.38203 2.23834 +2.25106 0 1.40175 1.37125 +>MA1523.1 MSANTD3 lnR0: 0.18 +2.8785 0.925264 0 2.6277 +2.00884 0.577331 0.517936 0 +0 -0.236135 -0.110405 1.17791 +3.96338 0 4.45579 2.50037 +0 9.32087 7.75142 5.79337 +5.28184 0 4.95264 4.7634 +4.60589 6.31186 9.28249 0 +4.6474 0 4.79888 4.30501 +0 1.91632 4.38759 3.65687 +1.57435 0 3.12142 3.04734 +>MA1524.1 MSGN1 lnR0: 1.348 +1.31717 0 0.361278 0.998156 +0.601093 2.48164 0 3.4932 +3.75095 0 1.96216 3.62146 +13.0342 0 8.38516 13.0342 +0 11.9943 3.52727 12.5143 +0.697339 2.10745 4.55767 0 +0 3.73971 1.66697 0.525279 +9.0887 3.90437 7.86521 0 +13.0342 9.0887 0 13.0342 +2.95585 0.994222 -0.445984 0 +3.16049 0 1.10952 0.593917 +1.02423 0 0.148349 1.19906 +>MA1527.1 NFIC(MA1527.1) lnR0: 4.268 +1.44422 0.437465 0 1.44064 +3.62105 1.24266 4.43583 0 +10.941 10.421 7.86139 0 +11.4609 10.941 0 11.4609 +11.4609 8.96058 0 11.4609 +4.86792 0 10.941 11.4609 +0 0.840155 -0.515845 0.587458 +1.36776 0 0.513009 0.924196 +1.1268 0.222672 0 1.21301 +1.39806 1.19165 0 1.72284 +3.34369 2.08979 3.8711 0 +11.4609 10.941 0 11.4609 +11.4609 0 7.17092 11.4609 +9.48053 0 10.941 11.4609 +0 10.421 10.421 10.941 +0 5.18783 -0.447159 2.7825 +1.44203 0 0.102084 1.26552 +>MA1528.1 NFIX(MA1528.1) lnR0: 4.268 +1.57058 0.624917 0 1.54566 +1.91782 1.60736 1.80895 0 +7.01306 5.64353 2.31345 0 +14.4645 13.9445 0 14.4645 +14.4645 13.9445 0 14.4645 +3.74078 0 13.9445 7.07808 +0 1.37104 -0.0437727 1.11165 +1.43245 0 0.616017 0.926027 +1.47903 0.325827 0 1.27747 +1.72207 1.63439 0 1.7096 +3.2574 2.36587 3.05141 0 +14.4645 13.9445 0 5.70559 +14.4645 0 13.9445 14.4645 +14.4645 0 13.9445 14.4645 +0 2.67213 7.48332 5.72657 +0.632991 2.03747 0 1.94601 +1.5159 0.112834 0 1.24995 +>MA1529.1 NHLH2 lnR0: 4.852 +1.51944 1.85529 0 1.73975 +2.19215 2.62096 0 1.92525 +2.79923 4.07315 0 3.23201 +0.836287 0 0.320115 0.705205 +1.96889 0 4.47891 7.12226 +3.48298 2.99583 0 3.33698 +13.1923 0 12.6724 12.2021 +0 13.7222 9.01387 13.2519 +11.8948 3.00058 0 4.72999 +5.73645 0 3.12948 14.6869 +14.2418 9.85316 11.7414 0 +14.762 12.6726 0 14.762 +5.36446 0 6.16175 4.54573 +7.09048 6.61174 0 5.29599 +3.47606 0.376899 2.5995 0 +2.78204 0 3.91549 3.34844 +1.58387 0 3.06074 2.5152 +2.14971 0 2.2925 1.92046 +>MA1530.1 NKX6-3 lnR0: -0.404 +1.47402 0 0.00418936 6.1793 +12.629 0.072271 12.109 0 +5.92129 0 3.62499 3.91558 +0 12.109 12.109 12.629 +12.629 12.109 12.109 0 +12.629 3.32551 12.109 0 +0 12.109 2.74627 12.629 +0 2.57756 3.62308 0.871019 +0 0.622805 1.24649 0.920309 +>MA1531.1 NR1D1 lnR0: 3.1 +0.575827 3.19609 0 6.71481 +9.03567 10.9937 0 3.67628 +7.43849 12.5632 0 9.41891 +12.5632 4.42505 1.46134 0 +13.0831 0 10.9937 1.14989 +0 10.4738 10.4738 9.59254 +3.31506 1.81636 0 4.35638 +8.21385 5.22796 4.37754 0 +0 4.69388 -0.277667 8.1391 +13.0831 12.5632 0 3.06067 +9.94423 12.5632 0 10.3032 +4.89749 3.38067 2.68249 0 +12.0929 0 6.13487 4.7352 +0 9.74402 2.29722 8.21385 +0.630684 0.237286 0 0.713192 +>MA1533.1 NR1I2 lnR0: 4.268 +0 1.09876 -0.445399 0.787396 +4.33565 0.242217 2.82549 0 +4.52475 7.29421 0 6.24471 +0 1.46915 2.17586 3.52413 +0 0.878351 6.77426 7.29421 +5.83374 0 6.304 7.81416 +3.80784 0.64163 4.2781 0 +3.61041 0 0.735235 2.69348 +0.651104 0.870092 0 1.53545 +0 0.946676 0.18165 0.84825 +6.81526 0.795102 6.29531 0 +3.39838 5.72476 0 4.52475 +0 1.43473 3.11004 4.73455 +0 1.12962 5.20481 7.29421 +7.81416 0 7.29421 5.83374 +5.72476 0.47026 3.63537 0 +3.29982 0 1.29208 1.65314 +>MA1534.1 NR1I3 lnR0: -0.404 +0 1.8281 0.325254 1.68988 +8.13432 1.57558 14.8912 0 +3.36118 8.81807 0 15.9311 +0 3.65024 6.55154 5.87601 +0 3.4664 14.8912 15.4111 +15.9311 0 15.4111 15.9311 +15.4111 4.12797 14.8912 0 +1.27075 0.620941 2.83957 0 +1.73952 1.65302 2.51032 0 +>MA1535.1 NR2C1 lnR0: -0.404 +0.676663 0 0.506888 0.872467 +0.984761 2.16695 0 2.58461 +0 3.85275 -0.487293 6.3784 +13.6227 13.1027 0 5.48398 +13.6227 13.1027 0 13.6227 +13.1027 12.5828 4.57449 0 +13.6227 0 4.85337 13.6227 +0 12.5828 1.9423 13.1027 +0.794938 0 0.445737 0.675201 +>MA1536.1 NR2C2(MA1536.1) lnR0: -0.988 +0.561486 1.03473 0 1.67431 +0 3.27165 -0.23729 13.1905 +14.5663 6.23488 0 4.27789 +14.5663 14.0464 0 2.45992 +14.0464 13.5264 2.99664 0 +14.5663 0 3.46798 2.57927 +0 13.5264 0.953775 14.0464 +0.0159838 -0.414361 -0.0492796 0 +>MA1537.1 NR2F1(MA1537.1) lnR0: 3.1 +0.659041 1.53087 0 2.32391 +0 4.97496 0.0747625 6.12574 +7.19252 8.02952 0 5.93289 +6.63745 9.53093 0 5.97633 +11.7652 5.60671 4.09673 0 +11.9985 0 5.66895 4.40369 +0 11.6042 5.22908 10.6245 +0 6.62166 2.78371 3.61058 +0 8.82438 3.18255 9.56454 +11.6539 14.9041 0 9.57496 +7.57679 14.9041 0 6.56037 +10.4883 4.92307 3.63321 0 +10.2275 0 4.41531 3.52313 +0 6.33442 1.90067 5.50316 +0.575269 0 0.366555 0.756792 +>MA1538.1 NR2F1(MA1538.1) lnR0: 3.1 +0 2.0106 -0.146527 2.37648 +0 4.45151 0.700353 4.89819 +6.74626 4.80151 0 3.78758 +5.99759 6.19491 0 6.15648 +7.18512 4.74825 3.35725 0 +7.83503 0 5.83935 4.83079 +0 4.81727 0.715327 8.86308 +0.281077 -0.310745 -0.315743 0 +11.6644 4.71615 5.4726 0 +5.88904 7.70356 0 8.52014 +0 4.62395 11.1444 11.6644 +12.1843 0 10.6742 6.71486 +5.20892 0 5.47764 6.56746 +5.41436 0.900094 5.70003 0 +2.53792 0.106206 2.5972 0 +>MA1539.1 NR2F6(MA1539.1) lnR0: 3.1 +0 2.57421 0.237438 2.73209 +0 7.77246 1.1468 8.65143 +8.95691 12.3978 0 7.01037 +8.6743 9.7238 0 6.78852 +8.67967 6.62599 4.95758 0 +11.6088 0 5.70244 5.19964 +0 7.23547 1.25296 7.52504 +0.935216 0 0.163716 0.693309 +7.38131 4.56643 6.84019 0 +5.39224 5.76984 0 10.6186 +0 4.94638 6.1793 11.4076 +6.65771 0 13.388 8.74951 +7.59533 0 10.0986 9.30957 +8.45204 1.11028 7.76383 0 +2.77987 0.240063 2.59804 0 +>MA1540.1 NR5A1 lnR0: 0.764 +1.23737 0.351802 0 0.731934 +1.40727 -0.00257971 0.893639 0 +6.06383 0 2.49756 5.39239 +0 11.3706 3.28063 9.59133 +0 4.42798 4.33164 4.79079 +12.4105 11.8905 0 6.0306 +12.4105 11.8905 0 12.4105 +2.09257 0.496511 2.87711 0 +6.32093 0 4.19185 3.15327 +0 3.52334 0.756971 3.80058 +1.15306 0 0.682699 0.750091 +>MA1541.1 NR6A1 lnR0: 4.268 +1.37981 0.658751 0 1.0478 +1.79125 0.391262 0.828598 0 +3.3353 0 1.37332 3.24667 +0 6.89379 3.7549 6.16307 +0 2.73329 3.06376 4.0683 +6.46281 6.42353 0 4.31412 +4.46052 4.55597 -0.488132 0 +8.72273 3.02515 4.48465 0 +7.26226 0 4.85408 4.92778 +0 9.19299 7.62354 5.84429 +0 2.65769 4.07367 3.72772 +5.81711 5.7521 0 4.31412 +4.60881 5.39785 0 1.00444 +3.25324 1.72763 0.800228 0 +4.96306 0 2.99796 2.3168 +0 4.84367 0.784266 4.37341 +0 0.142426 -0.0800808 0.290042 +>MA1542.1 OSR1 lnR0: 0.18 +0.833357 -0.0238536 0.827511 0 +3.93156 4.33046 0 8.52678 +12.6559 0 12.1359 8.44954 +9.83673 5.03717 11.616 0 +0 5.28624 6.38232 3.4244 +9.23032 0 12.1359 12.6559 +11.333 -0.11783 8.25336 0 +6.73712 9.83673 0 8.05749 +3.54841 2.44689 2.72375 0 +0.644633 1.12921 -0.326833 0 +>MA1544.1 OVOL1 lnR0: 2.516 +0 0.758343 0.50789 0.912328 +0 3.6779 0.282156 1.00629 +0 2.78591 0.735708 0.201573 +0 4.69451 13.2176 2.80872 +14.2575 0 13.7375 14.2575 +14.2575 0 13.7375 14.2575 +13.2673 13.7375 0 11.9583 +13.7375 13.2176 10.9184 0 +13.7375 13.2176 13.2176 0 +0 9.92817 13.2176 13.7375 +3.93958 0.846037 2.05993 0 +0.432311 -0.225499 -0.112955 0 +2.35917 -0.170982 3.44906 0 +1.2496 0.304701 0 1.08722 +>MA1545.1 OVOL2 lnR0: 1.932 +0.696938 2.1189 0 1.17648 +0.400774 1.40476 0.113181 0 +0 1.92662 3.73829 1.2876 +12.015 0 8.8771 13.9954 +13.9954 0 8.13596 13.9954 +13.9954 13.4755 0 13.9954 +13.4755 2.60359 12.9555 0 +13.4755 12.9555 9.66613 0 +0 9.18546 5.77857 13.4755 +1.86218 -0.243761 0.460076 0 +0.585366 0.377164 0 0.584046 +1.23946 -0.345694 1.34677 0 +1.04917 0.297451 0 0.981864 +>MA1546.1 PAX3(MA1546.1) lnR0: 3.684 +1.84565 0 1.23744 0.841498 +3.45376 0 0.912886 2.88723 +9.82138 8.7222 0 3.89133 +2.85735 3.51165 6.99182 0 +7.52219 0 5.75156 2.84595 +0 8.20225 5.49207 8.7222 +7.04151 0 8.7222 3.22835 +3.5436 9.30143 0 10.8116 +8.15356 0 0.710537 7.35411 +1.60037 0.0232641 1.70362 0 +0 0.632269 1.34548 0.131154 +0 2.58535 1.38698 3.91177 +4.67475 4.36571 5.1733 0 +3.9619 2.72244 4.09985 0 +0 3.76499 3.06977 2.61267 +0 -0.264597 -0.417731 0.544941 +>MA1548.1 PLAGL2 lnR0: 0.18 +0.538447 0.0184969 0.0184969 0 +4.82435 4.3044 0 3.40542 +10.3882 9.86822 0 10.3882 +10.1543 2.4574 0 10.1543 +10.0694 0 1.9733 10.0694 +10.3882 0 9.86822 10.3882 +10.3882 0 9.86822 10.3882 +10.2783 0 9.75839 4.1105 +3.40361 0 4.67332 2.28583 +0.80235 0.282399 0.282399 0 +>MA1549.1 POU6F1(MA1549.1) lnR0: 0.18 +0 2.17835 -0.0112289 1.05976 +5.22899 3.98449 8.57768 0 +0 4.58474 4.08157 12.5232 +0 12.0032 12.0032 12.5232 +12.5232 12.0032 3.85976 0 +6.87153 4.76128 0 3.72333 +0 5.46795 12.0032 3.92174 +4.82519 2.88379 0 2.29146 +1.27582 0.126126 0 1.70305 +0.384246 0.2098 -0.0962365 0 +>MA1550.1 PPARD lnR0: 3.684 +0 0.204253 0.482219 0.616183 +1.2818 2.51336 0 3.45303 +0.624383 6.42181 0 9.35844 +7.45273 9.19057 0 7.66364 +7.02667 10.0014 0 3.00999 +9.11204 8.19744 4.3926 0 +8.39799 0 3.61063 3.11681 +0 13.0241 5.84711 13.544 +0 7.88058 3.29531 4.9168 +0 10.0078 2.99765 13.4984 +8.94794 9.88309 0 8.59777 +9.10864 12.4573 0 3.23362 +13.5238 7.73406 4.41987 0 +7.13776 0 4.14271 3.38805 +0 7.66393 2.35709 7.80908 +0 -0.509783 0.379751 0.0922229 +>MA1552.1 RARB(MA1552.1) lnR0: 2.516 +0 2.26649 -0.16467 1.91635 +0 2.4272 1.15597 8.41663 +7.33824 4.66961 0 4.36761 +5.89309 6.49951 0 3.11322 +4.38293 2.31535 2.60691 0 +6.759 0 5.82808 5.27121 +0 7.73384 0.566296 6.27337 +6.81829 5.7191 8.27876 0 +5.27121 5.65982 0 7.01946 +0 3.57042 4.07242 5.02863 +3.11322 0 8.79871 6.34803 +5.65444 0 5.65982 5.27121 +5.03 1.32851 2.46612 0 +1.80867 0.287389 1.47948 0 +>MA1553.1 RARG(MA1553.1) lnR0: 2.516 +0 1.96398 0.259981 1.79814 +0 2.50229 1.47816 4.61766 +5.41366 6.43787 0 4.93117 +6.88455 6.824 0 2.13707 +3.28651 2.99508 2.85627 0 +7.34395 0 5.80937 4.98683 +0 7.42827 1.10535 6.75835 +6.59677 5.49758 7.34439 0 +5.69468 6.13422 0 8.49016 +0 3.56704 4.17189 4.05828 +2.28902 0 9.07477 8.49016 +5.47891 0 7.42808 6.59463 +5.59224 1.46306 2.7679 0 +2.00113 0.270278 2.07215 0 +>MA1554.1 RFX7 lnR0: -0.404 +7.81416 0 1.35295 1.9891 +8.56965 6.48025 0 8.56965 +8.0497 2.93135 7.52975 0 +8.0497 2.76946 7.52975 0 +2.04915 8.0497 0 3.33599 +7.0002 0 2.93039 4.29003 +7.29421 -0.0165858 3.00418 0 +0 3.05047 0.881234 3.28941 +1.51842 -0.480448 1.43473 0 +>MA1555.1 RXRB(MA1555.1) lnR0: 2.516 +0.985614 2.13616 0 3.01087 +0 3.4032 -0.418658 5.81137 +5.38198 5.85223 0 4.59619 +6.47075 5.44126 0 3.22801 +5.59178 3.82778 2.95886 0 +6.69096 0 5.37156 4.34492 +0 5.65738 0.486913 7.16754 +7.16122 4.34207 10.1911 0 +4.7559 5.59178 0 8.09215 +0 4.49259 4.85161 6.84244 +3.03594 0 7.16122 6.69096 +5.40599 0 5.71608 5.40599 +5.57044 -0.407506 5.38819 0 +3.28999 0 2.13478 1.00689 +>MA1556.1 RXRG(MA1556.1) lnR0: 2.516 +0.930925 2.67334 0 4.22746 +0 6.71346 0.0413298 10.204 +11.4603 4.25157 0 11.4603 +8.48964 5.98927 0 4.88146 +7.27611 7.86072 5.38272 0 +11.4603 0 9.95011 7.41283 +0 6.45953 10.4204 10.9403 +10.2209 0.0834847 9.70093 0 +5.49687 5.18982 0 6.75194 +0 2.74803 4.17831 4.10105 +4.35066 0 4.99906 5.49687 +4.35066 0 3.54583 6.26372 +5.63083 -0.0395071 3.85032 0 +3.3658 0 2.114 0.903957 +>MA1557.1 SMAD5 lnR0: 0.18 +1.70498 -0.44221 2.35566 0 +7.58671 8.09838 0 10.1061 +3.92334 4.92395 2.90474 0 +7.32625 0 6.876 10.1061 +11.1556 3.87595 2.52113 0 +0 2.62738 4.61834 9.00694 +8.25 7.10817 0 9.88591 +0 2.79728 7.27656 4.08596 +8.1865 0 9.58617 8.06738 +0 2.10347 2.79728 1.78778 +>MA1558.1 SNAI1 lnR0: 0.18 +0.798574 0.998031 0 0.843135 +1.40442 4.64762 0 2.38567 +5.94863 0 6.11748 6.33531 +0 5.48797 7.16698 5.08394 +3.98509 5.21809 0 6.48536 +8.53735 11.587 0 9.85615 +8.91297 13.6267 8.25353 0 +5.29367 14.1466 0 6.46228 +3.23086 0 1.0333 0.791554 +0 0.60421 -0.492213 0.659842 +>MA1559.1 SNAI3 lnR0: 0.18 +0 1.61621 0.423152 1.39652 +0 11.2991 0.221271 4.36914 +8.46584 0 12.486 7.8866 +0 11.966 6.88695 10.5055 +6.1786 7.62711 0 7.59993 +13.0059 8.27963 0 13.0059 +12.486 8.3018 7.15559 0 +6.50038 12.486 0 8.10022 +4.33343 0 1.85802 1.49312 +0 2.21723 1.04067 3.04872 +>MA1560.1 SOHLH2 lnR0: 0.18 +1.58251 0 1.37979 1.14397 +3.30218 2.17303 0 2.62971 +5.19454 0 5.28522 4.57448 +0 9.62412 4.2846 10.1441 +10.664 0 6.59421 7.69339 +6.79538 10.1441 0 6.70318 +4.98562 3.6389 9.62412 0 +5.3245 7.84488 0 8.36483 +2.65049 0 2.78223 3.46838 +0 0.144023 -0.474354 0.756172 +>MA1561.1 SOX12 lnR0: 0.764 +0 1.13736 2.40951 2.59518 +2.96873 0 3.81938 3.92231 +4.60464 0 4.56536 4.38859 +4.63409 4.93609 0 4.60464 +0 4.41614 7.55503 8.65422 +0 7.55503 6.82528 9.64443 +10.1644 0 9.64443 8.18396 +0 9.12448 9.12448 9.64443 +0 2.66478 3.68639 5.29511 +2.69081 1.47221 3.32385 0 +1.13464 0.531039 0 1.61675 +>MA1562.1 SOX14 lnR0: 0.18 +1.67004 0 1.45418 2.20434 +3.59774 0 3.68843 3.06765 +4.20838 4.92017 0 3.55692 +0 5.46767 3.84627 3.92996 +0 4.83648 8.60657 4.8469 +7.34727 0 5.70095 5.51736 +0 8.60657 8.60657 9.12652 +0 4.47746 8.60657 6.56686 +9.12652 7.03712 4.55912 0 +2.79259 2.43153 0 2.70156 +>MA1564.1 SP9 lnR0: 1.348 +0.708784 1.10081 0 2.56947 +2.61181 0 2.95441 2.73817 +3.4201 0 4.38352 3.59448 +0 0.589275 4.85378 4.61421 +10.1 0 7.02041 8.38006 +4.0172 3.57336 0 4.29938 +7.19019 0 11.1495 7.80082 +11.6695 0 11.1495 6.76377 +6.39964 0 6.55112 3.06454 +0.598009 0 4.96472 2.33362 +3.78957 0 3.24712 2.16574 +1.97769 0 2.48577 1.33323 +>MA1565.1 TBX18 lnR0: 1.348 +1.06139 1.84713 0 1.4878 +0.858523 2.0475 0 2.0538 +0 3.07273 1.74125 3.66238 +3.88273 3.71081 0 4.50111 +6.16275 9.51144 0 10.0314 +6.54081 2.71371 8.99149 0 +5.61562 6.73157 0 8.46195 +2.91842 2.42704 2.27652 0 +4.35955 2.24345 0 5.03638 +0 8.00128 6.43184 4.43238 +0 3.07273 1.01507 2.99095 +0 0.617666 -0.213955 1.73247 +>MA1567.1 TBX6 lnR0: 0.18 +0.932829 1.283 0 1.2176 +0 2.68783 1.19076 2.33812 +3.0528 1.90905 0 3.87501 +8.00007 7.36391 0 13.8251 +7.86708 2.91272 12.7852 0 +9.95648 13.3052 0 10.1609 +4.28323 1.32207 4.5403 0 +3.44494 1.17333 0 1.4056 +0 3.52582 1.75726 3.91819 +0 0.607548 0.556631 0.955785 +>MA1568.1 TCF21(MA1568.1) lnR0: 1.348 +2.30961 0 1.16925 1.6026 +0 4.80493 0.773574 2.14134 +3.76584 0 2.06294 5.38372 +7.89495 0 6.00998 8.6247 +0 9.15424 1.86004 5.80555 +9.67419 3.42948 3.12637 0 +0 3.74826 3.04472 9.67419 +5.25842 2.46548 9.15424 0 +7.89495 9.67419 0 5.9878 +5.21233 2.59213 0 1.16488 +2.82563 0 5.922 0.552642 +0.584687 1.05495 0 2.08038 +>MA1569.1 TFAP2E lnR0: 0.764 +1.61653 0 1.9207 0.669457 +14.2035 1.05079 0 14.2035 +14.2035 0 13.6835 14.2035 +14.2035 0 13.6835 14.2035 +12.8134 0.193653 1.39701 0 +2.54069 0 0.0395765 2.66924 +0 1.1367 0.262022 12.7874 +14.2035 13.6835 0 14.2035 +14.2035 13.6835 0 14.2035 +14.2035 0 1.07283 14.2035 +0.633558 1.79951 0 1.47063 +>MA1570.1 TFAP4(MA1570.1) lnR0: 0.18 +0 1.33518 0.745077 3.54987 +0 0.0625656 7.17219 0.738515 +9.33964 0 8.81969 9.33964 +0 8.29974 4.4311 8.81969 +8.81969 0.588083 1.03175 0 +0 1.14169 0.2098 8.81969 +8.81969 8.29974 8.29974 0 +9.33964 6.83927 0 9.33964 +0.983326 3.22958 -0.124989 0 +2.94702 0.654232 1.57184 0 +>MA1571.1 TGIF2LX lnR0: 1.348 +3.38236 2.28718 3.5605 0 +6.04799 3.71925 0 6.18955 +0 4.71652 3.69372 2.54066 +6.72482 0 6.34103 5.87077 +0 6.47359 2.45293 5.89478 +5.83328 1.42973 0 2.60926 +2.54194 0 1.48461 5.798 +6.00333 2.44395 6.13986 0 +5.75642 6.65981 0 7.24056 +2.54066 3.74846 4.55071 0 +6.25035 0 3.83804 5.71313 +0 3.69372 2.2633 3.41269 +>MA1572.1 TGIF2LY lnR0: 1.348 +2.79392 2.09221 3.09098 0 +5.46936 4.22317 0 6.09763 +0 4.42072 3.33777 2.09989 +5.86003 0 6.21949 5.63652 +0 6.50969 2.09734 5.49829 +4.89194 1.12913 0 1.96139 +1.96886 0 1.24937 4.8356 +5.15654 2.07187 5.55758 0 +5.35974 6.33029 0 5.88326 +2.24143 3.25068 4.5868 0 +5.72807 0 4.28236 5.3843 +0 3.28567 2.14258 2.90892 +>MA1573.1 THAP11 lnR0: 5.436 +0 0.536278 -0.501397 1.07567 +0.616141 3.39272 0 3.98595 +0.832884 5.29344 0 5.23416 +0 5.62871 6.61892 7.71811 +9.24427 0 7.73411 7.67482 +7.10633 4.19499 7.16562 0 +0 4.03406 4.65595 4.73282 +8.24768 0 7.72773 7.25747 +0 4.91107 2.97089 5.59928 +0.3695 1.88256 2.11473 0 +2.98141 0.767714 1.92619 0 +6.67213 4.0035 5.57294 0 +6.91939 0 7.70843 6.43871 +8.25406 0 7.73411 8.25406 +7.65883 0 7.13887 6.92907 +0 5.42131 2.15591 5.94126 +3.87322 3.89226 0 4.09343 +0.781955 0 1.02935 3.32318 +0 1.00973 0.993023 2.75701 +>MA1574.1 THRB(MA1574.1) lnR0: 3.1 +1.1971 1.39273 0 2.10724 +0.696345 4.24267 0 6.39419 +6.14665 7.2748 0 4.93258 +6.81808 9.078 0 2.68671 +8.59733 5.44048 3.01394 0 +8.34728 0 3.35324 2.71799 +0 8.37925 2.84546 9.17656 +0 5.12386 1.54981 2.41774 +0 7.02071 1.64079 9.39678 +8.8682 10.1668 0 7.57069 +8.30814 9.078 0 2.60033 +8.40657 4.55614 2.07678 0 +6.43805 0 3.53389 2.25774 +0 5.2782 0.701446 5.20302 +0.270625 -0.42535 -0.405655 0 +>MA1575.1 THRB(MA1575.1) lnR0: 5.436 +1.2119 1.37901 0 1.48001 +7.17975 2.18513 7.4073 0 +4.5032 2.65074 0 4.63316 +0 2.99153 2.69566 1.18973 +7.54919 0 10.3186 12.408 +11.4178 0 10.3186 9.26915 +11.8881 1.26468 5.14427 0 +2.89476 0 0.785592 0.588613 +0 2.78997 0.33014 5.21 +0.025356 -0.45777 -0.321613 0 +5.21928 0.434294 2.43173 0 +0.538297 0.711322 0 3.05771 +0 4.69267 1.19955 10.3186 +12.408 9.90767 0 12.408 +12.408 11.8881 0 7.50235 +1.2711 2.57549 3.20096 0 +4.83902 0 2.55619 4.29839 +0 8.80849 2.15997 9.32844 +1.49124 0 1.41919 1.20986 +>MA1576.1 THRB(MA1576.1) lnR0: 5.436 +0.912955 2.28123 0 1.4396 +8.49346 4.83462 7.97351 0 +4.23259 2.09477 0 3.57353 +0 3.7235 3.87401 2.41354 +9.04302 0 6.22387 4.91391 +9.04302 0 2.674 4.6937 +4.75298 1.81635 2.76946 0 +3.62711 -0.350514 0.166601 0 +0 2.63527 1.01739 4.67623 +2.86492 0 1.60859 2.5133 +1.51016 1.23138 0 8.1312 +8.53764 8.01769 5.23782 0 +9.04302 8.52307 0 7.0626 +0 4.45325 8.00312 2.1432 +9.04302 0 8.52307 7.47357 +6.07239 0 6.54265 6.74382 +8.52307 4.71371 8.00312 0 +7.67234 -0.234016 1.00373 0 +0 4.59936 1.57041 8.25821 +>MA1577.1 TLX2 lnR0: -0.988 +1.87291 0 0.469723 0.631339 +2.48145 -0.456018 2.3255 0 +0 12.2827 6.00495 12.8027 +0 12.2827 12.2827 12.8027 +12.8027 12.2827 12.2827 0 +12.8027 12.2827 12.2827 0 +0 12.2827 12.2827 12.8027 +1.16832 1.36402 0 2.51205 +>MA1578.1 VEZF1 lnR0: 0.18 +3.94371 0 2.49435 10.0532 +9.3951 0 9.86536 10.3853 +8.08325 0 9.8625 10.3824 +8.81587 0 9.86536 10.3853 +7.59394 0 9.85386 8.07462 +6.93083 0 7.85602 7.2175 +0 -0.336693 1.33617 1.67504 +4.09863 0 2.92722 1.23081 +0.642996 0.604906 0.306204 0 +0.0254352 0.437036 0.620775 0 +>MA1579.1 ZBTB26 lnR0: 3.1 +0.1394 -0.33335 -0.391224 0 +0 -0.132069 -0.397379 0.0816549 +2.17019 0 2.78808 1.7894 +7.25826 7.46806 7.46806 0 +6.70402 0 6.86918 9.07292 +8.41156 0 6.68118 4.29574 +0 5.83229 4.37278 5.773 +6.28315 8.54307 0 6.996 +0 5.52517 6.71504 6.65575 +0 2.47993 1.79825 3.06291 +0 0.500427 0.522371 1.10101 +0 0.0977134 0.257051 0.819776 +0.679018 0.345591 0 1.04987 +0 -0.465262 -0.404765 0.0828389 +0.299196 -0.454793 -0.00302985 0 +>MA1580.1 ZBTB32 lnR0: 0.18 +1.05659 0.741571 4.24189 0 +3.58821 9.4846 0 4.76177 +9.12411 10.1736 9.1834 0 +0 8.60296 11.1626 11.6826 +12.2025 0 10.6924 12.2025 +0 9.18059 8.86181 8.54207 +12.2033 9.70295 0 9.42345 +11.6818 8.86262 11.1618 0 +0 3.8786 1.18673 2.78646 +0.0136706 2.33153 2.31824 0 +>MA1581.1 ZBTB6 lnR0: 1.932 +0.782813 1.15547 0 0.7566 +0.855127 -0.303665 0.0652007 0 +2.38887 0 0.953672 3.2949 +4.92956 0 6.26072 6.62468 +6.02997 3.72036 4.69702 0 +2.88483 4.52044 1.39542 0 +7.71095 5.11202 0 8.5104 +0 5.63734 6.09845 6.55194 +5.64731 6.6031 0 7.60372 +5.66411 0 5.68629 5.93969 +4.61868 0 4.30743 3.5088 +0.78041 0 0.591394 1.12053 +0.983961 0.333134 0 1.62928 +>MA1583.1 ZFP57 lnR0: 1.932 +1.17493 0.0868994 0 0.687919 +0.572298 0 0.0115674 0.556755 +0 0.0367927 -0.0799457 1.23859 +2.37653 1.13309 0.893409 0 +8.79755 6.74526 4.87215 0 +8.3995 6.36842 0 8.3995 +8.29895 0 8.43989 7.84883 +9.29838 0 2.92937 9.87762 +6.52735 8.41965 0 7.13798 +7.67286 0 4.33687 5.42589 +0 3.38746 2.26188 4.97725 +0.902837 0.156636 0 1.07307 +0.318777 -0.499518 -0.466556 0 +>MA1584.1 ZIC5 lnR0: 3.684 +0.698713 0 0.395961 1.65519 +5.43342 2.36111 0 2.11149 +0 2.50347 2.25289 14.0945 +6.85766 0 14.2312 10.6221 +7.60973 0 8.4036 8.94797 +4.42741 0 5.37095 6.40348 +12.1957 0 14.2354 13.7651 +8.72559 0 12.6641 13.184 +11.0666 0 13.9722 2.80276 +3.76139 9.76126 0 10.1569 +13.0701 0 6.31409 2.24927 +2.79976 1.68582 1.92468 0 +6.84874 11.0891 0 13.1785 +0.95666 -0.400749 2.02751 0 +8.99323 3.49057 0 3.34808 +1.03846 0 3.83363 1.62453 +>MA1585.1 ZKSCAN1 lnR0: 0.18 +0 2.78932 2.43657 3.31554 +4.09708 0.0190592 2.62934 0 +0 6.22241 7.57165 12.4409 +8.76346 9.89019 0 9.30559 +12.458 11.9381 11.9381 0 +0 6.36711 11.9268 12.4468 +9.27908 5.81624 0 7.86423 +9.19573 8.78165 0 8.20552 +2.4929 0.878218 1.66648 0 +1.68563 0.9506 0 3.03614 +>MA1587.1 ZNF135 lnR0: 2.516 +4.06026 0 2.25437 2.20674 +6.1236 0 5.17182 4.4992 +7.40736 3.99005 5.22576 0 +7.04972 0 6.07483 2.7701 +4.30501 5.00331 0 9.18748 +0 7.19655 3.50513 6.72629 +6.10378 0 5.0046 6.94348 +9.30957 0 8.21038 7.51991 +8.78962 6.48001 7.69043 0 +8.31479 0 6.99539 8.31479 +4.91273 0 6.5806 3.40912 +2.96744 -0.361245 2.63825 0 +1.29776 2.93828 0 3.68915 +0 3.08823 -0.428176 3.32151 +>MA1588.1 ZNF136 lnR0: 3.1 +1.20162 3.63471 0 4.51654 +0 2.86839 1.96039 0.513676 +0 6.096 4.88557 6.82038 +6.24901 5.88365 5.88365 0 +6.71451 4.88557 6.19456 0 +6.11396 0 6.44359 4.31728 +6.18394 4.60408 5.43361 0 +2.2959 3.96131 1.53984 0 +3.76911 7.21 0 5.2946 +5.22781 5.87602 0 6.39597 +3.85044 1.26028 5.52511 0 +5.08731 5.02442 4.27605 0 +4.60881 6.0866 0 5.43651 +0 3.40654 0.321106 3.668 +2.27954 0 4.52711 2.28949 +>MA1589.1 ZNF140 lnR0: 6.604 +1.58108 1.3146 1.3898 0 +0 2.16663 1.20126 2.58365 +2.62722 4.92331 0 2.52391 +6.36026 7.2736 0 7.44903 +0 6.24521 3.41193 7.20824 +6.50997 7.14849 0 7.17086 +6.32354 -0.44994 4.0707 0 +1.70041 7.34284 0 3.81535 +7.68828 9.72799 0 7.1907 +0 8.63744 7.23626 7.58795 +0 6.91199 6.53718 8.74093 +7.50325 3.72599 5.3619 0 +4.50747 5.05938 4.53729 0 +6.95379 7.2879 0 8.67376 +6.20699 0 6.06661 3.61593 +2.65406 2.90964 3.78295 0 +2.49807 3.20239 0 3.45648 +2.28838 2.84104 0 3.22484 +1.6503 2.37352 0 2.89347 +2.16413 1.33884 1.56152 0 +2.28544 0 1.90981 2.00479 +>MA1592.1 ZNF274 lnR0: 3.684 +0.579048 0.187132 0 0.648757 +1.20717 1.84147 0 2.89874 +4.59796 0.850232 2.9083 0 +0 8.84451 -0.206099 2.64085 +7.63668 6.02321 2.21367 0 +11.7525 12.2228 0 15.3024 +0 9.93302 3.81756 4.55361 +4.55802 3.33848 0 7.94853 +8.67147 9.91173 7.61253 0 +7.82279 0.512105 14.0813 0 +11.3414 0 12.0024 12.1633 +14.7822 14.2623 14.2623 0 +12.6836 0 14.7233 3.80936 +1.75864 4.45548 0 2.42657 +2.42172 0 1.12553 0.822265 +0.277896 0.22515 -0.464094 0 +>MA1593.1 ZNF317 lnR0: 1.348 +0.83728 1.60476 0.887425 0 +0 0.467255 -0.302351 1.61632 +0 4.14579 3.72388 2.88408 +5.73056 0 5.82057 6.37988 +0 6.32278 4.45463 3.81113 +4.38791 5.69209 0 6.112 +5.21716 0 5.51116 5.9445 +0 4.64418 4.43786 2.5162 +5.70338 5.7854 0 5.81273 +0 5.11915 5.13289 5.53372 +1.5951 0 1.70382 0.7834 +0.196771 0.837333 1.04176 0 +>MA1594.1 ZNF382 lnR0: 8.356 +0 4.32575 2.82541 3.94135 +2.67042 4.48696 0 2.46706 +4.00902 3.36827 0 5.63561 +0.773725 5.41945 0 3.36494 +4.26963 6.44446 0 5.53794 +0 3.30285 2.98755 4.93995 +4.19958 0 2.71716 0.750891 +0 7.34344 5.9528 7.95 +3.00002 3.3252 3.82688 0 +5.34963 0 6.16165 1.53047 +0 7.7318 6.74159 7.37588 +6.50113 0 4.461 5.23641 +1.66595 -0.334366 5.33579 0 +0 7.35264 6.8017 8.78115 +8.52614 0 6.605 5.47451 +0 -0.0879061 3.84846 1.35382 +3.17236 6.28378 0 6.06106 +0 5.38979 3.9886 5.55072 +4.26268 0.0722724 4.09678 0 +2.20662 0 4.32982 4.29051 +4.7636 0 5.80539 3.65845 +3.34927 0 4.82966 1.64523 +0 3.90297 3.21082 2.90063 +4.78957 0 4.52345 3.19814 +>MA1596.1 ZNF460 lnR0: 3.684 +1.81713 2.92667 0 4.92184 +5.13539 0 2.73869 3.94552 +6.65016 0 4.38196 4.92307 +5.46616 2.00782 3.37676 0 +6.85723 0 4.93609 6.12748 +0 0.252922 1.68516 3.27606 +5.06578 5.90166 0 5.84237 +8.26988 0 7.55917 7.49988 +10.0667 0 7.24757 8.27705 +6.74344 6.32936 5.86447 0 +9.06573 0 6.56536 7.62059 +8.48559 0 6.56446 7.75584 +7.33521 0 5.71918 5.69432 +1.36026 3.03818 0 4.51025 +0 1.94462 0.695303 4.99212 +2.73225 2.8241 0 4.62194 +>MA1597.1 ZNF528 lnR0: 4.268 +2.66302 0 2.48301 2.6298 +2.89079 0 2.04392 2.46965 +2.5039 0 2.61357 3.53719 +0 4.76355 2.53186 4.66809 +4.60012 7.09476 0 6.45624 +6.68541 6.57643 0 6.87617 +5.15755 7.54743 0 8.06738 +0 6.65937 6.65937 7.59029 +0 6.27089 3.86175 6.11941 +7.12003 8.16953 0 8.11024 +4.01246 0 2.88706 2.36578 +5.67599 0 7.13646 6.49794 +0 7.06564 5.66446 8.16483 +5.4591 2.95873 4.93915 0 +7.90202 1.82232 4.50363 0 +5.06196 1.13826 2.17311 0 +5.50986 0 5.89846 4.47824 +>MA1599.1 ZNF682 lnR0: 3.684 +1.55118 0 0.970136 1.47686 +0.716553 0.569068 0 1.53486 +3.29614 3.14074 0 3.59574 +3.56746 4.30921 0 5.04385 +3.46921 0 2.88023 4.23718 +4.09391 0 3.3832 1.24891 +0 3.15177 4.93168 6.03087 +0 4.39722 4.86899 7.08835 +7.66296 6.95225 0 7.4722 +6.61809 0 6.09814 5.35051 +7.87628 0 6.62658 6.88607 +7.46669 0 6.4918 7.46669 +4.22618 0 4.71793 4.26948 +0.309429 1.41433 1.40228 0 +0 -0.173434 -0.410358 0.836183 +1.0868 0.13566 0.552118 0 +>MA1600.1 ZNF684 lnR0: 4.852 +0 1.09933 0.00718579 1.32954 +3.09026 0.309493 0.664982 0 +0 5.05603 3.6057 5.89475 +7.42211 0 6.90216 6.4319 +0 6.04089 2.86286 3.13528 +4.69766 2.36482 0 4.40249 +6.90897 5.80979 3.82937 0 +6.92193 0 5.51764 7.26645 +5.36948 0 8.58519 4.64672 +0 6.07732 3.56609 2.17501 +8.7 0 4.21921 4.78451 +5.27342 0 6.766 7.93164 +7.71328 0 7.19333 4.20876 +10.7229 0 10.2029 8.74244 +2.12693 2.54116 5.28844 0 +4.38235 3.78912 5.76954 0 +1.49975 1.33694 -0.254875 0 +0 1.05185 0.363719 2.22357 +>MA1602.1 ZSCAN29 lnR0: 1.348 +3.34351 0 1.97469 1.19253 +6.00708 9.83644 0 10.3564 +9.83644 5.26904 7.01729 0 +8.08038 0 9.85962 10.3796 +9.79495 3.71525 9.275 0 +0 7.03472 9.33391 7.55467 +7.8382 0 9.61744 2.92331 +0 8.72846 0.355913 9.24842 +10.3328 0 5.21448 6.66861 +0.538444 0.57465 0 1.33325 +3.11452 4.22094 0 4.6079 +1.2223 0.147121 0 1.37281 +>MA1100.2 ASCL1(MA1100.2) lnR0: 0.18 +0.756171 0.683709 0 1.55084 +1.71423 2.53574 0 3.60647 +12.5093 0 11.9893 8.64065 +0 4.23711 5.59671 4.29066 +5.82053 1.75845 0 3.31022 +3.09065 0 1.72342 8.15997 +5.16202 6.87099 4.6065 0 +6.83744 11.9893 0 7.65044 +4.58616 0 1.89277 1.69176 +1.33 0 0.734238 0.833217 +>MA0605.2 ATF3(MA0605.2) lnR0: 1.348 +1.5003 1.02904 0 1.79365 +0 3.62962 0.12021 14.4518 +15.1575 14.6375 13.6473 0 +15.6774 15.1575 0 5.36258 +0 14.6375 14.6375 15.1575 +15.6774 0 15.1575 6.64517 +5.97245 15.1575 0 15.6774 +15.1575 14.6375 14.6375 0 +5.21008 0 15.1575 15.6774 +0 14.6375 14.6375 15.1575 +14.4557 0.130233 3.93784 0 +1.78883 0 1.01895 1.48416 +>MA0462.2 BATF::JUN lnR0: 0.764 +0.30314 0.948211 -0.0104609 0 +0 0.838346 0.946835 1.78742 +6.59928 6.4903 7.07733 0 +5.77844 6.30631 0 3.61897 +0 6.91323 6.14498 6.79257 +4.95274 0 2.86709 4.95274 +5.5433 6.65064 5.50402 0 +3.54039 0 5.91103 5.64289 +0 6.26513 5.85527 5.98371 +1.50022 1.02495 0.68509 0 +0 -0.0529125 0.911093 0.396698 +>MA0463.2 BCL6 lnR0: 3.684 +0 -0.173842 -0.113135 0.192307 +1.97206 0.358327 1.81096 0 +3.00808 5.21202 0 4.36696 +5.35628 0 5.70102 5.73839 +3.98008 3.91607 5.73934 0 +3.01084 2.20783 2.14937 0 +6.85702 8.89673 9.3077 0 +11.9153 0 10.0864 5.43253 +5.33068 2.22308 0 1.06497 +0 5.08499 5.65164 4.65317 +3.6399 6.91476 0 5.98668 +7.81836 5.98128 0 5.29313 +0 4.61805 3.0517 4.01079 +0 5.4115 4.79529 3.22449 +1.15269 0.351046 2.94016 0 +0.545132 0.307344 -0.251667 0 +>MA0864.2 E2F2 lnR0: 3.684 +1.02364 1.50226 0 2.04331 +0.410233 2.46859 1.12488 0 +1.43908 2.23619 1.21262 0 +1.61327 3.06464 1.60187 0 +1.93775 4.1751 1.69915 0 +4.49273 1.71871 0 7.52 +11.0155 7.06996 0 11.5947 +8.24051 0 12.0699 12.5898 +8.46195 12.0711 0 10.2919 +10.602 0 7.35418 11.5923 +4.15168 0 1.98785 4.74738 +0 1.31831 3.43035 1.92337 +0.638686 1.70856 3.97128 0 +0.695851 1.83027 1.79749 0 +0.00261404 0.574522 1.38667 0 +1.74267 0 1.07891 0.77026 +>MA0469.3 E2F3 lnR0: 3.684 +0 1.52487 -0.0851202 0.926966 +1.35062 6.7578 5.63905 0 +2.5738 7.83969 7.80526 0 +3.26362 5.85258 7.38253 0 +3.40386 7.51821 2.24514 0 +9.08465 2.901 0 15.2139 +11.6694 14.6993 0 11.555 +11.0888 0 11.4085 10.6195 +10.5092 10.8289 0 10.5631 +11.3509 0 14.6996 12.0806 +15.2167 0 2.93798 9.10713 +0 2.28532 7.8421 3.40931 +0 7.33546 6.08792 3.34594 +0 7.85847 7.66111 2.62257 +0 5.39802 7.17162 1.35107 +0.957406 -0.092267 1.56184 0 +>MA0470.2 E2F4 lnR0: 2.516 +1.0666 2.5894 1.8232 0 +1.88248 3.23619 3.17289 0 +2.27962 4.14994 1.50974 0 +3.79179 4.21312 2.55695 0 +5.8884 2.62486 0 9.77507 +10.7266 8.01527 0 14.1521 +10.1928 0 12.0643 10.6038 +10.8638 10.6627 0 9.49882 +14.1521 0 7.93362 14.1521 +9.27168 0 1.76409 5.04543 +0 0.900064 2.97442 2.26981 +0.753235 1.50819 3.42034 0 +0.916902 2.72515 2.82292 0 +0.355281 0.729347 0.983038 0 +>MA0612.2 EMX1 lnR0: -0.988 +1.92978 0 0.158134 1.45696 +8.4249 1.14901 12.1846 0 +0 2.40025 12.5712 13.0911 +0 12.5712 12.5712 13.0911 +13.0911 12.5712 12.5712 0 +13.0911 12.5712 2.80047 0 +0 12.5712 12.5712 13.0911 +2.26233 0.770492 0 2.58674 +>MA0766.2 GATA5 lnR0: 0.18 +1.91081 0 0.894993 1.78817 +0 1.24683 6.65098 0.125176 +14.2916 13.7717 0 14.2916 +0 13.2517 13.2517 13.7717 +13.7717 13.2517 13.2517 0 +0 13.2517 13.2517 5.47863 +0 13.2517 5.67558 6.16738 +5.65906 0.0334619 0 4.21087 +0.704039 1.33365 0 4.09661 +0 -0.388906 0.148072 0.925125 +>MA0038.2 GFI1 lnR0: 1.348 +2.1614 0 0.643667 1.13467 +0 0.38588 3.99315 5.03044 +0 12.6457 14.2151 14.7351 +0 14.2143 14.2143 13.744 +14.7348 14.2148 14.2148 0 +11.2928 0 14.7337 11.8281 +0 14.1712 14.1712 4.15602 +5.51924 0 2.80829 15.1367 +0.844685 7.39329 0.218023 0 +4.06852 6.62177 0 5.42336 +7.02841 0 14.623 3.40452 +0 1.142 1.49455 1.99537 +>MA0734.2 GLI2 lnR0: 3.1 +0 -0.42606 -0.366856 1.68625 +7.93292 6.14634 0 4.92858 +0 1.7454 2.45322 13.6482 +14.3867 0 13.8668 11.2478 +14.388 0 13.8681 13.3978 +0 3.97895 6.73784 5.64527 +14.3882 0 13.8683 14.3882 +2.68196 0 13.7445 14.2644 +7.04831 0 10.0782 7.18192 +0 10.3541 4.33678 9.2463 +4.16124 0 4.43102 4.67687 +2.47957 1.66827 0 4.01286 +0.00636503 1.538 0.700848 0 +1.56168 0 2.72223 1.16201 +5.4126 3.58594 0 4.79239 +>MA0893.2 GSX2 lnR0: -0.988 +2.23921 0.254384 0 11.8187 +3.27774 0.407366 3.08438 0 +0 -0.203231 4.28636 6.46796 +0 11.6472 2.27025 12.1671 +12.1671 4.7843 11.6472 0 +12.1671 11.6472 5.42331 0 +0 11.6472 1.77041 7.81782 +0.912109 2.08525 0 2.13227 +>MA1099.2 HES1 lnR0: 0.18 +2.97518 2.38353 0 2.62662 +2.16459 3.1289 0 1.71822 +5.78416 0 14.0385 10.3522 +0 12.5564 -0.463661 5.28916 +14.5585 0 14.0385 5.02341 +10.1427 14.0385 0 14.5585 +6.12807 1.64939 13.5186 0 +13.5683 14.0385 0 8.85995 +2.99227 0.0357019 0 0.910928 +2.68823 0 1.0468 2.46052 +>MA0616.2 HES2 lnR0: 0.18 +3.93679 2.80125 0 3.89506 +2.99336 2.90804 0 2.91923 +6.6154 0 6.55941 7.29405 +0 12.0126 1.13357 12.5325 +13.4427 0 12.9228 6.4891 +13.4427 12.9228 0 13.4427 +12.9228 2.39974 12.4028 0 +7.74417 8.96193 0 13.4427 +3.6644 0 1.82713 0.785041 +2.70542 0 1.34955 2.26086 +>MA0650.2 HOXA13 lnR0: 0.764 +0.772316 0 0.271868 4.69023 +4.38113 0 1.88635 10.3224 +10.3224 0 9.80244 4.59763 +0 0.741229 9.28249 9.80244 +0 9.28249 9.28249 9.80244 +9.80244 9.28249 9.28249 0 +0 9.28249 5.15339 9.80244 +0 9.28249 8.29228 9.80244 +0 9.28249 9.28249 9.80244 +0 1.41773 4.12404 3.48982 +2.4468 0 2.85325 2.46138 +>MA0900.2 HOXA2 lnR0: -0.988 +1.85978 0.219701 0 2.43628 +15.6428 3.41007 15.1228 0 +0 0.667768 6.5017 15.1264 +0 15.1228 15.1228 15.6428 +15.6428 15.1228 15.1228 0 +15.6428 15.1228 15.1228 0 +0 15.1228 4.22701 15.6428 +1.57338 0.441631 0 2.02972 +>MA0158.2 HOXA5 lnR0: -0.988 +4.10599 1.06862 0 2.64369 +10.9138 0.451826 10.3938 0 +0 0.409955 4.68346 11.4987 +0 10.9788 10.9788 11.4987 +11.4987 10.9788 10.9788 0 +11.4987 10.9788 1.28346 0 +0 10.9788 10.9788 11.4987 +2.11004 0 0.364887 5.20794 +>MA0594.2 HOXA9 lnR0: 0.18 +1.12237 1.36617 0 5.34192 +2.53982 1.08466 2.93989 0 +4.87536 0 6.53183 4.98971 +1.8956 6.45018 0 11.0992 +10.5793 4.52904 10.0593 0 +0 3.17321 3.89149 0.377501 +0 3.67946 5.51925 3.17673 +0 0.381866 2.38036 0.900185 +0.905674 0 0.523037 0.617253 +1.02255 0.147655 0 1.03481 +>MA0902.2 HOXB2 lnR0: -0.988 +2.35828 0.515967 0 1.97452 +6.20186 -0.0303058 11.3265 0 +0 0.528769 4.52358 12.6126 +0 12.0926 12.0926 12.6126 +12.6126 12.0926 12.0926 0 +12.6126 12.0926 1.32485 0 +0 12.0926 12.0926 12.6126 +1.71167 0.52478 0 2.81138 +>MA0904.2 HOXB5 lnR0: -0.988 +2.24066 0.182772 0 2.60987 +11.4697 1.96708 10.9497 0 +0 1.03652 10.9497 11.4697 +0 10.9497 10.9497 11.4697 +11.4697 10.9497 10.9497 0 +8.68982 6.2414 0.995581 0 +0 10.9497 1.89713 11.4697 +2.76177 0 0.0881443 1.94158 +>MA0485.2 HOXC9 lnR0: 0.18 +2.33971 3.11095 0 14.3075 +13.7876 6.12875 13.2676 0 +14.3075 0 13.7876 14.3075 +2.37194 13.7876 0 14.3075 +11.2279 10.708 9.71776 0 +0 13.2676 13.2676 2.86285 +0 13.2676 13.2676 13.7876 +0 9.60341 13.2676 13.7876 +0 2.38511 2.9528 2.11265 +0.628807 -0.514291 0.674559 0 +>MA0909.2 HOXD13 lnR0: 0.764 +2.49259 0 0.488502 4.29786 +2.97872 0 0.159577 8.96395 +8.96395 0 8.444 8.96395 +0 0.854388 7.92404 8.444 +0 7.92404 5.36439 8.444 +5.66412 7.92404 7.92404 0 +0 7.92404 7.92404 8.444 +0 7.92404 4.25983 8.444 +0 1.77538 7.92404 8.444 +0 0.0362434 4.15396 8.444 +2.81446 0 6.18676 7.11769 +>MA0912.2 HOXD3 lnR0: -0.988 +5.85727 0 3.77304 2.47889 +13.6946 6.66914 13.1747 0 +0 3.73083 13.1747 13.6946 +0 13.1747 13.1747 13.6946 +13.6946 13.1747 13.1747 0 +13.6946 13.1747 1.17245 0 +0 13.1747 2.18074 13.6946 +4.13618 0 1.48071 2.92006 +>MA0910.2 HOXD8 lnR0: -0.988 +2.58791 2.47011 0 3.01133 +11.4824 0 10.9624 1.05312 +0 -0.250965 5.65975 11.71 +0 11.19 11.19 11.71 +11.71 11.19 11.19 0 +4.29943 11.19 2.28934 0 +0 11.19 11.19 11.71 +1.34681 0 1.5934 2.39571 +>MA0913.2 HOXD9 lnR0: 0.18 +4.13702 4.18701 0 5.11521 +13.6449 0 7.75183 1.08284 +0 0.39179 4.0324 4.09972 +0 5.59132 4.64586 11.562 +6.18223 13.3412 13.3412 0 +0 10.2024 13.3412 1.57172 +0 13.3412 13.3412 6.97508 +0 13.3412 13.3412 13.8612 +0 2.34471 3.19247 2.86986 +0.999395 0 1.4057 0.968072 +>MA1140.2 JUNB(MA1140.2) lnR0: 1.348 +2.17984 1.77658 0 2.26645 +0 4.68597 3.69576 5.39668 +7.18634 6.66639 5.3574 0 +8.6965 8.17655 0 4.92642 +0 6.66639 6.66639 8.17655 +8.6965 0 8.17655 7.12705 +8.6965 7.18634 0 8.6965 +7.18634 5.67618 6.66639 0 +4.5674 0 6.19613 7.70629 +0 6.08715 6.66639 7.18634 +7.51071 0.212283 3.56519 0 +2.69548 0 2.07465 2.88127 +>MA0701.2 LHX9 lnR0: -0.988 +4.43909 0 2.49845 2.81352 +11.8429 0.398921 11.323 0 +0 3.03086 11.9259 8.09654 +0 11.9259 11.9259 12.4459 +12.4459 11.9259 11.9259 0 +12.4459 11.9259 4.58068 0 +0 11.9259 3.74936 12.4459 +0 0.626259 -0.305722 1.38652 +>MA0702.2 LMX1A lnR0: -0.988 +5.76112 0.675803 3.5087 0 +12.719 7.24796 7.91939 0 +0 12.199 12.199 12.719 +0 8.9096 12.199 12.719 +12.719 6.58212 12.199 0 +12.719 12.199 12.199 0 +0 5.57797 3.31529 12.719 +0 -0.384758 0.746755 1.74713 +>MA0703.2 LMX1B lnR0: 0.764 +0 1.08074 0.558092 1.49813 +0.0372539 1.06064 0.909496 0 +1.39925 1.88504 1.12135 0 +11.6439 1.98552 3.62074 0 +11.8717 11.3517 11.3517 0 +0 11.3517 11.3517 11.8717 +0 11.3517 11.3517 11.8717 +11.8717 11.3517 11.3517 0 +11.8717 11.3517 11.3517 0 +0 7.68751 11.3517 11.8717 +0 1.02629 2.17796 1.90838 +>MA0623.2 NEUROG1 lnR0: 0.18 +0.684092 3.92821 0 6.23782 +0 0.583729 0.845818 6.91576 +12.1856 0 8.52673 12.1856 +0 11.1457 5.20441 11.6656 +9.36642 4.36719 11.1457 0 +0 11.1457 4.86788 11.6656 +11.6656 4.7658 11.1457 0 +12.1856 11.6656 0 12.1856 +6.27042 1.0246 0.560194 0 +5.21442 0 3.26256 0.658898 +>MA0842.2 NRL lnR0: 1.932 +0 1.6736 0.832982 1.78476 +0 4.09301 1.9786 1.79304 +0 5.19406 4.2128 0.831248 +0 2.8624 3.53188 0.0880643 +0.741717 0.488929 0 0.761498 +5.49367 2.74547 8.01995 0 +14.1184 14.5886 0 15.1086 +5.22755 0 10.1093 11.2399 +14.5886 10.9298 14.0687 0 +8.95991 14.5886 0 5.18845 +0 14.0687 11.7695 14.5886 +9.57829 0 5.54872 3.99266 +1.78288 3.09046 0 2.03499 +>MA0682.2 PITX1 lnR0: -0.988 +1.5827 0 1.34276 0.975968 +13.2317 12.7117 12.7117 0 +0 12.7117 12.7117 13.2317 +0 12.7117 12.7117 13.2317 +13.2317 12.7117 2.78747 0 +6.65189 0 13.2317 6.67187 +7.7029 0 6.22414 4.74266 +1.34838 0 1.14888 1.49897 +>MA0075.3 PRRX2 lnR0: -0.988 +3.5985 0 2.03789 2.29945 +5.20812 0.697871 4.58729 0 +0 7.21118 10.0896 12.59 +0 12.07 12.07 12.59 +12.59 12.07 12.07 0 +12.59 12.07 12.07 0 +0 11.0798 3.5108 12.59 +0 0.321241 -0.223898 0.814489 +>MA0867.2 SOX4 lnR0: 0.18 +1.31908 1.63945 0 1.79493 +0 2.00707 0.91271 3.65579 +0 11.805 11.805 9.03557 +12.8449 0 7.12842 7.80727 +0 10.8148 9.02515 12.325 +0 9.02515 8.25516 12.325 +0 4.95389 6.18813 1.02728 +2.94981 6.36156 0 6.51519 +1.2497 1.28162 0 4.79548 +0.608827 0.389469 0 2.4749 +>MA0868.2 SOX8 lnR0: 0.18 +0 0.173534 0.565587 1.32115 +1.80992 2.11814 0 2.17972 +0 3.03305 2.24438 3.00544 +0 10.21 10.21 5.26048 +9.2695 0 5.61066 5.16038 +0 10.21 10.21 6.68252 +0 4.80403 10.21 5.57151 +2.71121 5.05156 5.8607 0 +0.945588 3.09806 0 3.15998 +2.10513 1.10247 0 2.73263 +>MA0746.2 SP3 lnR0: 1.932 +1.09467 0.00831226 0 0.811487 +1.55986 3.03302 0 3.88389 +3.79684 0 4.81237 4.7302 +5.8231 0 6.83754 5.49196 +0 1.433 10.1488 8.68834 +10.3024 0 12.5623 9.41804 +4.30485 12.5623 0 4.19003 +13.0823 0 12.5623 13.0823 +13.0823 0 12.5623 9.79285 +11.5128 0 10.9929 3.68531 +0 -0.40286 5.83966 2.6075 +3.68818 0 4.06176 2.296 +1.29457 0 2.29046 0.940264 +>MA0632.2 TCFL5 lnR0: 0.18 +3.67636 1.26254 0.197898 0 +16.5084 0 15.9885 16.5084 +0 15.4685 0.755301 2.92535 +16.5084 0 15.9885 5.93004 +5.99857 15.9885 0 16.5084 +5.48561 0 15.6463 2.38701 +4.84202 6.71821 0 16.5084 +5.97416 0 3.94175 7.28674 +0 0.181573 1.38671 1.47014 +2.66529 0 3.01814 2.95076 +>MA0871.2 TFEC lnR0: 0.764 +1.03036 0 0.980475 1.29204 +1.1624 0 0.323359 2.14951 +13.3504 0 10.85 13.3504 +0 12.3105 5.19105 4.3634 +13.3504 0 12.8304 5.70487 +7.28111 12.8304 0 13.3504 +12.8304 12.3105 12.3105 0 +13.3504 10.5312 0 13.3504 +0 3.70902 5.21075 7.30015 +9.01859 0 6.80269 3.2057 +1.12595 0 0.720021 1.36389 +>MA0753.2 ZNF740 lnR0: 1.932 +1.9335 0 1.44443 1.94116 +2.55623 0 3.18384 1.35082 +1.0513 1.60229 0 2.25715 +4.59334 0 4.74951 4.87741 +3.73811 0 6.07742 9.4758 +6.25967 0 7.64687 6.41856 +5.98674 0 6.97543 6.50517 +5.92594 0 7.96564 6.91615 +7.04045 0 6.97543 7.68614 +8.89657 0 7.96564 8.48559 +3.67517 0 7.16619 8.16682 +0 1.59663 3.37739 2.93853 +2.84096 0 4.2213 2.59546 +>MA1707.1 DMRTA1 lnR0: 1.348 +0 1.55651 1.13817 1.18481 +0 1.90018 0.914363 0.971013 +1.27178 1.51052 2.1578 0 +2.77134 1.70223 1.83763 0 +11.7922 8.7126 0 11.7922 +0.561887 0.536205 9.02592 0 +1.77371 4.32401 10.7523 0 +0 8.45311 6.79147 11.2723 +10.2228 0 11.2723 11.7922 +0 10.7523 5.48248 2.93265 +0.930525 2.60405 1.6427 0 +2.16022 1.4973 1.64757 0 +>MA1708.1 ETV7 lnR0: 0.764 +0 1.73496 -0.115682 0.945922 +1.5132 1.18967 0 1.54291 +2.10769 0.70018 0 3.58316 +2.36511 0 2.86533 3.37908 +13.1344 10.3152 0 13.1344 +11.5649 10.3152 0 8.78507 +0 12.0945 12.0945 7.49512 +0 6.26943 10.1141 5.78712 +1.6633 6.18614 0 13.1344 +4.08771 2.80693 2.28012 0 +1.45021 3.21154 0 3.05045 +>MA1709.1 ZIM3 lnR0: 3.1 +0 1.38092 0.414904 1.42242 +0.569142 0.742417 0 1.62978 +1.15749 0 2.62467 2.41057 +0 6.55972 6.71157 7.31396 +0 6.66457 5.58465 5.37609 +4.69343 0 5.13389 8.13075 +0 8.16776 8.13159 7.71594 +6.89247 7.77615 0 8.20146 +0 3.67751 5.99552 5.5039 +0 6.94608 6.66226 7.51392 +0 4.96032 4.06138 2.72521 +2.09437 0 1.0143 1.56728 +3.96506 0 7.04391 5.3586 +1.3463 -0.177193 2.5969 0 +0 0.3479 1.13345 1.28736 +>MA1710.1 ZNF257 lnR0: 1.348 +1.48819 0.403615 0 1.73996 +0 0.80821 -0.00496577 0.429048 +9.42571 8.90576 0 9.42571 +0 8.27762 8.27762 3.5942 +9.42571 8.90576 0 9.42571 +9.42571 8.90576 0 9.42571 +1.91955 0 8.26635 2.8535 +0 2.75363 -0.0531873 8.054 +0 8.1281 1.77896 8.64805 +9.42571 8.90576 0 9.42571 +0.663513 2.45484 0 8.38249 +2.96583 2.59903 0 2.44441 +>MA1711.1 ZNF343 lnR0: 4.268 +1.80585 0 1.19049 3.56925 +3.63772 0 4.18222 2.4701 +3.98766 8.19334 0 7.04112 +15.9394 0 15.4195 12.8005 +11.1399 10.1393 14.8996 0 +15.4194 9.82038 12.6002 0 +15.9393 0 15.4193 15.9393 +0 0.145457 4.71834 3.17684 +6.74235 0 4.3321 4.9996 +4.04274 0 2.13854 3.07121 +0 1.68252 -0.304039 0.713492 +6.22953 0 7.57603 3.98196 +5.82553 6.86656 0 7.53903 +4.89784 4.54721 0 5.41991 +5.01525 0 4.71178 1.79548 +0 0.33692 3.34289 3.07132 +0.759549 0 0.0260002 1.69814 +>MA1712.1 ZNF454 lnR0: 4.852 +0 0.839608 0.44514 0.965091 +4.38668 3.86673 0 7.34303 +5.20703 3.34892 0 7.34303 +7.30074 0 6.78079 3.14795 +6.69228 1.56134 6.17233 0 +7.50065 0 6.9807 7.50065 +2.97098 0 0.821747 1.83415 +1.789 0.312041 0 2.03639 +3.44735 4.6448 0 7.30074 +7.50065 6.9807 0 7.50065 +2.5749 0 1.80756 2.5749 +3.21484 0 4.41229 2.91545 +3.01303 0 6.64588 3.69167 +6.59339 0 3.11709 0.833648 +3.83405 2.79628 0 1.68696 +1.17626 0.523801 0 4.1437 +2.33579 1.26905 0 0.720232 +3.16343 2.09669 0 4.88083 +>MA1713.1 ZNF610 lnR0: 2.516 +1.93858 0 0.287168 2.24637 +3.28125 0 0.719663 2.78225 +2.42604 0 1.76081 2.69538 +5.41223 4.07811 0 5.20091 +6.34755 0 4.67751 7.19478 +7.37975 0 5.72662 7.62525 +7.37975 5.59666 0 8.03623 +9.31442 0 6.6779 9.31442 +6.84553 5.45285 5.06243 0 +8.80807 0 5.14923 9.60753 +4.47574 0 3.3689 4.75475 +3.32216 0 0.187597 1.64809 +2.56573 0 0.757274 2.19134 +1.53749 0 0.511685 2.11979 +>MA1714.1 ZNF675 lnR0: 6.604 +0 1.43578 -0.436232 1.6936 +2.68671 3.9743 0 2.45576 +3.62851 4.43449 0 3.82088 +0 0.0564255 0.13319 1.92283 +1.46857 0 1.421 0.691945 +1.58956 -0.187192 1.62943 0 +0 0.318636 0.803624 1.63451 +1.55264 4.9799 0 5.34422 +4.93068 6.38627 0 6.39864 +0 4.40634 1.03376 3.71065 +5.0339 6.58225 0 3.35848 +5.25172 7.05709 0 3.46863 +0 0.423069 2.35038 4.3071 +3.05773 0 4.15568 2.21722 +0 2.67201 3.97975 2.87854 +0 2.09148 1.43156 3.87524 +0 7.41345 7.41345 9.21556 +0 6.74552 7.41017 9.21228 +4.44188 1.09986 3.33187 0 +5.09587 7.18434 0 5.87273 +0.68656 1.74372 0.450052 0 +>MA1715.1 ZNF707 lnR0: 3.1 +5.13479 0 4.73232 3.41108 +5.27216 0 4.99771 5.4737 +6.87304 0 6.7279 5.77697 +5.11153 0 6.79221 4.48764 +0 6.9377 5.36825 5.30897 +7.25042 0 7.46022 5.54482 +7.49575 5.98559 7.96601 0 +7.80895 0 6.03833 1.85879 +6.8339 0 6.68876 4.69748 +5.8129 3.09231 6.86239 0 +5.06279 5.95514 0 4.40807 +4.68018 6.00003 0 6.2012 +4.55739 3.37914 3.51749 0 +0 2.00337 3.5342 2.91486 +3.08659 0 2.72183 3.79204 +>MA1716.1 ZNF76 lnR0: 6.604 +0.800149 0 0.665191 1.17521 +1.07552 0 0.938806 0.54323 +1.49003 0.825152 1.51741 0 +0 1.45048 2.4557 0.39767 +5.94787 0 10.9281 8.66821 +10.4626 0 9.94268 11.4528 +10.4633 0 9.94335 9.88407 +0 6.53409 3.52818 7.37281 +3.71813 0 1.3676 0.795198 +0 1.63201 2.53002 7.40546 +0 4.20731 3.45488 6.68876 +5.82575 5.01172 3.94078 0 +4.08724 2.93923 0 4.57318 +9.88271 0 8.95179 11.4522 +0 1.9284 4.92318 2.65401 +1.3054 0 2.32931 1.08765 +2.51201 0 4.54653 0.800909 +2.29371 5.06845 0 2.93489 +7.06921 0 3.45645 4.61542 +2.38915 2.94107 0 3.30212 +1.5212 0 1.22358 1.82737 +>MA1717.1 ZNF784 lnR0: 0.764 +1.83607 1.05268 0 3.48316 +1.87056 1.02585 0.987002 0 +0 9.24898 12.0289 12.5488 +8.36042 0 12.5488 6.99947 +6.37824 0 5.74395 1.50426 +4.93063 4.26017 5.49355 0 +0 6.90954 6.65571 8.06953 +7.79893 0 9.12324 6.17116 +6.05068 0 3.51913 5.86386 +3.30491 3.06442 0 1.95906 +1.43009 0 1.28133 0.728998 +>MA1718.1 ZNF8 lnR0: 6.02 +3.12013 5.41012 0 3.61877 +2.92159 2.01809 4.66331 0 +0 3.19252 1.67809 4.3801 +5.36467 4.4459 5.59071 0 +1.71483 7.9501 0 5.24322 +5.79995 4.54443 0 2.24765 +0 5.02401 4.08983 6.77282 +7.41668 2.25931 7.27153 0 +0 5.81903 0.730719 5.59631 +5.64683 7.16562 5.95519 0 +0 9.68916 3.58959 7.90991 +9.0118 0 10.2815 8.02159 +6.1124 0 7.27624 7.55069 +0 7.03804 4.42447 6.94259 +5.52076 0 4.83968 3.23442 +0 4.86736 3.62095 5.02829 +1.60429 3.69146 0.382879 0 +4.28085 3.86298 3.41287 0 +3.88486 3.3263 3.04222 0 +3.8266 3.67497 3.09974 0 +>MA1719.1 ZNF816 lnR0: 4.852 +0 0.522653 -0.33877 0.815369 +0 0.984103 -0.0578895 1.29899 +0 0.713223 -0.215489 1.84488 +1.81044 2.60866 0.429586 0 +5.44709 7.57899 0 6.73392 +7.01037 7.13611 0 8.13674 +7.46807 7.13887 0 7.87904 +6.45702 6.2337 0 7.63799 +0 7.42113 5.97599 7.94108 +6.13123 0 6.12082 7.63098 +0 1.90636 2.57779 4.40673 +4.03867 2.68565 2.30829 0 +5.08124 5.03465 0 5.04507 +2.6605 0 3.47054 1.7842 +0 0.411519 0.678765 0.600558 +1.55289 2.22803 0 1.89794 +2.78639 2.98041 0 3.63181 +2.92534 2.40539 0 3.01829 +>MA1720.1 ZNF85 lnR0: 3.684 +0 0.550388 0.075612 0.877863 +0 -0.0444849 0.673185 0.895568 +0 0.997065 -0.0499171 0.546242 +1.58595 2.27338 0 3.68072 +0 6.02708 2.21676 4.43046 +7.29095 6.51054 0 7.29095 +0 6.98579 5.99558 6.77599 +6.49548 6.96574 4.87097 0 +6.09456 5.98559 6.56482 0 +0 0.996383 2.65178 4.99501 +8.03808 0 7.10715 8.61732 +0 3.77741 2.97796 0.553023 +3.90002 3.77471 0 0.95423 +5.85686 0 5.13248 5.65243 +0 3.13165 2.97706 2.8119 +2.22267 1.09208 0 1.22296 +>MA1721.1 ZNF93 lnR0: 3.684 +2.18388 2.39776 0 3.86767 +3.88677 2.95991 0 4.38706 +3.73608 0 2.37913 0.769998 +0 2.48243 0.601715 3.9145 +5.05618 3.65366 0 1.5315 +6.33128 0 6.56571 5.94805 +0.851784 3.72777 0 5.72785 +7.39328 6.37133 0 8.17405 +7.02549 0 5.67247 6.12748 +0 3.537 0.989665 4.79161 +6.69025 6.72667 0 8.17038 +7.29407 0 6.01608 6.1356 +2.88465 3.64671 0 4.29565 +5.34981 3.95155 0 6.28249 +2.05746 0 2.35988 1.17955 +1.98488 2.64155 0 3.23278 +>MA1722.1 ZSCAN31 lnR0: 5.436 +3.05866 5.76378 0 2.50991 +7.46976 0 5.40811 2.81323 +0 1.55714 8.40007 10.285 +10.6978 11.168 12.1582 0 +0 10.501 11.0803 1.99731 +0 9.37736 6.06769 12.6772 +7.81793 0 10.5512 1.44481 +7.09742 8.40075 2.13922 0 +9.63401 6.38614 0 6.73979 +9.90733 0 9.38738 8.71746 +7.53702 0 8.79306 5.072 +8.37264 0 5.78857 7.11379 +7.4495 3.43396 7.41776 0 +8.71786 12.6772 0 9.77157 +8.3809 0 10.691 6.34019 +1.7202 4.54758 0 1.22095 +0.903766 0.947998 -0.50842 0 +3.7948 0 3.75508 3.17239 +1.33357 0 1.25298 1.72061 +>MA1723.1 PRDM9 lnR0: 8.356 +0.964379 3.54976 0 1.94109 +2.72642 4.55114 0 3.21159 +0.702005 4.51734 -0.249372 0 +5.04119 8.0698 0 4.50224 +4.55647 8.12404 0 8.64399 +2.35124 1.50073 0 1.69256 +0.852263 0 0.823606 2.31258 +0 5.43868 1.38044 5.95863 +2.21995 1.356 0 2.7851 +3.25385 6.09719 0 6.61714 +5.45386 8.11067 0 5.08206 +0 1.76662 -0.139828 1.92339 +8.72167 8.20172 0 8.72167 +6.02345 8.17629 0 8.69624 +0 -0.247866 0.261111 1.20505 +0 0.624261 0.00727495 1.37188 +0.76706 7.04268 0 1.74504 +1.18495 0 1.94853 1.55932 +0 7.34194 1.66476 4.01858 +1.35765 2.77585 0 4.75829 +0 -0.362654 -0.138023 1.61762 +0 1.81188 0.84126 3.3917 +0.717931 1.32304 0 2.80517 +1.39985 1.9014 0 2.23512 +>MA1631.1 ASCL1(MA1631.1) lnR0: 1.932 +1.30095 0 0.491022 1.19735 +0 -0.35899 -0.462816 0.0236505 +2.17382 1.46651 0 2.99243 +7.9497 0 6.63804 7.30752 +0 5.26328 4.65894 5.6503 +7.96957 0 3.20082 5.67736 +7.85309 0 5.72318 8.22355 +6.40868 4.89272 5.47485 0 +7.50172 6.16622 0 7.51311 +6.6317 0 3.37329 4.07503 +2.49399 0 2.56622 1.49807 +1.08974 0 0.23737 0.955862 +1.51625 0 0.51651 1.09295 +>MA1632.1 ATF2 lnR0: 1.932 +0 0.369603 0.229194 0.2777 +0 0.367559 -0.50247 0.789753 +0 3.39025 2.41419 5.02761 +6.73448 5.4226 6.86022 0 +6.02746 7.01022 0 4.94456 +0 6.59455 7.18281 5.82946 +4.93967 0.44713 0 0.869794 +5.84725 5.94415 0 8.20625 +5.84889 6.91778 7.07482 0 +4.09649 0 6.29973 6.339 +0 7.44777 5.65345 6.76009 +3.5866 0.826373 2.05911 0 +0.414276 -0.305954 0.139891 0 +>MA1634.1 BATF lnR0: 0.764 +0.256308 0.963283 -0.0277978 0 +0 0.804688 0.854156 1.69836 +6.50268 6.42152 6.74431 0 +5.6245 6.09225 0 3.60605 +0 6.92261 6.48067 6.54038 +4.66436 0 2.71685 4.66436 +5.25386 6.59678 5.16395 0 +3.57593 0 5.76505 5.45044 +0 6.12721 5.8957 5.8496 +1.39398 0.979531 0.627428 0 +0 -0.102352 0.912855 0.319773 +>MA1635.1 BHLHE22(MA1635.1) lnR0: 0.18 +1.04716 0 0.334618 0.869095 +1.21949 0.50298 0 2.74877 +14.5434 0 10.4736 10.6747 +0 8.30194 7.82664 14.0184 +13.5498 8.32153 0 10.6714 +10.6714 0 8.32153 13.5498 +14.0184 7.82664 8.30194 0 +10.6744 10.0623 0 14.5431 +2.74917 0 0.502814 1.22117 +0.87141 0.335635 0 1.04818 +>MA1636.1 CEBPG(MA1636.1) lnR0: 3.1 +0 0.131901 -0.0466509 0.422555 +0 0.778947 -0.322443 0.0998768 +0 2.5246 1.24456 5.09384 +6.76906 6.59729 6.30388 0 +5.96992 6.34798 0 2.73343 +0 5.46886 3.08006 3.70751 +3.87639 2.97527 4.26599 0 +6.57275 7.31609 0 6.98828 +3.2169 0 6.47851 3.44208 +0 5.38152 7.52531 6.75842 +0 6.9738 6.31263 6.46681 +4.70687 2.06998 3.11461 0 +0.735683 0 1.88406 2.01708 +0 0.353616 0.752422 0.122465 +0.607268 0.0663215 0.652255 0 +>MA1637.1 EBF3 lnR0: 1.932 +0.863151 -0.0856172 -0.326502 0 +2.02099 0.272589 1.2418 0 +7.05244 0 5.82103 7.29227 +6.2185 0 6.24096 5.27955 +6.42431 0 5.95616 6.23038 +0 1.51351 2.8393 2.95725 +0 3.23346 1.69665 3.27131 +5.82728 6.28102 0 8.17148 +5.02048 6.41449 0 6.28875 +5.63898 5.26122 0 5.93292 +0 2.64341 2.51872 3.35009 +0 -0.413515 -0.335497 0.874063 +0.148808 -0.318752 -0.0563132 0 +>MA1638.1 HAND2 lnR0: 0.18 +0 0.336757 -0.0826639 0.504491 +0.871046 0 0.685027 2.34196 +10.9704 0 7.74386 9.16048 +0 5.57165 4.92122 12.3904 +11.5897 9.36082 0 8.89056 +0 9.31059 8.98263 10.1962 +10.758 3.06294 9.15562 0 +7.44055 7.56196 0 9.65136 +1.27934 0.205197 0 0.582437 +1.24292 0 0.736237 0.910034 +>MA1639.1 MEIS1(MA1639.1) lnR0: 1.932 +0.579739 0.412226 0 0.78026 +0.191142 -0.414288 0.947989 0 +2.73335 0 4.58967 2.67286 +0 6.10064 4.29788 6.34866 +6.26554 5.95409 5.69363 0 +1.15491 0 3.78573 3.04843 +0 3.60868 6.88543 4.27116 +0 4.26224 4.41645 4.75586 +5.60193 5.61726 6.07219 0 +5.80966 0 6.61701 5.84653 +0 3.71668 4.58004 2.61214 +0.557121 0.241158 0.92116 0 +0.137336 -0.105739 0.181447 0 +>MA1640.1 MEIS2(MA1640.1) lnR0: 3.1 +0 0.378752 -0.414029 0.34412 +0 0.146793 -0.0637972 0.361461 +0 1.52913 0.816269 1.30468 +1.87329 4.3741 2.81076 0 +4.03552 5.78041 0 4.50063 +0 5.95652 5.84429 5.60807 +4.97917 5.5494 4.66384 0 +4.68831 5.97009 5.50875 0 +3.28306 4.22662 2.61453 0 +0 6.17777 4.71378 6.86799 +5.20405 3.54548 4.60228 0 +2.79089 3.52597 0 2.33912 +1.02377 2.32557 0 1.34453 +1.26011 0 0.635897 0.737539 +0.615044 -0.106868 0.529562 0 +>MA1641.1 MYF5 lnR0: 1.348 +0.789292 0.268283 0 0.867619 +0 -0.29027 -0.364359 1.1458 +0 1.90808 1.53705 3.65736 +7.28177 0 6.01432 8.39628 +0 7.23913 6.70013 6.33574 +7.17572 5.47392 0 6.04422 +6.03769 0 5.47378 7.17559 +6.33587 6.72082 7.23926 0 +8.42925 6.01445 0 7.2819 +3.65717 1.53606 1.90789 0 +1.1458 -0.364813 -0.289791 0 +0.867619 0 0.267755 0.789821 +>MA1642.1 NEUROG2(MA1642.1) lnR0: 1.932 +0.83217 0.550853 0 1.03588 +0.680472 0.559338 0 0.790208 +0 0.373638 -0.399832 1.34307 +0 0.482383 0.502672 3.20011 +7.36263 0 6.65577 7.58969 +0 6.72189 6.21641 7.64386 +6.70282 5.20698 0 3.92294 +0 4.53284 5.70676 6.82309 +5.58931 4.59655 6.06397 0 +7.34659 7.27018 0 6.56688 +4.51638 3.04469 0 2.84649 +1.16112 0 0.457227 0.624515 +0 -0.453529 -0.401195 0.393722 +>MA1643.1 NFIB lnR0: 6.604 +0.395674 0.0313579 -0.0803174 0 +0.654789 0.622783 0 0.758799 +3.26925 0 2.44199 2.88542 +4.00539 0 3.97868 2.45871 +4.8877 7.01535 4.08788 0 +9.94184 8.43168 0 8.95163 +8.44851 8.31179 0 8.44851 +5.29794 0 7.16619 8.24009 +0 2.06647 3.6141 2.51934 +2.2706 0.341042 1.29923 0 +0.348918 0.280787 -0.250205 0 +2.74423 2.38148 0 3.08417 +2.11436 3.52287 2.22334 0 +8.56693 6.96457 0 5.00915 +8.4436 0 7.43102 8.14173 +9.36033 0 8.4294 8.53838 +0 2.84315 6.14792 5.73678 +0 3.64495 0.966885 3.78063 +2.92132 2.63978 0 3.28404 +0.0449694 0 0.444058 0 +0 -0.0949842 -0.050717 0.376582 +>MA1644.1 NFYC lnR0: 0.764 +0 0.760396 -0.362531 1.61422 +0.713088 1.49704 0 1.48289 +5.90733 0 4.93605 5.33805 +5.54954 0 6.77859 6.17449 +0 4.72077 6.35292 4.90279 +0 4.46087 3.92133 4.98842 +5.57901 4.53585 6.89337 0 +4.87335 0 2.90898 5.29418 +0 3.49442 3.17244 5.90913 +1.96653 0.679499 0 2.25225 +0 0.154464 0.46037 0.986906 +>MA1645.1 NKX2-2 lnR0: 2.516 +0.0512493 -0.469933 0.0299586 0 +0 0.219898 0.433752 0.635102 +0 -0.131511 -0.317056 0.0917802 +3.54242 0 3.11003 4.73153 +5.76546 0 7.03401 5.24832 +0 5.10207 5.94053 3.89346 +6.15226 0 5.81669 6.29649 +5.60233 5.19745 5.80536 0 +6.37968 0 4.79436 5.51117 +0 2.3944 4.62716 3.94691 +0 2.69664 2.59073 3.56364 +0.654039 0.193612 0 1.14538 +0 -0.0987367 -0.00228583 0.28272 +0 -0.280987 -0.229741 0.23487 +>MA1646.1 OSR2 lnR0: 1.348 +0 -0.237564 -0.0735615 0.345337 +0 -0.507105 -0.0273807 0.336981 +0 1.40023 1.46871 2.10599 +6.23582 0 5.04794 6.49965 +0 5.52228 3.64274 5.56775 +6.49365 5.89059 0 6.94694 +0 3.49258 3.13853 2.90641 +0 4.99522 4.16434 5.56037 +5.53782 6.29133 0 6.32109 +4.66137 0 3.80858 3.83075 +0 -0.483006 0.423176 0.174339 +0.741123 0.51122 0 1.3037 +>MA1647.1 PRDM4 lnR0: 0.764 +0.882892 1.12257 0 1.2242 +0.0562448 0.537742 -0.490046 0 +5.00341 0 4.31632 5.85838 +2.66054 3.71003 2.73735 0 +5.01017 5.88172 0 7.85974 +5.48659 5.06658 5.79289 0 +5.15823 3.39463 3.43749 0 +5.06904 5.04 5.34854 0 +4.20409 0 5.55615 4.91519 +0.483667 0.494082 1.48724 0 +0 0.224264 0.411168 0.514843 +>MA1648.1 TCF12(MA1648.1) lnR0: 0.764 +1.08975 0 0.188467 1.1504 +0.839959 0.076354 0 1.28195 +6.38114 0 5.55201 5.40898 +0 4.14326 2.67604 4.87279 +6.68072 0 3.84025 5.45666 +5.33705 0 3.93984 6.85159 +5.23702 3.23875 3.799 0 +4.78743 4.69613 0 6.20151 +6.12321 0 4.52721 4.49262 +0.860725 0 0.297552 0.64629 +1.32545 0.142617 0 1.22471 +>MA1649.1 ZBTB12 lnR0: 0.764 +0 -0.00230674 -0.455072 0.712615 +1.31542 -0.0300295 0.736017 0 +5.38797 0 4.59123 6.38807 +4.96462 3.72367 3.90599 0 +1.11717 5.18942 0 6.08225 +6.1503 5.73244 0 5.64406 +0 4.71084 4.81384 5.88004 +0 5.51459 4.86496 5.56006 +6.89602 0 6.40381 5.32658 +0.948312 0 1.45234 1.34536 +1.13432 0 0.572024 0.672395 +>MA1650.1 ZBTB14 lnR0: 1.348 +2.14421 0 0.0919839 2.24796 +2.47525 0 0.339195 2.42492 +3.87825 0 2.49471 6.03974 +7.13005 0 4.73555 6.62052 +5.9131 3.75932 0 6.48476 +6.34781 0 3.63612 6.0839 +5.39801 3.68772 0 6.35635 +6.65534 0 3.9564 6.75929 +0 6.30072 8.07171 12.0172 +5.66872 0 2.47038 5.36142 +1.25029 0 0.155524 2.17297 +2.84851 0 0.858137 2.39857 +>MA1651.1 ZFP42 lnR0: 6.604 +0.962513 0.0969393 0 0.798128 +0.0371883 -0.371813 -0.344405 0 +0.449164 -0.0601909 -0.0170066 0 +1.26637 0 1.00106 1.3297 +2.09228 0 2.29488 2.57729 +0 5.03271 3.76768 5.51001 +0 4.25327 3.90875 4.29255 +0 1.79329 -0.232696 2.90576 +0 7.15654 6.35709 7.50823 +7.8689 6.35874 7.15819 0 +8.62142 8.10147 0 10.1909 +6.38268 5.6583 0 4.13952 +6.19852 0 7.65899 7.5997 +4.83653 2.88662 1.42273 0 +4.38515 2.11796 0 3.54928 +3.93725 0 4.0842 3.48437 +3.1867 0 2.49753 2.2532 +0.311925 -0.33858 0.00537058 0 +1.79003 0 0.611365 1.17917 +1.1338 0 0.328944 1.09539 +0.710306 0.311722 0 0.842267 +>MA1652.1 ZKSCAN5 lnR0: 2.516 +0.931745 0.858755 0 1.32587 +1.05631 0.757444 0 1.49592 +0 1.71546 0.384933 1.09513 +4.98144 6.58433 0 6.39309 +6.83258 6.786 0 7.3579 +0 5.09115 5.47963 7.25025 +0.853851 5.96968 0 6.48963 +5.55218 6.31082 0 6.43871 +5.33262 4.58146 4.75589 0 +6.66686 6.9545 0 8.78344 +0 5.67039 5.09115 6.87544 +2.93232 2.4315 0 2.3916 +0 0.796372 -0.288244 1.39482 +0 0.507368 -0.369436 1.10986 +>MA1653.1 ZNF148 lnR0: 1.348 +2.21749 0 1.02483 1.14452 +2.18625 0 0.332217 1.12065 +7.47489 0 5.65632 7.02153 +6.74698 0 4.41756 6.15705 +6.7224 0 4.66464 6.7224 +7.36371 0 5.6198 7.78531 +6.16656 8.77488 2.75685 0 +7.80118 0 6.53452 7.78001 +5.28587 0 4.38459 4.88913 +4.86635 0 4.51748 3.58932 +3.5852 0 1.89242 3.09828 +3.56878 0 1.76725 3.08544 +>MA1654.1 ZNF16 lnR0: 7.772 +0 2.30576 2.94041 4.93609 +0 0.176094 0.144417 3.9413 +3.52783 2.30759 1.62504 0 +0 3.99612 -0.344102 1.17982 +5.95804 7.99775 0 7.52749 +6.41408 7.25915 0 6.30821 +9.11794 6.16264 0 9.11794 +0 9.08724 8.09703 9.60719 +6.32935 8.58927 0 8.11901 +7.08981 0 7.24129 5.25002 +6.54973 0 9.45534 3.78853 +0 4.90218 5.36707 7.25203 +4.18265 1.23548 3.6627 0 +1.90273 3.97728 0 1.5874 +5.44032 5.47131 0 6.48884 +0 2.17167 2.12631 4.04745 +0 4.29866 0.748792 2.72384 +3.89622 7.08377 0 4.23107 +3.50244 6.44015 0 6.26652 +3.13889 1.20886 2.28124 0 +4.16238 2.86165 1.58819 0 +2.51357 -0.0906441 0.883839 0 +3.01967 1.81262 2.00709 0 +>MA1655.1 ZNF341 lnR0: 1.348 +0.9582 0.441601 0 0.911433 +1.29957 1.99816 0 2.26707 +3.67926 2.722 0 3.73936 +0 3.59807 4.48455 6.44895 +0 5.80118 4.37081 6.13206 +6.26215 0 3.98397 5.32495 +0 4.88831 4.66097 6.16808 +7.1867 5.58646 0 6.74645 +6.76138 0 5.99461 6.75513 +2.33018 0 2.23502 2.68082 +0 -0.262826 -0.338469 0.293359 +1.12693 0 0.013489 1.21313 +>MA1656.1 ZNF449 lnR0: 2.516 +1.10024 0 0.786236 1.30345 +0.659497 0 0.269474 1.33052 +0 0.700643 0.963702 3.72922 +0 2.86655 4.22667 3.30784 +6.53951 6.24634 0 6.76629 +6.1266 0 4.41235 6.44538 +7.31098 0 7.94402 8.46397 +7.21407 0 7.01808 7.41373 +0 3.9446 4.65549 4.34183 +0 5.51332 2.44659 5.77773 +5.75954 0 5.37729 7.23197 +2.63551 0 3.37424 2.80502 +0 -0.0559078 0.183988 0.686036 +0.937322 0.0270644 0 1.03643 +>MA1657.1 ZNF652 lnR0: 1.348 +1.51539 0.575588 0 0.757019 +0 0.998909 0.930713 1.71048 +0 4.36784 4.59574 5.36541 +0 6.37395 3.52546 4.74522 +5.82648 4.21847 0 4.83627 +0 5.57147 0.301644 4.2697 +6.52045 6.69608 0 6.80181 +5.68447 5.6621 5.43406 0 +5.53559 4.8271 4.96326 0 +0 5.1841 5.25182 5.51826 +0 2.36823 2.6024 3.2617 +0 0.0458979 0.356022 0.228676 +>MA1683.1 FOXA3 lnR0: 0.764 +0 0.577923 0.00277293 0.973055 +0.20885 1.86942 0.525125 0 +3.66093 4.73843 0 4.44052 +5.88154 5.11183 5.49567 0 +0 3.94724 5.56808 5.25157 +0 2.91813 4.88829 5.40678 +0 4.98863 5.04701 5.49254 +5.84244 0 4.98464 2.93764 +0 5.03313 5.63006 4.58522 +0.0651234 -0.0287182 -0.225836 0 +0 0.066541 -0.0995832 0.189787 +>MA1725.1 ZNF189 lnR0: 1.932 +1.39477 0 0.863484 1.09894 +0 -0.230991 0.338315 0.277468 +3.01844 1.04022 1.3192 0 +3.2895 3.75587 0 2.03042 +6.17066 0 5.73731 6.13165 +5.48189 4.58955 4.58611 0 +5.65182 3.90584 0 5.36715 +5.42027 4.72501 5.29863 0 +6.49983 5.54035 4.92887 0 +6.75626 0 6.33487 6.52043 +6.45755 0 6.73705 5.77789 +0.969973 0 2.38848 1.13002 +1.67658 0.149571 0.189066 0 +>MA1726.1 ZNF331 lnR0: 2.516 +0.971463 0 0.959706 1.41411 +1.46245 0 1.84181 1.86303 +2.34871 0 1.95774 0.871237 +2.46309 3.23358 2.79975 0 +6.88075 6.15637 0 6.88075 +6.41458 0 6.73432 6.7736 +0 4.33067 3.703 1.96891 +6.50517 6.6071 0 7.77275 +0 4.94305 5.20351 6.233 +4.52941 6.423 0 8.5124 +6.32317 0 6.04872 6.40041 +2.84642 0 4.25617 3.54216 +2.51122 0 2.1476 2.33909 +0.049266 0.466805 1.04604 0 +>MA1727.1 ZNF417 lnR0: 3.1 +0.629019 0 0.460683 1.72454 +0 1.26887 0.158499 1.17312 +1.99214 0 0.355895 0.600961 +0 -0.148551 -0.464376 1.09135 +0.573452 -0.434068 0.0956242 0 +1.41581 1.48689 2.28253 0 +1.97002 1.21854 0 2.0212 +9.0759 8.55595 0 9.0759 +9.0759 8.55595 0 9.0759 +7.23993 0 8.46742 4.53425 +9.0759 8.55595 0 9.0759 +9.06729 0 8.54734 7.31985 +5.35135 0 8.49456 6.50423 +0 5.50844 8.01873 8.53868 +0 -0.0921214 0.940258 2.42805 +>MA1728.1 ZNF549 lnR0: 1.348 +0.860189 0.635628 0 1.16551 +0.824819 0 0.0261946 1.28269 +2.82552 2.76864 2.26196 0 +6.40445 4.74573 0 5.87162 +6.95848 0 5.83156 6.33331 +4.18194 4.04427 4.48809 0 +7.74754 5.76023 0 5.36232 +6.74284 0 4.57084 4.71229 +5.84092 0 5.43198 5.02818 +4.96576 0 5.70895 3.73005 +0 0.823823 0.509054 0.383895 +0.712889 1.1649 0 1.84183 +>MA1729.1 ZNF680 lnR0: 3.1 +1.82305 3.5428 0 3.75151 +0.022959 0.246123 0.202489 0 +4.0245 0 5.13316 4.29797 +2.44879 0 5.89096 4.56971 +0 5.88341 4.12418 5.62753 +0 7.37513 1.47795 5.28347 +7.46656 8.48395 0 8.6662 +0 7.29006 6.39204 8.14374 +0 8.00834 4.18111 6.18885 +3.86455 6.90316 0 6.31587 +0 6.48557 6.55527 7.69062 +0 1.77075 4.05065 2.35019 +4.5645 3.08636 3.96916 0 +0.761448 1.26649 0 0.790678 +0 2.40709 2.45029 1.59155 +>MA1730.1 ZNF708 lnR0: 3.1 +1.45413 0 0.550946 1.15008 +1.3686 0 0.444432 1.07704 +1.1337 2.70301 0 2.05395 +5.45845 5.76681 0 5.70752 +7.16165 0 7.31313 8.15186 +6.54448 3.2704 5.85626 0 +6.34846 6.62796 0 8.54909 +5.98522 4.20471 4.73552 0 +0.63212 6.38642 0 6.4257 +7.45884 0 3.90995 5.42011 +7.82107 0 5.9361 7.56061 +6.99157 4.08023 5.2612 0 +1.74913 0 1.35874 2.35756 +2.03648 0 2.80403 2.23096 +2.1449 -0.0744587 1.16384 0 +>MA1731.1 ZNF768 lnR0: 4.852 +2.61191 0.0560562 1.36096 0 +1.52035 0 0.926099 0.790045 +1.36728 0.6665 0 1.5377 +3.34568 0 1.67001 3.1306 +2.24692 0.39674 1.00963 0 +1.88307 -0.462775 0.254532 0 +0 1.10581 -0.483534 1.27882 +1.68079 0 0.826221 3.92283 +5.14344 0 3.57525 2.92873 +4.37346 0 1.85033 2.90447 +4.67198 3.97242 5.73533 0 +9.21047 0 4.92749 5.9763 +7.04198 6.52203 3.85586 0 +9.26556 0 6.36039 9.26556 +8.74561 8.22566 5.84044 0 +9.24515 5.20227 0 9.24515 +0.892224 2.87814 0 0.778718 +2.91502 5.12799 0 1.51628 +>MA0833.2 ATF4 lnR0: 2.516 +0 0.726356 -0.101357 0.759588 +0 0.89835 -0.307253 0.748422 +0 1.31453 1.26858 4.9677 +5.9484 5.79157 6.1649 0 +7.5908 7.27145 0 6.37593 +0 6.61111 5.30475 6.16065 +6.9245 3.69409 5.97757 0 +8.1582 9.21682 0 8.64069 +2.72691 0 7.68551 2.62605 +0 7.00231 8.17132 7.90549 +0 8.25218 7.58831 7.88624 +4.8236 1.40055 2.51652 0 +0 -0.166858 0.883956 1.0358 +0 0.337044 0.417715 0.0820808 +>MA0835.2 BATF3 lnR0: 0.764 +0.316083 1.3158 0.260048 0 +0 1.00753 1.20732 1.68123 +6.40034 7.01754 7.67005 0 +5.87173 7.29778 0 3.56212 +0 6.38328 6.46223 6.57527 +5.16845 0 4.19706 5.16845 +5.37054 6.57767 6.02245 0 +3.54059 0 6.79416 5.66152 +0 6.49442 6.0258 5.55554 +1.27969 1.24286 0.812712 0 +0 0.19889 1.31008 0.383647 +>MA0465.2 CDX2 lnR0: 1.348 +0 0.305269 0.0868776 0.725151 +0 1.65026 -0.111409 0.393873 +3.43 3.49495 0 3.7299 +4.91408 0 5.3972 3.37364 +0 2.46233 6.58412 3.8451 +0 5.5933 4.08002 5.96618 +6.74885 5.72249 5.74083 0 +0 4.68966 4.30137 4.75707 +0 5.86908 5.80133 5.46781 +0 5.0842 5.32655 5.17472 +0 0.842264 0.692693 0.946128 +0 0.0373283 0.25379 0.180851 +>MA0102.4 CEBPA lnR0: 2.516 +0.0185021 0.187501 0.0920783 0 +0.679015 0.620981 -0.0208416 0 +0 2.3516 1.54944 3.53645 +6.3967 5.94916 6.14115 0 +6.17031 7.45793 4.42435 0 +3.13933 5.89083 0 2.90151 +6.49175 0 6.72327 5.6619 +0 3.58109 2.65703 3.27393 +3.82286 0 5.22817 3.1464 +0 3.11261 7.12489 5.98084 +0 5.60213 5.18909 5.67836 +3.4658 1.11869 2.25438 0 +0 0.162618 0.586211 0.439486 +0.155756 -0.030567 0.0643215 0 +>MA0836.2 CEBPD lnR0: 1.932 +0.485412 0.468472 -0.150302 0 +0 0.895948 0.229685 1.97777 +6.55464 5.5415 6.10405 0 +6.64443 7.39819 5.90019 0 +3.70054 5.79322 0 3.61881 +6.75019 0 6.52354 6.6013 +0 3.40617 2.05943 3.09374 +4.18523 0 5.47531 3.42995 +0 4.40662 7.47926 6.72062 +0 5.43194 5.07744 5.76566 +2.20949 0.112413 1.11916 0 +0 -0.0180775 0.492016 0.407446 +0.169707 -0.238532 1.65842e-05 0 +>MA0018.4 CREB1 lnR0: 1.932 +0.208088 -0.0514027 0.142129 0 +0.0802128 0.0425093 -0.440821 0 +0 0.601196 -0.480866 1.47831 +5.25244 5.70046 5.50934 0 +5.85826 4.93126 0 5.08826 +0 4.82051 4.61968 4.9617 +4.65478 1.46792 2.61433 0 +6.17743 5.24248 0 5.81149 +2.91112 5.21443 5.24254 0 +4.82566 0 4.99718 5.74798 +0 5.63654 5.37584 5.61753 +1.65958 0.0811582 0.619838 0 +0 -0.480536 0.203715 0.0555698 +>MA1102.2 CTCFL lnR0: 1.348 +0 -0.0459788 -0.256546 0.86089 +1.92147 0.0123354 0 2.99802 +3.79258 0 2.63534 3.30082 +0 4.80993 5.13389 9.28384 +8.07958 5.11387 0 6.9941 +5.06627 4.73321 0 6.54678 +5.92835 3.71896 0 4.26288 +6.8949 4.40933 0 6.48209 +6.05917 5.91281 0 5.82052 +7.05039 0 7.91601 6.94452 +1.66683 1.60869 0 3.07225 +2.62387 0 0.282366 2.31545 +>MA0471.2 E2F6 lnR0: 1.932 +1.2727 0.60784 0 1.71075 +0.990605 0.647165 0 1.5497 +0.794988 1.16855 0 1.25792 +4.28199 4.63099 0 6.47744 +7.34808 5.19417 0 7.71861 +3.26912 0 5.19942 4.12005 +5.17671 5.76619 0 5.69987 +7.01521 6.13905 0 6.95335 +6.93319 5.19136 0 7.18803 +0 4.0803 3.10294 6.70275 +0 3.45148 1.81387 5.03511 +0.993416 0.750343 0 2.09385 +1.09675 0.423807 0 1.53594 +>MA0154.4 EBF1 lnR0: 3.1 +0 0.14852 -0.145003 0.29648 +0.759081 0.491844 0 0.812167 +3.77567 2.32723 2.0433 0 +5.18654 0 4.13273 2.70308 +6.70714 0 6.79431 5.60471 +6.4961 0 6.51845 5.0604 +4.4465 0 5.4687 4.55757 +0 3.78397 3.77065 2.23846 +3.95276 5.51594 0 4.50373 +4.47272 6.32933 0 6.43471 +5.29171 6.48795 0 6.46462 +2.38861 3.69698 0 5.07908 +0 1.7728 2.12766 3.63839 +0.761629 0 0.428119 0.785618 +0.181217 -0.204579 0.0334106 0 +>MA0162.4 EGR1 lnR0: 2.516 +1.22502 0 0.802222 1.64543 +2.38488 0 1.02214 2.17152 +0 -0.0310406 1.37348 2.87883 +5.93158 0 5.17846 5.62306 +2.62053 4.25402 0 3.87697 +7.45899 0 5.40769 6.7712 +4.72331 0 4.18857 6.61625 +6.97861 0 5.31998 5.99067 +0 1.50036 2.83957 4.82705 +8.02776 0 5.34477 7.39392 +2.62808 2.84357 0 3.49902 +5.17307 0 3.51078 3.95405 +0.747573 0 0.711445 1.5979 +2.34683 0 0.793644 1.88829 +>MA0598.3 EHF lnR0: 3.1 +0.928952 0 0.0808809 0.761713 +0.785415 -0.503077 -0.043661 0 +2.57088 0 2.50324 2.15585 +0 4.30783 3.55144 4.17048 +6.72833 0 5.06681 3.43305 +5.04461 5.8606 5.99421 0 +6.65439 5.90989 5.63507 0 +6.70075 0 6.66148 6.65768 +7.01533 0 7.12957 7.50321 +4.8505 3.83004 2.50565 0 +4.18637 1.58689 0 2.28724 +1.52306 0.619218 0.497275 0 +2.14585 1.97308 2.44729 0 +0.73834 0.0294077 0.276392 0 +1.16083 0 0.590371 0.698341 +>MA0473.3 ELF1 lnR0: 2.516 +0 0.58346 0.167898 1.0549 +0 0.718895 0.194991 0.892584 +0 -0.0667766 0.213026 1.26551 +4.09966 0 2.94687 4.77063 +0 2.8309 4.92425 5.98939 +7.63257 6.72182 0 7.36177 +6.60394 6.44176 0 6.61055 +0 5.27154 5.50466 6.89157 +0 5.42321 5.28081 5.3843 +3.84748 4.68532 0 7.15956 +3.72259 3.79092 3.78092 0 +3.10549 3.00651 0 3.97743 +0.945492 0.50962 0 1.89844 +0.682854 0.0864343 0 1.00443 +>MA0640.2 ELF3 lnR0: 2.516 +0.245359 -0.387717 -0.0866559 0 +0.462402 -0.475984 -0.329221 0 +2.62033 0 1.81728 1.65701 +2.61439 0 2.73528 1.99638 +0 3.75349 3.39891 3.62877 +6.69894 0 4.89231 3.66721 +5.21757 4.47566 5.29958 0 +6.67062 5.03726 5.02071 0 +6.59144 0 6.29494 6.33386 +7.17053 0 6.56999 7.08392 +5.7801 4.50742 3.91665 0 +4.05896 1.59402 0 2.23437 +1.14387 0.0686148 0 0.704373 +1.08345 0.791738 1.38408 0 +>MA0592.3 ESRRA lnR0: 1.932 +1.29612 0.821949 0 0.944522 +1.8164 0 0.472862 0.775737 +2.71218 0.723518 2.50622 0 +4.96538 0 3.20163 5.1635 +0 5.53562 4.89614 5.87488 +0 5.31675 4.86682 6.46485 +6.14532 6.11678 0 6.08998 +7.27455 7.35633 0 6.88122 +4.51429 5.38231 4.07332 0 +6.80825 0 4.88166 5.16618 +0 6.17654 4.40953 6.11516 +1.23638 0 1.02645 0.928791 +0 0.211998 0.135822 0.836421 +>MA0761.2 ETV1 lnR0: 2.516 +0 0.229706 -0.135401 0.723502 +0 -0.128791 -0.394917 0.704819 +0 1.85001 1.38351 2.42192 +4.59917 0 3.71258 5.52962 +0 2.88818 5.28128 6.32434 +7.74551 6.97747 0 7.15401 +7.03012 6.98408 0 6.44712 +0 5.67709 6.00193 6.56822 +0 5.51879 5.75424 3.40664 +3.37513 4.53392 0 6.31243 +2.9818 2.24579 2.54859 0 +1.76707 1.88741 0 2.31713 +0 0.117327 -0.410945 0.65826 +0 -0.407425 -0.496142 0.184523 +>MA0477.2 FOSL1 lnR0: 1.932 +0.0361588 -0.224324 -0.471244 0 +0.601386 0.607265 0 0.796638 +0 1.84329 0.883232 3.61255 +7.68914 6.35651 7.6686 0 +7.18002 7.42533 0 5.07824 +0 7.02927 7.03424 7.47669 +4.58155 0 2.32675 4.56269 +5.66236 7.8097 5.95914 0 +4.57899 0 7.51454 7.03917 +0 6.76125 6.05151 7.20461 +3.76993 1.33244 1.99642 0 +0.611314 0 0.341539 0.574311 +0.854343 0 0.665969 0.749103 +>MA0148.4 FOXA1 lnR0: 1.348 +0 0.799256 0.525524 0.910104 +0.258789 2.55126 0.82838 0 +4.08086 5.51357 0 5.03145 +4.67468 3.82509 5.00669 0 +0 3.7824 5.24996 5.77263 +0 3.89514 5.70611 4.73504 +0 6.40661 5.8377 6.30355 +5.67451 0 5.77057 3.34948 +0 5.81074 5.99645 5.41018 +2.42013 2.76818 2.52659 0 +0.711382 0.633521 0 0.664127 +0.17701 0.112849 -0.0333158 0 +>MA0047.3 FOXA2 lnR0: 0.764 +0 1.18279 0.286899 1.09842 +0.322037 2.68806 1.07189 0 +4.13829 6.27213 0 6.29602 +6.02959 6.37618 6.48313 0 +0 4.1272 5.9441 5.22624 +0 2.76155 4.53428 4.41004 +0 5.63908 5.88367 4.942 +6.80937 0 5.71572 2.23798 +0 5.73839 5.78639 4.66472 +0.126928 0.206509 0.207893 0 +0 0.144752 0.0670252 0.357984 +>MA1103.2 FOXK2 lnR0: 0.764 +0 0.657129 0.386595 0.781729 +0.346824 0.960369 0.327788 0 +2.73721 4.484 0 4.67485 +5.39687 5.64409 5.01387 0 +0 5.26195 6.15292 5.48592 +0 2.9232 4.47179 4.62222 +0 4.98365 4.74202 5.36001 +5.30883 0 5.01434 3.76533 +0 5.1539 5.93775 4.90788 +0 -0.204272 -0.230913 0.26537 +0.565407 0.399903 0 1.24156 +>MA0481.3 FOXP1 lnR0: 0.764 +0 0.426722 0.170961 0.643781 +0.0323166 1.60554 0.430348 0 +3.00459 5.19081 0 4.73698 +5.83449 6.04036 5.70442 0 +0 4.48404 5.43924 5.1086 +0 3.13016 4.58457 4.61131 +0 4.9822 5.37158 5.03056 +5.97995 0 5.30139 2.99603 +0 4.5968 5.92846 4.20357 +0.0835307 -0.208953 -0.0889244 0 +0 0.33143 0.489919 0.261901 +>MA0062.3 GABPA lnR0: 2.516 +0.610107 0 0.0849509 0.536678 +1.49157 0 0.650294 0.703274 +2.93403 0 2.54111 2.62969 +0 3.15535 2.8691 3.54858 +6.36555 0 4.63518 3.54075 +3.89046 4.78474 5.35904 0 +6.10074 5.0734 4.66883 0 +5.92171 0 5.68051 5.76701 +6.44976 0 6.85265 6.65662 +5.01487 4.65255 3.10393 0 +5.02312 3.00654 0 3.85951 +2.88988 1.21375 1.84453 0 +0.765447 -0.357462 -0.0925423 0 +0.654978 -0.223688 0.170863 0 +>MA0035.4 GATA1 lnR0: 0.764 +0.0779767 0.412722 0.221788 0 +0.731843 0.467497 0.849647 0 +4.4616 0 4.47976 4.98296 +5.66307 6.27362 6.14314 0 +0 5.54712 5.28031 1.25997 +0 5.13136 5.51425 5.02891 +4.89206 5.19686 6.18823 0 +5.1565 0 5.43156 5.62191 +3.0054 3.76254 5.72514 0 +0 0.714516 0.35791 0.423189 +0.116784 0.161266 0.864923 0 +>MA0482.2 GATA4 lnR0: 1.348 +0.552266 0.344323 0.429139 0 +0.665816 0.236382 0.415367 0 +3.75482 0 2.87993 2.21978 +4.47075 0 5.44906 3.89955 +5.07149 4.70035 5.62229 0 +5.01317 4.75143 5.51227 0 +0 4.42829 4.87549 4.99685 +6.15042 6.02975 6.13921 0 +7.32984 0 6.56987 5.78034 +2.62728 4.18179 4.55891 0 +0.590148 -0.464982 -0.3888 0 +0.387351 -0.0591768 0.637103 0 +>MA1104.2 GATA6 lnR0: 1.932 +0.296212 0.231499 0.501709 0 +0.634912 0.668138 0.917344 0 +0 0.871825 1.22903 0.789748 +3.17649 1.6656 2.40185 0 +4.27722 0 3.25215 3.99804 +4.82186 5.12442 6.42106 0 +3.8053 5.12281 6.2895 0 +0 5.97015 5.96317 6.03136 +5.61172 5.90574 6.79728 0 +6.57316 0 6.66871 5.9415 +2.1981 3.68422 4.51036 0 +0.299735 -0.230976 -0.161778 0 +0.317887 0.0981818 0.722727 0 +>MA1105.2 GRHL2 lnR0: 1.348 +0 0.0466183 0.134307 0.762407 +0 0.817378 0.200331 1.49519 +0 4.42064 3.2272 4.44947 +0 5.1243 3.1489 4.82971 +6.78448 0 5.99184 7.42896 +0 3.89822 5.54954 2.52085 +4.20356 5.94046 0 5.37065 +6.40719 5.27362 0 6.44547 +4.25438 3.42588 5.04837 0 +4.35296 3.64398 4.34967 0 +1.29769 0.378041 0.606384 0 +0.646718 0.18261 -0.11942 0 +>MA0043.3 HLF lnR0: 2.516 +0.0239193 -0.072628 -0.223228 0 +0.353061 0.453777 -0.191138 0 +0.674458 1.13242 0 3.28777 +6.26365 6.02556 6.72429 0 +7.08751 7.30904 4.133 0 +0 6.90277 3.52011 6.69297 +6.75679 3.29813 5.88103 0 +3.65457 7.51137 0 7.28898 +6.0048 0 6.36369 1.87698 +0 7.02311 8.33792 7.85316 +0 7.86381 6.39593 7.64563 +3.72941 0 1.98409 1.5385 +0 -0.0520943 0.932558 0.587447 +0 -0.1338 -0.201588 0.0356218 +>MA0114.4 HNF4A(MA0114.4) lnR0: 1.932 +0.611802 0.580397 -0.3725 0 +1.0749 0 0.628926 0.670949 +5.29104 0 5.01549 4.6156 +0 4.53596 4.77792 5.58933 +0 4.30687 2.9214 4.89949 +0 5.72907 3.94654 5.7007 +6.38582 5.51439 0 5.48714 +5.46986 5.36088 3.72656 0 +4.25314 0 4.32824 3.69172 +5.4276 0 5.97977 4.77223 +0 3.16294 3.08599 3.11792 +0 -0.0637533 -0.459769 0.428942 +0 0.224996 -0.140415 0.543869 +>MA0484.2 HNF4G lnR0: 1.932 +0.644138 0.583541 -0.403333 0 +1.14457 0 0.561555 0.672402 +5.71295 0 5.24313 4.70317 +0 4.66923 4.64718 5.73547 +0 4.38184 2.76356 5.12013 +0 6.03085 3.89785 5.67665 +6.82175 5.64929 0 5.661 +5.86592 5.62922 3.76289 0 +4.22014 0 4.37444 3.81012 +5.34002 0 6.12275 4.61584 +0 3.00593 2.88082 3.0336 +0.607882 0.38309 0 0.996501 +0 0.118109 -0.205039 0.522975 +>MA0901.2 HOXB13 lnR0: 2.516 +0 0.994882 0.730592 0.416177 +0 0.505125 0.311128 0.238348 +2.50298 0 2.36637 2.74414 +4.43569 0 6.74108 3.41478 +0 3.29032 6.96572 3.14566 +0 6.06563 4.68274 4.5455 +7.44086 6.53987 6.44946 0 +0 6.54446 5.506 4.35274 +0 6.39652 6.68293 5.48963 +0 6.05845 6.33743 5.86603 +0 4.26461 4.64994 4.04511 +0.640215 0.999064 1.74281 0 +0.0791951 0.54134 0.701263 0 +0.151491 0.533076 0.670236 0 +>MA0490.2 JUNB(MA0490.2) lnR0: 1.932 +0 -0.0668973 -0.195879 0.0266569 +0 0.0502196 -0.314373 0.228017 +0 2.30822 1.74861 3.83382 +7.11305 6.31464 7.32462 0 +7.0547 7.01468 0 4.78357 +0 6.62902 6.55724 6.77039 +4.13616 0 2.48211 4.1233 +5.20883 7.44748 5.80755 0 +4.28582 0 6.82066 6.97544 +0 6.45416 5.8469 6.73976 +3.96522 2.20394 2.44303 0 +0.0677887 -0.289847 -0.0703499 0 +0.120541 -0.366319 0.0840653 0 +>MA0491.2 JUND(MA0491.2) lnR0: 1.932 +0.098869 -0.0506746 -0.235903 0 +0.619642 0.662675 0 0.806365 +0 2.23868 1.23179 3.7675 +7.26268 6.51211 7.2762 0 +6.65018 6.76818 0 5.14381 +0 6.72532 6.90515 6.7419 +4.51635 0 1.86311 4.51143 +5.58233 7.08946 5.89348 0 +4.80405 0 6.62637 6.54824 +0 6.51409 6.15633 6.9279 +4.84701 2.24345 2.84212 0 +0.534231 0 0.341124 0.559584 +0.597842 0 0.624959 0.573144 +>MA0039.4 KLF4 lnR0: 1.348 +0.994247 0 0.295806 1.12332 +1.19861 0.392179 0 1.15791 +4.79638 0 4.90878 4.74238 +4.98226 0 5.24809 3.85564 +3.18652 0 4.94697 5.00225 +5.95928 0 5.99803 6.22169 +0 7.53738 2.24156 3.6851 +6.40177 0 5.10333 6.00003 +5.45259 0 4.72509 5.8571 +5.87411 0 5.60964 4.79192 +0.68445 0 1.52104 0.798877 +1.45891 0 0.410033 1.16677 +>MA1107.2 KLF9 lnR0: 3.684 +1.46865 0 0.99172 1.6843 +0 0.123529 -0.47726 0.769384 +3.05232 1.93709 0 3.95308 +2.43617 0 3.39146 4.13838 +6.87995 0 6.3403 6.85537 +0 2.54645 4.3806 5.66911 +7.26066 0 6.07411 7.889 +0 3.60247 1.60316 4.2449 +7.21258 0 4.99959 7.02819 +3.67554 0 5.13895 6.14904 +7.83915 0 6.83713 5.96198 +0 1.57719 3.90129 3.56619 +5.17624 0 3.50203 3.61463 +0.856989 0 1.4052 0.942337 +1.86239 0 1.23761 1.20199 +1.20926 0 0.737274 1.58882 +>MA0700.2 LHX2 lnR0: 0.764 +0 0.731561 0.383335 0.468456 +0 0.72129 0.325812 0.27453 +2.42576 0 1.68945 2.30397 +7.41449 0 7.13608 3.61968 +0 5.74776 6.18543 3.7449 +0 5.30629 5.68952 5.43643 +5.49388 6.1025 5.96414 0 +6.45993 9.40819 9.40819 0 +0 8.20209 9.1923 7.2223 +0 0.618726 0.0409533 0.324058 +0.0628283 0.0635307 0.435364 0 +>MA0495.3 MAFF lnR0: 3.684 +0 0.573086 -0.413917 0.397051 +0 1.5557 1.26031 0.687947 +3.30679 2.69055 0 4.39287 +5.92293 6.03527 5.88862 0 +4.81767 0 6.65941 6.17412 +0 7.3006 5.7754 5.7301 +6.1942 6.33988 0 4.09069 +6.93252 0 6.37106 6.1681 +0 5.36509 4.47801 4.30627 +1.46513 1.74617 1.71956 0 +1.88268 3.17755 3.30846 0 +2.25431 2.9775 3.6641 0 +1.86418 1.77711 2.80943 0 +0.28517 0.476891 1.05512 0 +0.424984 0.299194 0.473873 0 +0.0513757 0.1583 0.18362 0 +>MA0659.2 MAFG lnR0: 3.1 +1.11744 1.77082 0 1.38702 +0 2.0111 1.93379 1.27211 +3.17814 1.94384 0 3.79819 +6.18271 6.37009 6.11965 0 +5.33179 0 7.19982 6.34056 +0 7.57707 6.30833 5.97056 +6.66628 6.11435 0 4.40422 +7.05753 0 6.62042 6.58262 +0 5.4383 4.37011 4.50499 +1.16086 1.56855 1.41965 0 +1.84763 2.798 2.9566 0 +2.1472 2.86239 3.31979 0 +1.19793 0.297676 1.91853 0 +0.950904 0.384582 1.21536 0 +0.304873 0.250296 0.369004 0 +>MA0496.3 MAFK lnR0: 3.1 +0.665127 0.290692 0.403605 0 +1.69801 1.02942 0 1.70233 +1.44911 0 1.9896 3.26951 +4.82859 4.35168 4.91327 0 +5.86309 5.04434 0 4.66468 +0 4.26147 4.61245 5.16781 +4.45324 0 2.34581 4.42375 +4.06304 4.79449 4.86155 0 +5.19176 0 5.5878 5.92597 +0 5.17842 4.66146 4.59543 +5.40547 4.47306 0 3.8222 +4.50797 0 3.67064 4.72711 +0 0.282946 1.88986 1.58032 +0 0.0438585 0.0741103 0.129511 +0.32618 0.403266 0.593251 0 +>MA0052.4 MEF2A lnR0: 3.1 +0.0665339 0.79388 0.0169385 0 +0.488092 0.998576 -0.186122 0 +2.95563 0 3.40375 2.77471 +4.25275 1.51072 5.12492 0 +0 3.06127 2.98849 2.88829 +0 5.11655 3.8626 2.57332 +0 6.10645 4.28833 4.09383 +0 5.38289 5.3226 3.51068 +0 5.84273 5.62252 4.12729 +5.04996 4.86341 5.55291 0 +0 7.65449 4.63228 7.08941 +2.61232 3.35455 0 3.44513 +0 0.403297 1.72115 1.44191 +0 0.280658 1.23168 0.401746 +0 -0.0617166 0.552794 0.184598 +>MA0620.3 MITF lnR0: 4.852 +0.0746657 -0.219028 -0.215062 0 +0 -0.176991 -0.27946 0.128127 +0 0.328049 0.0138162 0.34108 +0 1.17988 -0.167578 0.734728 +1.42999 2.79236 0 4.59506 +4.41443 2.85661 3.5896 0 +8.48184 0 7.16072 8.66746 +0 5.77267 6.44411 6.27563 +7.69827 0 5.33508 2.2428 +2.24228 5.33496 0 7.69815 +6.27753 6.44413 5.7727 0 +8.66746 7.16072 0 8.48184 +0 3.59011 2.85606 4.41564 +4.59589 0 2.79279 1.43029 +0.735233 -0.167578 1.17889 0 +0.340598 0.013779 0.328036 0 +0.128294 -0.278908 -0.177418 0 +0 -0.214906 -0.219863 0.0743405 +>MA1108.2 MXI1 lnR0: 0.18 +0.647396 0.417084 0 0.796623 +0 -0.438445 -0.495255 0.642035 +8.04834 0 7.69341 6.00131 +0 12.7654 6.41041 11.305 +11.3491 0 10.0483 5.98805 +0 13.6637 3.17582 14.1836 +14.2539 4.8333 13.734 0 +5.7974 7.45483 0 7.36685 +1.85768 0.435356 0 0.637281 +0.875565 0 0.231481 0.758865 +>MA0499.2 MYOD1 lnR0: 1.932 +1.16608 0 0.469749 1.06002 +0 -0.110334 -0.357358 0.0260509 +2.76377 1.94134 0 3.77231 +7.02888 0 6.48866 7.39961 +0 5.212 4.6758 5.7222 +6.23099 0 1.76704 4.84178 +6.38693 0 5.07249 7.07285 +7.02755 5.29886 5.91271 0 +7.77144 6.37136 0 7.57982 +6.14016 2.98126 3.56386 0 +3.88345 0 2.08049 1.59122 +0.666596 0 0.750011 0.879633 +1.55771 0 0.643456 0.846308 +>MA0500.2 MYOG lnR0: 1.348 +0.782381 0 0.187501 0.848441 +0 0.635178 0.0941114 0.83658 +1.10595 1.96292 0 3.17783 +8.42336 0 7.67618 7.36111 +0 6.35539 5.93837 6.98431 +8.28111 7.31709 0 7.46475 +7.48172 0 7.30629 8.28118 +6.98398 5.92604 6.33105 0 +7.36091 7.66205 0 8.3907 +3.18748 0 1.9758 1.09965 +0.852154 0.0984127 0.656883 0 +0.860477 0.16857 0 0.779692 +>MA0056.2 MZF1 lnR0: 1.932 +0.597189 0 0.318619 0.671098 +0 -0.173965 0.155871 0.119593 +0 1.98092 2.005 3.93378 +0 3.50588 3.65009 4.61346 +6.16034 6.54008 5.75141 0 +6.75682 0 6.23687 6.85943 +6.32997 0 7.10334 6.56957 +6.60373 0 6.99944 6.13955 +6.48411 0 6.44968 4.85151 +0 2.74995 3.08221 2.41678 +1.34021 0 0.971338 1.08878 +0.299987 -0.207648 0.274952 0 +0.500105 -0.340727 -0.0287312 0 +>MA0089.2 MAFG::NFE2L1 lnR0: 3.684 +0 0.294496 0.360953 0.745133 +0.775254 0.148855 0 1.63064 +0 -0.304523 -0.105615 0.363343 +0 4.90328 1.33102 7.674 +7.92597 8.51057 9.50078 0 +7.96856 8.60709 0 7.49927 +0 8.77061 7.64424 8.80988 +6.24721 0 2.96714 5.5621 +3.78215 7.29666 5.84156 0 +4.51588 0 6.80686 5.43128 +0 7.70795 4.75529 4.95285 +6.166 7.24035 0 4.001 +8.03851 0 6.52835 7.37762 +0 4.88504 3.75867 3.249 +0 0.862147 0.442237 0.790049 +0.549 2.35467 1.9154 0 +>MA0025.2 NFIL3 lnR0: 1.932 +0.157228 0.336113 -0.182975 0 +0 0.68244 -0.206772 1.67517 +4.54172 4.37121 4.76139 0 +5.40398 6.03869 3.03179 0 +0 6.00981 3.86616 5.56564 +4.89694 3.19278 4.79375 0 +4.29045 5.3968 0 5.53585 +3.6322 0 4.6754 0.903075 +0 4.75571 6.40064 5.59509 +0 5.85914 5.34564 5.47354 +2.55748 0.872278 1.74001 0 +0 -0.0781073 0.35683 0.464087 +0.0422704 -0.0409327 0.094848 0 +>MA0502.2 NFYB lnR0: 1.348 +2.72259 0 1.4057 1.92967 +2.92894 -0.189188 1.38026 0 +5.28444 0 1.85979 4.50833 +0 4.69058 6.32424 4.85151 +5.61024 4.25648 4.34162 0 +6.34803 6.97817 5.55368 0 +7.51982 7.35889 0 6.49047 +7.28144 6.8777 0 7.32679 +5.85486 0 5.16973 3.82909 +5.7004 0 5.32586 2.62004 +0 0.37298 0.40322 1.58555 +0.718699 0.830075 0 1.93985 +>MA0063.2 NKX2-5 lnR0: 0.764 +0 0.222842 -0.489804 0.762439 +0.628023 0 0.317259 1.29852 +6.15292 0 7.56988 4.43444 +0 6.15661 5.51092 6.06846 +5.60576 0 6.60682 5.51973 +5.19628 5.38177 5.7985 0 +4.75401 0 6.03982 2.85599 +0 4.74396 3.90296 4.02015 +0 4.32507 5.06345 4.25435 +0 -0.44191 -0.513205 0.461196 +0 0.0207355 0.225253 0.505745 +>MA1112.2 NR4A1 lnR0: 1.348 +0.516243 0.0811575 -0.256632 0 +0.0184416 -0.179849 -0.104546 0 +0 5.33853 3.55837 4.64032 +0 6.42704 4.94068 6.12353 +0 7.36194 6.33812 8.10211 +5.33302 6.99382 0 2.56319 +6.10046 6.42211 0 5.38119 +5.14137 3.46035 2.74732 0 +8.1625 0 6.55512 4.77964 +0 6.05199 4.94454 5.49955 +0 -0.361113 -0.392294 0.382519 +0 0.11021 -0.0936268 0.60454 +>MA0679.2 ONECUT1 lnR0: 3.684 +0 0.871303 0.635037 0.92539 +0 1.25857 0.677947 1.12605 +0 1.2881 1.10226 1.08902 +0 1.78479 2.07892 1.8225 +0 5.11168 2.19517 5.30834 +0 6.79297 5.10887 6.39829 +6.91705 7.10144 7.38435 0 +5.94886 0 7.67702 7.6263 +0 6.49554 5.02722 5.89624 +0 7.3416 6.78169 6.30561 +8.0084 6.83531 7.95529 0 +0 3.25594 2.44894 3.50492 +0 1.07171 1.47881 1.20698 +0 0.738719 1.11219 0.420242 +0.289628 0.612653 0.648857 0 +0 0.223217 0.302675 0.0509216 +>MA0712.2 OTX2 lnR0: 1.348 +0 0.271178 0.41369 0.425332 +0 0.644983 -0.223449 0.272687 +1.10126 3.35715 0 1.82491 +4.83874 7.00705 0 5.85066 +5.75364 6.07397 0 6.09411 +0 5.13602 6.77128 6.37461 +7.20248 7.03385 6.64208 0 +5.85835 5.44852 5.77701 0 +0 6.90029 5.87793 4.8157 +1.27899 2.06705 0 1.57897 +0 0.117262 0.0263608 0.489986 +0 0.276132 -0.250377 0.0720092 +>MA1113.2 PBX2 lnR0: 1.932 +0.720709 0.708051 0 1.25704 +0.173982 -0.437866 1.08651 0 +2.49616 0 3.59523 3.00827 +0 4.82824 3.40094 5.33017 +6.90852 5.02016 5.90069 0 +0 2.8727 4.32891 3.47101 +0 4.9919 5.72579 4.20535 +0 4.60356 5.00511 4.70076 +5.26541 5.37418 5.83858 0 +3.86451 0 5.37237 3.55759 +0 4.36535 5.61906 3.37016 +0.722173 0.18921 1.01733 0 +0.192928 -0.17224 0.170574 0 +>MA0681.2 PHOX2B lnR0: 3.684 +0.0531922 0.863666 0.702683 0 +0.0412764 0.973264 1.03381 0 +1.84369 3.21697 3.32825 0 +0 3.89934 3.65944 2.72983 +0 6.10246 6.06837 5.6322 +4.80663 5.77256 6.1651 0 +4.38237 0 4.24646 2.07921 +0 3.94176 5.61187 2.46332 +0 4.4919 4.52671 4.69426 +0 6.22223 5.47614 5.17907 +5.75003 6.69787 6.52289 0 +3.45175 4.01402 4.64967 0 +0 3.90438 3.75136 2.74469 +0.722059 1.89763 1.71745 0 +0 0.765695 0.882474 0.261428 +0.12502 0.917214 0.998529 0 +>MA0782.2 PKNOX1 lnR0: 3.1 +0.169878 -0.30451 -0.318868 0 +0.0152553 -0.445338 -0.402105 0 +2.48753 3.63465 2.61358 0 +4.92379 4.91029 0 5.58199 +0 5.18226 4.22073 4.89227 +3.97847 2.64041 0 2.33794 +4.96689 4.81962 4.59592 0 +6.54426 5.17863 0 6.23167 +0 5.8844 3.32822 5.60143 +6.32175 0 5.96651 5.88204 +0 4.59781 3.26098 3.65554 +3.80456 2.49875 0 2.9221 +1.46169 0 0.831832 1.94115 +0.57636 -0.0656947 -0.0152001 0 +0 -0.338682 -0.488935 0.0903618 +>MA0627.2 POU2F3 lnR0: 1.932 +0 0.0861371 0.171591 0.0736219 +0 1.42663 1.06827 0.943248 +2.12011 1.90484 3.07759 0 +0 7.52847 6.67258 5.81366 +5.55728 6.77619 4.84069 0 +6.19122 7.6129 0 4.67872 +6.19458 0 5.48689 4.24119 +0 8.79306 8.0216 5.87786 +0 5.91568 5.41751 3.93197 +0 7.78667 7.28757 7.31209 +3.0524 3.08335 2.84906 0 +0 0.0943544 -0.223667 0.0336317 +0 0.13711 0.719221 0.131436 +>MA0508.3 PRDM1 lnR0: 0.764 +1.33397 -0.197469 1.21056 0 +0.00987601 -0.0336076 0.448509 0 +5.92466 0 6.17063 6.45131 +5.3122 6.23405 5.42072 0 +4.50069 4.66983 5.07833 0 +4.8108 6.16361 5.96483 0 +5.74625 0 7.92752 7.40004 +3.76337 4.94737 4.58188 0 +5.41974 0 7.43051 6.77842 +1.36163 0.478606 2.18856 0 +0.970963 -0.332242 0.812393 0 +>MA0684.2 RUNX3 lnR0: 1.348 +0 -0.170695 -0.305485 0.181516 +0 0.403544 0.895905 0.0444733 +0 2.29744 1.90659 3.17037 +0 5.79355 5.34686 6.01659 +6.40277 0 6.97684 6.29976 +6.1875 0 6.02574 6.9542 +1.54047 4.90225 2.73704 0 +5.87671 0 5.9968 6.62684 +0 5.39756 5.68653 5.63711 +0 1.84704 1.24327 2.19657 +0 0.0249591 0.111402 0.330869 +0.0702934 -0.454011 -0.340302 0 +>MA0743.2 SCRT1 lnR0: 3.684 +0 -0.312906 -0.331902 0.0769617 +0 0.621446 0.13347 0.872652 +0.508856 0.949983 0.728079 0 +2.82886 1.56576 0.434174 0 +5.70276 0 5.34789 4.86339 +0 1.83831 4.0693 3.4704 +0 6.67914 4.62098 5.77831 +8.56099 0 7.96944 8.5477 +0 7.36807 7.91723 5.73731 +3.36255 6.45956 0 5.7647 +5.55486 6.85098 0 5.62971 +5.97603 5.14509 7.20433 0 +2.89467 3.60744 0 2.87704 +1.83778 1.60196 0 1.48496 +0.459072 -0.214657 -0.0702418 0 +0.264642 0.101893 0.316149 0 +>MA0744.2 SCRT2 lnR0: 3.684 +0 -0.0262156 -0.428035 0.258854 +0 0.343947 -0.110181 0.940052 +0 1.70244 0.73112 0.81946 +3.23319 2.28272 0 1.56156 +5.88984 0 5.41087 4.46719 +0 2.7184 3.99474 3.57158 +0 6.64423 4.48333 5.97161 +8.56738 0 7.58803 8.74414 +0 7.16262 7.38203 5.69611 +3.43196 6.20475 0 5.72084 +5.49526 5.90325 0 5.29657 +4.77683 3.52261 5.07937 0 +2.36487 2.72476 0 2.25298 +1.42896 1.14425 0 1.2111 +0.221473 -0.300878 -0.173812 0 +0.260166 0.105539 0.259646 0 +>MA0745.2 SNAI2 lnR0: 1.932 +0 0.0218702 -0.131632 0.552254 +1.08105 -0.115516 0.25659 0 +1.87981 2.04416 0 3.98797 +7.21812 0 7.03099 6.61693 +0 7.19492 6.13938 7.54896 +9.07745 0 7.03954 8.03145 +7.94743 0 6.45473 7.47006 +9.07153 6.58022 7.24621 0 +8.41592 7.39839 0 8.91416 +5.46119 1.98205 4.31432 0 +1.15704 0 1.56383 1.61072 +0 -0.220416 -0.377555 0.601488 +1.51152 -0.11394 0.592366 0 +>MA0143.4 SOX2 lnR0: 0.764 +0 0.864675 -0.0829231 0.265179 +0 0.468845 0.291511 0.382636 +0 6.98414 7.04422 5.85517 +6.36677 0 5.91849 4.49495 +0 5.50058 6.61962 5.02973 +0 4.96104 4.76241 6.03102 +4.00145 6.17086 5.82927 0 +3.37752 6.4535 0 5.93502 +2.38258 3.08809 0 2.89711 +0 0.222861 0.173199 0.389603 +0 0.201652 0.327798 0.309361 +>MA0080.5 SPI1 lnR0: 6.02 +0 0.372976 -0.385302 0.487005 +0 0.650393 -0.0317998 0.706235 +0 0.889992 0.0110946 1.31798 +0 2.23936 1.07049 2.18688 +0 2.19205 1.14249 2.58072 +0 4.52676 2.33913 2.52161 +3.2134 3.17034 0 4.52257 +0 4.47544 2.62126 4.7222 +5.06185 7.71115 0 6.66501 +5.73144 6.99323 0 7.08584 +0 6.00651 5.93579 6.59079 +0 6.74161 6.02562 5.26146 +3.77089 3.43275 0 6.1112 +2.92993 4.29712 3.34665 0 +3.71839 2.99713 0 4.58949 +0 2.45682 1.5978 3.10907 +0 1.06105 0.462671 1.4737 +0 1.27484 0.496519 1.09494 +0 0.0607904 -0.343392 0.265921 +0 0.256026 0.0705006 0.203666 +>MA0081.2 SPIB lnR0: 3.684 +1.12581 0.490444 1.01115 0 +0.997209 -0.339303 0.519989 0 +2.76765 0.702485 1.70206 0 +6.44062 0 3.762 5.27382 +0 4.72196 4.61116 4.15806 +7.02116 0 3.1438 4.45556 +5.7968 6.19601 6.77524 0 +7.03568 6.44283 6.16588 0 +7.43243 0 7.335 6.39805 +6.98532 0 7.54089 5.0971 +4.46501 1.58514 2.87622 0 +4.778 0 3.08735 3.02539 +1.78067 1.59694 3.90088 0 +2.52115 1.07584 2.44012 0 +1.76731 0.717031 2.0272 0 +1.32079 -0.281417 0.752358 0 +>MA0829.2 SREBF1(MA0829.2) lnR0: 2.516 +0 0.538327 -0.175024 0.840597 +0.662394 0.437618 0 1.43429 +0 2.79051 1.10604 4.88581 +5.16877 4.75653 5.11678 0 +6.48568 0 5.35929 6.39263 +0 6.21023 6.3055 5.65066 +7.26456 0 1.8877 5.92671 +4.9235 0 0.625516 6.5383 +5.65612 5.50771 6.63125 0 +7.18264 4.88584 0 7.01438 +0 5.24059 5.26481 5.03319 +5.09763 1.25153 2.74833 0 +1.45685 0 0.502695 0.613918 +0.934972 -0.125131 0.68489 0 +>MA0522.3 TCF3 lnR0: 0.764 +1.2167 0 0.255572 1.22355 +0.749459 0.0249011 0 1.56811 +6.42757 0 5.32031 5.84631 +0 5.60612 3.63744 6.20371 +6.9857 0 4.35022 5.38435 +5.06677 0 3.32504 7.03709 +6.11514 3.22361 3.79858 0 +5.18957 4.73807 0 6.32303 +7.05679 0 4.81495 5.01266 +0.77969 0 0.119786 0.788156 +1.39511 0 0.133014 1.16762 +>MA0830.2 TCF4 lnR0: 1.932 +1.24563 0 0.488598 1.20443 +0.810053 0.348123 0 0.804985 +2.64858 1.85108 0 3.8985 +7.32999 0 6.41378 7.50412 +0 4.83617 3.81925 5.66315 +7.39851 0 3.90957 5.62302 +6.7376 0 4.48812 7.64615 +6.13812 4.18526 4.76029 0 +7.2712 5.65984 0 7.32316 +3.96764 0 1.82394 2.90913 +1.72572 0 1.36997 1.58056 +0.948688 0 0.119346 0.944907 +1.44992 0 0.357798 1.04257 +>MA0769.2 TCF7 lnR0: 0.764 +0.515762 -0.277042 -0.398282 0 +1.08023 0 0.520435 0.691823 +6.29167 0 6.05839 6.96423 +5.82348 6.26511 7.14622 0 +5.49398 5.25443 5.15472 0 +5.27477 7.24873 6.83776 0 +6.17371 5.59096 0 5.33878 +0 7.23489 6.3853 5.86661 +0.933366 2.75924 2.25188 0 +1.38148 0.156009 0 1.93136 +1.00585 0.833877 1.52557 0 +>MA0090.3 TEAD1 lnR0: 1.932 +0.642387 0 0.413423 0.539654 +0.921716 0 0.863385 0.686238 +0 4.96381 2.11426 4.85323 +3.81653 0 4.94428 6.25776 +0 6.13218 5.58796 6.53761 +6.9296 6.02625 6.14077 0 +3.63949 6.08816 5.13866 0 +6.09801 0 6.38654 6.11506 +7.04358 0 7.42139 5.79223 +0 4.47759 4.23374 2.57515 +2.88738 2.91584 0 3.22507 +1.51124 0.403204 0 1.82765 +0.672555 0 0.382216 1.17504 +>MA0809.2 TEAD4 lnR0: 1.348 +0.756595 0 0.55867 0.561664 +1.13277 0 0.777 1.01631 +0 4.09933 1.8992 4.24197 +3.62283 0 4.2858 6.44811 +0 5.36114 6.44706 5.5819 +6.21665 5.47268 5.61061 0 +4.70715 5.3595 4.53172 0 +6.19386 0 5.46614 5.28316 +6.29787 0 8.37835 6.1146 +0 3.43634 5.12051 2.43751 +1.46585 1.20464 0 1.57589 +0.749401 0.155145 0 1.02568 +>MA0003.4 TFAP2A(MA0003.4) lnR0: 2.516 +0 -0.437559 -0.430561 0.318282 +0.906121 -0.348018 0.100861 0 +1.22507 0.813653 0.293639 0 +3.68212 1.44773 0 3.42363 +6.23237 0 6.28658 6.86073 +7.48685 0 6.11101 6.19012 +5.56984 2.99709 3.63533 0 +5.14626 0 3.23424 5.2408 +0 3.63551 2.90962 4.91775 +6.82446 6.08538 0 7.30056 +7.09165 5.97719 0 7.05525 +3.44153 0 1.19264 3.46154 +0.698815 0 0.642114 0.806324 +0 -0.113452 -0.0861982 0.782874 +>MA0814.2 TFAP2C(MA0814.2) lnR0: 2.516 +1.10477 0.102525 0 0.556379 +1.07711 0.673166 0 0.988808 +3.80558 1.34785 0 3.51911 +6.73442 0 4.60489 6.80189 +7.35077 0 4.75806 6.90257 +5.11222 2.5942 2.76637 0 +5.84955 4.14358 0 5.94434 +0 2.87749 3.13795 5.502 +6.51124 5.23373 0 7.41437 +6.79778 5.14874 0 7.01301 +3.79669 0 2.09469 3.94742 +1.93207 1.11365 0 1.86081 +0.725016 0.289615 0 1.31524 +1.03781 0.075928 0 0.739001 +>MA1123.2 TWIST1 lnR0: 1.932 +0 0.00659063 -0.162497 0.298555 +0.0776521 0.0529865 0.00423724 0 +0.319951 0.506005 0.180904 0 +2.94665 0 3.09615 5.0559 +6.60031 0 7.74351 7.70046 +0 7.01285 6.39589 6.53739 +6.23952 4.15228 0 4.58112 +0 3.30312 4.18734 6.76687 +6.13463 5.26589 5.92054 0 +6.55156 5.97285 0 5.94387 +3.33043 2.12093 1.64656 0 +1.06656 -0.307669 -0.282556 0 +0.179383 -0.284638 -0.206795 0 +>MA0093.3 USF1 lnR0: 2.516 +0.130554 0.0684006 -0.411806 0 +0.885455 1.71076 0 1.28418 +3.0036 3.79216 0 5.19215 +3.27517 1.45533 2.72906 0 +7.10243 0 6.0652 7.19641 +0 5.7739 6.22393 6.54345 +6.44172 0.994572 2.82283 0 +4.33999 5.12243 0 7.35345 +6.84303 7.07636 5.90418 0 +7.50358 5.97585 0 7.25436 +0 3.3455 2.73197 4.44938 +4.96494 0 3.74227 2.6983 +1.29865 0 1.4719 0.658709 +0.220563 -0.3382 0.143304 0 +>MA0748.2 YY2 lnR0: 0.764 +0 -0.212706 0.356247 0.870862 +1.25571 0.410974 0 2.17097 +0 6.22076 3.31225 7.08247 +6.41179 3.69814 4.80792 0 +7.26638 5.45504 0 8.06583 +5.87095 5.66416 0 6.18411 +6.07837 0 7.61897 5.32033 +6.78875 3.94347 0 6.49213 +3.92743 3.08317 0 4.36171 +2.08493 0 1.6272 2.10588 +1.84345 0.621992 0 1.97385 +>MA0528.2 ZNF263 lnR0: 1.348 +1.12419 0.631049 0 1.56882 +1.21205 0.25982 0 1.02752 +1.66165 2.20332 0 2.31184 +5.478 4.91524 0 5.81664 +6.52366 5.0455 0 5.93481 +6.27527 5.72265 0 6.22219 +0 4.45109 7.75868 6.37653 +6.45291 5.71644 0 5.45328 +6.70255 4.54436 0 6.65809 +0 4.33157 4.60853 6.29809 +1.88623 0.680879 0 2.41971 +2.07835 1.09253 0 1.68595 +>MA0609.2 CREM lnR0: 3.684 +0.924908 0.276074 0 0.949131 +0.992422 0 0.476077 1.13707 +0 0.485889 -0.129393 0.637356 +2.4251 2.34412 0 4.30278 +4.71898 3.81834 4.34106 0 +5.56666 3.8029 0 4.94323 +0 5.0682 4.0963 5.23521 +5.23298 0 3.92704 3.63712 +3.63661 3.92018 0 5.22972 +5.23849 4.08913 5.06338 0 +4.94323 0 3.80152 5.56995 +0 4.33506 3.81797 4.71351 +4.30123 0 2.34636 2.42535 +0.641471 -0.127617 0.486363 0 +1.13838 0.476233 0 0.993299 +0.948755 0 0.276074 0.925277 +>MA1928.1 BNC2 lnR0: 1.348 +0.0303234 -0.459656 -0.381856 0 +0.0419285 0.82546 0.0327523 0 +1.4713 1.68467 0 3.13917 +5.12893 5.74115 5.21256 0 +5.73174 6.09009 0 4.67435 +0 4.91652 5.83588 4.74103 +4.72662 2.34544 0 4.45369 +5.89776 5.08221 5.47989 0 +5.06851 0 5.48071 6.0786 +0 6.0547 6.00368 6.03938 +1.90626 -0.0651752 0.387689 0 +0 -0.195467 0.191356 0.0762548 +>MA1929.1 CTCF(MA1929.1) lnR0: 14.196 +2.58308 0 1.61942 2.78242 +2.46249 3.10335 3.4434 0 +5.72131 5.50067 0 5.30165 +4.72551 0 4.45416 3.31875 +0 2.31225 2.98915 1.9179 +1.51231 1.50843 0 2.891 +2.93218 1.6844 2.46373 0 +1.42925 1.44756 0.270036 0 +2.95836 0 2.35379 2.1053 +2.83161 0 2.81647 1.85714 +0 -0.37067 0.320023 0.254912 +1.01193 0.117326 0 1.19138 +1.00869 0 0.672548 1.25632 +0.00509295 -0.0473871 -0.0644718 0 +0.997372 0.608855 0 0.992829 +1.59453 -0.487371 0.888789 0 +1.12715 0.6976 0 0.999241 +1.44506 1.97364 0 1.93007 +3.28636 0 3.25571 3.97628 +5.28522 0 6.24252 5.93273 +0 3.02592 1.65295 1.82751 +3.52312 0 0.510915 4.05064 +1.64351 0 2.12984 0.87105 +0 3.84812 2.17921 3.28203 +5.39183 5.73892 0 7.28684 +1.22463 5.49916 0 5.79188 +3.30639 3.73689 0 0.978113 +5.23644 6.29825 0 6.03743 +4.43888 3.78576 0 3.58421 +2.68646 0 4.21333 3.10528 +0.690413 2.69711 0 3.17784 +2.7389 0 0.738952 2.6219 +1.08417 -0.422293 1.08328 0 +0 -0.113989 -0.346659 1.55757 +>MA1930.1 CTCF(MA1930.1) lnR0: 14.78 +2.8461 0 1.88275 2.45347 +3.06998 3.7085 3.28764 0 +6.34443 6.04469 0 7.08556 +5.08848 0 6.29397 3.15394 +0 3.39769 3.11509 2.65863 +2.21112 1.96968 0 2.73075 +3.58974 2.26649 2.89257 0 +1.53331 1.10693 -0.337012 0 +2.05972 0 1.99983 2.03168 +1.69048 0 1.41388 1.59614 +0.671464 0 0.345988 1.3457 +1.18605 0 0.149403 1.55079 +1.79058 0 1.00915 1.97611 +0.48374 0.0988734 0.774564 0 +0.393774 -0.49669 -0.0693362 0 +1.1183 0 0.858807 1.1328 +1.05946 -0.240437 0.738854 0 +1.40449 1.17121 0 1.51841 +1.5486 2.02596 0 2.03306 +4.02042 0 3.69694 4.09412 +6.47261 0 7.89692 7.83763 +0 3.72051 2.24131 2.64692 +3.94754 0 0.546186 4.61898 +1.55711 -0.490752 2.01515 0 +0 4.73683 2.8026 4.00611 +6.71806 7.90371 0 8.57418 +0.812189 6.48025 0 6.32877 +3.32245 4.02983 0 0.617752 +5.76288 7.29305 0 6.87122 +4.621 3.89108 0 3.86998 +2.94444 0 4.35478 3.00081 +0.703352 2.7885 0 2.82778 +2.72204 0 0.811791 2.87824 +1.79419 -0.214353 1.51578 0 +0 -0.111391 -0.266724 0.539899 +>MA1931.1 ELK1::HOXA1 lnR0: 2.516 +0 2.50081 1.61647 1.52102 +6.58923 0 2.10844 3.29982 +5.59902 0 6.06928 5.59902 +6.58923 6.06928 0 6.58923 +6.58923 6.06928 0 6.58923 +0 5.54933 5.54933 6.06928 +0 5.54933 5.54933 5.07907 +6.58923 5.07907 0 6.58923 +3.77008 2.5787 2.76946 0 +0 1.50188 2.76946 4.08886 +0 2.5787 2.25992 3.09865 +3.28941 1.88512 1.58849 0 +4.08886 2.25992 2.25992 0 +0 1.50188 1.77925 1.41486 +>MA1932.1 ELK1::HOXB13 lnR0: 3.684 +0 3.42378 0.800764 3.33564 +5.52549 0 2.67188 5.77932 +5.99071 0 6.94557 7.77062 +13.1123 12.5923 0 13.1123 +13.1093 12.5894 0 4.96581 +0 12.0751 5.25987 12.5951 +0 12.0602 5.7476 4.13618 +4.76951 6.15252 0 13.1008 +6.25609 3.07792 8.65217 0 +0.369412 -0.453961 2.06074 0 +1.54421 6.02432 0 3.98152 +6.14866 3.73186 3.63617 0 +0 4.96001 3.36456 1.88762 +0 3.45504 3.14188 4.47755 +0 1.94769 2.47363 2.56114 +0 0.328006 0.311423 1.1714 +>MA1933.1 ELK1::SREBF2 lnR0: 3.684 +0 2.75349 -0.243349 0.867247 +2.64682 0 1.98777 4.41633 +6.58046 0 5.86975 4.50147 +8.37012 5.70149 0 10.3505 +10.3505 6.16637 0 5.27147 +0 5.88507 8.32043 4.87954 +0 5.76077 6.17174 2.22629 +3.27977 8.06492 0 10.1543 +6.16637 4.40494 5.3498 0 +3.20998 0.0322358 0 3.06519 +0.816987 5.55709 0 6.07704 +5.44484 0 3.05211 3.58454 +4.7059 3.78186 0 7.79088 +3.41825 2.37917 4.35959 0 +4.7059 4.27084 0 4.88105 +0 4.11409 2.93077 2.35758 +>MA1934.1 ERF::FIGLA lnR0: 3.684 +0 1.58869 0.432357 1.7814 +2.7565 0 1.46681 4.99134 +2.06722 0 5.31117 8.05106 +10.1997 8.59102 0 10.1997 +8.93217 11.4695 0 8.14477 +0 7.49184 8.33153 9.17026 +0 4.18038 7.01116 1.13389 +0 0.712653 0.0726504 4.83177 +8.46961 0 13.4499 10.009 +0 7.49184 7.31303 10.1605 +8.55901 0 0.513269 6.29317 +5.85529 0 1.00096 7.64009 +8.9706 4.24431 5.43418 0 +9.01877 8.49882 0 6.35857 +1.7216 0.605361 0 0.608209 +0.283898 -0.468629 -0.19114 0 +>MA1935.1 ERF::FOXI1 lnR0: 2.516 +1.36396 2.03055 0 3.37245 +1.22706 0.962889 0.730719 0 +0 0.789036 1.97001 1.98838 +0 1.61098 1.71144 1.66164 +0 3.26209 1.49257 5.73472 +3.52269 0 2.64552 4.24704 +0 -0.173503 3.29321 8.57345 +4.79957 4.58851 0 9.91888 +9.91888 4.36127 0 5.56956 +0 7.88877 6.09911 5.97337 +0 2.45068 6.31932 1.58742 +1.10578 2.27958 0 5.14828 +2.13598 0.683876 1.51831 0 +1.0141 1.17142 0 1.61167 +>MA1936.1 ERF::FOXO1 lnR0: 2.516 +0.80745 3.46326 0 8.03066 +0.99021 2.60668 1.77106 0 +0 0.0354469 1.90855 3.34544 +0 7.84034 1.79162 2.21162 +0 4.17613 3.49102 8.36029 +5.33037 0 8.36029 8.88024 +0 1.23323 3.132 8.36029 +5.59083 4.81042 0 8.88024 +4.9194 8.36029 0 4.28185 +0 2.08984 7.84034 4.31284 +0 4.41477 3.634 2.35359 +1.42503 3.98613 0 8.27616 +1.00314 -0.155404 -0.370865 0 +2.34624 0.478867 0 2.63292 +>MA1937.1 ERF::HOXB13 lnR0: 3.684 +0 0.266087 -0.346143 1.21492 +1.60067 0 0.976894 2.45502 +2.05408 0 2.65007 5.93851 +7.19675 8.65722 0 8.50574 +6.66595 10.9564 0 6.31792 +0 4.84787 5.62605 5.61689 +0 2.36149 4.08983 1.54564 +1.13036 2.71422 0 5.56313 +4.04143 0.0484764 3.10034 0 +0.554101 0 0.909305 0.712318 +0.529283 3.466 0 2.40154 +6.54065 3.05007 3.87201 0 +0 2.77079 2.04371 0.764859 +0 6.23013 4.0566 2.83217 +0 1.66521 2.36149 2.2972 +0 -0.0511144 -0.0567946 0.650679 +>MA1938.1 ERF::NHLH1 lnR0: 4.268 +0 0.407945 0.407945 4.25258 +8.6247 4.2361 0 4.20892 +6.1918 0 4.36286 4.54511 +0 7.74266 7.74266 8.26261 +7.62464 4.54503 0 3.80442 +3.96937 0 6.58831 5.53881 +4.83704 3.39334 3.97257 0 +7.76124 4.56729 0 4.79061 +8.74695 0 5.44713 5.60806 +5.13147 0 4.72587 7.80547 +4.02665 8.267 0 5.81632 +6.43417 4.78785 0 4.02503 +0 3.32688 5.76224 4.59839 +0 7.32139 3.77152 1.49469 +1.14845 5.41408 0 2.60935 +7.64551 0.423636 3.07811 0 +0 -0.170524 -0.0257349 0.676835 +>MA1939.1 ERF::SREBF2 lnR0: 4.268 +1.24584 0.295735 0 1.15243 +1.6818 0 0.37548 4.04311 +3.15812 0 7.47301 3.9041 +6.42352 5.49259 0 8.98317 +7.41373 4.50238 0 5.11453 +0 4.97264 7.94327 3.51217 +0 2.04737 7.94327 2.31456 +0 7.23626 0.107068 6.766 +6.08147 5.56152 4.09064 0 +3.78662 0 5.49259 5.31896 +0 6.37383 5.64408 7.47301 +8.98317 0 5.90357 5.02233 +8.98317 1.92792 0 6.42352 +3.55753 4.51771 4.80438 0 +8.98317 8.46322 0 5.55761 +0 7.62831 3.02992 2.53137 +4.89992 0.609892 4.21171 0 +>MA1940.1 ETV2::DRGX lnR0: 2.516 +0 1.62355 0.147931 1.66283 +1.47298 0 0.753123 3.09125 +2.43532 0 4.48202 9.46039 +11.0298 7.95023 0 11.0298 +11.0298 8.94044 0 8.73064 +0 7.0193 7.21006 6.7398 +0 3.48439 5.44986 1.36903 +1.57217 1.86544 0 4.72138 +3.99714 -0.326507 2.52963 0 +0 2.09643 1.50022 2.79822 +0 2.68709 2.951 3.63533 +7.08432 5.28159 5.51066 0 +3.22436 2.57938 4.45965 0 +0 4.58395 3.84127 2.71657 +>MA1941.1 ETV2::FIGLA lnR0: 3.684 +0 1.92024 -0.0645237 1.64121 +2.31196 0 0.962477 3.84141 +2.79557 0 3.74047 5.59942 +6.33605 5.10736 0 6.63027 +6.16458 6.17613 0 6.00715 +0 4.15646 4.36453 4.70263 +0 4.10783 4.28409 1.95771 +0 1.66929 0.355066 5.65697 +7.01916 0 5.21581 5.01153 +0 4.82387 3.79472 5.63007 +5.92519 2.02183 0 6.07707 +4.46991 0.906567 0 6.12407 +5.40287 4.60947 4.5006 0 +5.84344 5.99049 0 5.5114 +2.20235 0.887934 0 1.30462 +0.263658 0.261249 -0.316816 0 +>MA1942.1 ETV2::FOXI1 lnR0: 3.1 +1.65071 0 0.314524 0.97458 +2.03121 2.45473 0 3.9834 +1.9481 1.40595 1.19024 0 +0 1.09558 2.36173 3.10054 +0 1.88788 1.61571 2.72221 +0 4.39559 2.69618 5.46949 +5.95233 0 4.31939 6.14833 +0 1.26814 5.91889 10.3075 +7.31735 5.76034 0 6.90637 +6.14833 10.666 0 4.52393 +0 5.02678 10.1461 6.7974 +0 3.79944 5.93975 1.19741 +1.95009 5.87044 0 8.75929 +2.00044 -0.0870344 2.07129 0 +1.05468 1.77666 0 1.55299 +>MA1943.1 ETV2::HOXB13 lnR0: 3.1 +0 1.28239 0.882357 2.12807 +3.21588 0 2.48927 4.55168 +3.4882 0 6.73358 9.8468 +12.6267 12.1067 0 10.6462 +12.6267 12.1067 0 12.6267 +0 7.81669 7.92255 12.1067 +0 2.02842 7.71813 1.21231 +0 -0.165266 0.544425 6.28388 +2.36362 0 5.71825 0.796812 +0 5.49723 1.29513 5.90128 +8.96783 3.58374 11.5868 0 +0 4.27535 3.80571 0.866902 +0 5.99816 7.53932 3.83535 +0 2.08452 3.37791 3.40162 +0.862673 0 1.57325 1.72103 +>MA1944.1 ETV5::DRGX lnR0: 2.516 +0 1.69264 -0.273706 2.32927 +1.88725 0 0.377094 3.2493 +1.35764 0 4.40575 4.54247 +6.91939 6.71822 0 7.64914 +9.21859 5.14877 0 9.21859 +0 4.75312 8.17868 7.70843 +0 2.90561 3.80363 1.54371 +3.57395 3.054 0 9.21859 +3.00917 0.0297184 2.32096 0 +0 3.97234 1.09893 6.71822 +0 2.53405 1.91865 2.92285 +4.65119 4.4086 3.31983 0 +3.50208 1.91865 3.18367 0 +0 3.82937 1.76635 3.50208 +>MA1945.1 ETV5::FIGLA lnR0: 3.1 +0.903816 2.2574 0 2.68723 +2.14122 1.11667 0 3.45373 +1.75518 0 2.17296 5.13004 +7.59505 8.44012 0 8.69961 +11.2593 8.75889 0 4.69481 +0 4.87984 5.56494 6.14092 +0 4.68908 4.44358 1.60323 +1.21463 2.65286 0 5.45604 +8.28864 0 6.39 6.66087 +0 6.7938 5.51103 8.75889 +7.29843 2.2609 0 7.8337 +5.29586 1.92559 0 8.69961 +6.53297 6.55515 4.91426 0 +7.29843 7.0751 0 6.1802 +2.47452 1.63218 0 1.80384 +>MA1946.1 ETV5::FOXI1 lnR0: 1.932 +2.68359 3.59011 0 9.18913 +2.48242 2.53234 1.48717 0 +0 0.945554 4.57266 5.67185 +0 4.18839 4.02013 7.09973 +0 8.14923 1.92536 6.36998 +9.18913 0 4.07079 3.62939 +0 0.846389 4.18839 8.66918 +5.52492 3.16897 0 9.18913 +5.52492 7.09973 0 3.88403 +0 7.15902 3.94289 4.70834 +0 3.05556 3.40574 0.87782 +3.3036 5.70232 0 9.00215 +2.06881 0.258231 0.959532 0 +>MA1947.1 ETV5::FOXO1 lnR0: 1.932 +1.55523 3.70928 0 4.80847 +1.26758 3.87201 0.853494 0 +0 0.277153 3.36761 4.87778 +0 2.30257 6.30737 5.83711 +0 7.29758 1.85949 4.67864 +5.77782 0 7.81753 4.20838 +0 2.10103 4.32695 6.24808 +4.13114 4.8469 0 8.33748 +8.33748 7.81753 0 5.55761 +0 4.73792 2.94826 2.86648 +0 0.551253 1.86024 0.179555 +1.31705 1.53234 0 3.21765 +1.72915 0.314261 0.614683 0 +>MA1948.1 ETV5::HOXA2 lnR0: 2.516 +0 2.40887 -0.0463306 2.2101 +1.3718 0.139794 0 1.53458 +3.09622 0 2.60155 3.96631 +8.87201 8.35206 0 6.89159 +5.32214 8.35206 0 8.87201 +0 4.69321 5.85168 4.58197 +0 1.99264 2.69618 0.592972 +4.16367 3.75366 0 6.89159 +8.35206 1.40381 7.8321 0 +0 -0.0463306 1.14453 3.30362 +0 3.703 1.31161 5.06265 +8.35206 2.88105 5.53291 0 +8.35206 1.31161 2.75304 0 +0 3.87126 7.8321 3.44636 +>MA1949.1 FLI1::DRGX lnR0: 3.1 +0 2.45068 1.01422 1.76021 +3.35977 0 2.80455 3.06986 +2.47001 0 5.07566 7.57603 +8.15527 8.62553 0 8.15527 +5.71992 8.62553 0 5.48127 +0 5.80638 8.10558 8.62553 +0 7.56999 3.70135 1.12538 +3.09676 2.64031 0 3.94893 +4.92097 0.500983 3.76983 0 +0 1.63706 2.70451 2.90568 +0 4.14474 1.61516 3.71983 +6.06587 2.87192 2.48869 0 +3.286 1.47074 3.5655 0 +0 2.25652 2.20967 2.92698 +1.26965 1.32893 0.615146 0 +>MA1950.1 FLI1::FOXI1 lnR0: 2.516 +1.06563 2.05856 0 2.59583 +2.14183 1.30238 1.68473 0 +0 1.41987 2.31592 3.32954 +0 2.71324 2.86031 3.16497 +0 9.17294 3.27703 5.0945 +6.39263 0 5.06621 6.0446 +0 1.7909 4.49945 10.4254 +5.73356 10.6831 0 6.54863 +11.2031 10.6831 0 6.99671 +0 5.12549 6.39307 6.40348 +0 3.70345 4.89332 1.16434 +0.908338 3.93266 0 4.54481 +2.25221 -0.187357 1.30562 0 +0.694756 0.891823 0 0.808365 +>MA1951.1 FOS(MA1951.1) lnR0: 2.516 +1.2005 -0.331517 -0.349991 0 +2.78507 1.79691 0 2.20402 +0 3.72256 1.01789 5.42872 +8.62553 6.66044 6.03855 0 +5.83201 5.34822 0 5.22916 +0 6.2148 4.96413 8.30419 +7.69007 0 9.02624 4.83785 +5.50132 9.02881 0 7.24957 +6.00243 10.0809 5.22202 0 +4.36262 0 6.09129 6.18482 +0 10.0826 5.87624 10.6025 +6.21468 1.62229 4.38575 0 +3.07209 0 3.27628 3.86313 +0 2.96407 -0.447384 3.98805 +>MA1952.1 FOXJ2::ELF1 lnR0: 2.516 +0 0.736684 -0.189344 1.21539 +1.02857 1.08211 1.49308 0 +0 1.3577 3.34869 2.36678 +0 1.66599 3.13862 2.02544 +0 2.38705 2.70944 5.42401 +4.46113 0 4.11503 3.75841 +0 0.0326609 4.38198 5.34236 +3.28949 3.6224 0 6.50235 +6.44155 10.4617 0 10.9816 +0 9.94172 7.64252 7.17227 +0 9.94172 9.94172 4.0818 +2.05585 3.56408 0 5.45134 +1.16697 1.44282 5.04464 0 +0 1.42287 -0.21892 1.09901 +>MA1953.1 FOXO1::ELF1 lnR0: 2.516 +1.01835 1.92289 0 4.21382 +1.21043 1.69986 1.51879 0 +0 0.301998 5.16085 2.65185 +0 2.65379 4.39149 4.21786 +0 5.06293 2.94635 5.58288 +8.40203 0 7.88208 3.02888 +0 3.40128 4.39149 7.88208 +5.11262 4.59267 0 5.62215 +6.10283 4.33221 0 6.42161 +0 2.88285 5.06293 5.90166 +0 7.36213 4.22323 1.77255 +2.00583 2.88706 0 5.62215 +1.89685 0.949787 2.0923 0 +0 0.234432 -0.214845 0.260459 +>MA1954.1 FOXO1::ELK1 lnR0: 2.516 +0 1.0916 -0.339037 3.73302 +0.477432 2.70251 0.900605 0 +0.633971 0 5.04682 2.55218 +0 4.62698 3.9848 4.60683 +0 5.36966 3.82202 6.25794 +6.61899 0 5.76531 5.07483 +0 2.02297 5.82459 7.74573 +9.25589 8.00619 0 8.04546 +7.53593 7.33475 0 7.05525 +0 4.74777 5.73799 7.33475 +0 4.66612 5.30616 2.81717 +2.94326 3.67054 0 6.54572 +2.30065 0.842447 1.52146 0 +0.647695 1.70357 0 1.35848 +>MA1955.1 FOXO1::ELK3 lnR0: 2.516 +0.943853 3.17803 0 3.24305 +0.707602 1.10642 2.36407 0 +0 -0.186215 5.58957 6.10952 +0 5.42131 3.85186 5.36203 +0 6.41152 3.12211 6.93147 +7.45142 0 6.93147 5.15223 +0 1.6011 3.44089 5.94126 +5.88198 4.63227 0 7.45142 +5.471 4.63227 0 5.15223 +0 6.41152 6.41152 3.79258 +0 2.74731 5.42131 3.26726 +2.85303 3.50591 0 4.89177 +2.88402 1.10642 2.20518 0 +0.71071 0.561489 0 0.979356 +>MA1956.1 FOXO1::FLI1 lnR0: 2.516 +2.58698 3.28941 0 7.85681 +1.03888 1.31132 3.15111 0 +0 0.584606 6.56983 4.79058 +0 4.5523 7.11196 7.63191 +0 7.11196 7.11196 4.85203 +8.15186 0 7.63191 6.17144 +0 3.68639 6.12175 7.63191 +4.48764 5.33271 0 8.15186 +5.01296 7.63191 0 7.16165 +0 7.11196 7.11196 6.6417 +0 4.81276 7.11196 2.55284 +2.62157 3.96769 0 8.15186 +5.07225 1.67387 3.06451 0 +2.25008 2.07465 0 0.982504 +>MA1957.1 HOXB2::ELK1 lnR0: 2.516 +0 2.40872 -0.231341 2.46964 +3.6012 0 1.65605 4.94697 +5.08044 0 7.50538 6.52559 +7.66631 10.2853 0 8.02533 +10.8052 10.2853 0 7.83457 +0 9.7653 9.7653 7.98606 +0 9.7653 5.55896 3.87292 +5.24546 5.68686 0 8.82478 +6.73539 2.51506 5.28603 0 +1.08144 0 2.00928 2.78387 +0 3.65005 0.108321 3.2982 +5.0516 4.20556 4.53164 0 +3.87292 1.38464 4.23502 0 +0 3.80189 2.49731 2.58658 +>MA1958.1 HOXD12::ELK1 lnR0: 4.268 +0.943995 1.20005 0 1.48693 +0.677868 1.70893 0 2.55684 +1.24778 0.0409026 0 3.49058 +2.84276 0 3.76424 6.8036 +7.38284 8.84331 0 9.36326 +9.36326 8.84331 0 6.22437 +0 7.33315 8.32336 8.84331 +0 6.75391 8.32336 3.98445 +5.23416 6.86289 0 9.36326 +5.87268 8.32336 8.32336 0 +3.01529 0 5.60753 1.75566 +3.6385 8.84331 0 9.36326 +8.84331 8.32336 5.35273 0 +0 4.89779 5.7637 2.65655 +0 8.32336 5.7637 8.84331 +0 2.47429 6.34294 4.08302 +0 0.705513 0.447996 0.640361 +>MA1959.1 KLF7 lnR0: -0.404 +1.11998 2.53934 0 1.13829 +9.50835 8.9884 0 9.50835 +9.50835 8.9884 0 9.50835 +9.50835 8.9884 0 9.50835 +4.58048 0 8.65135 2.73263 +9.50835 8.9884 0 9.50835 +9.04386 4.76902 0 2.00406 +2.58744 3.87778 0 2.44031 +9.50835 8.9884 0 9.50835 +>MA1960.1 MGA::EVX1 lnR0: 1.348 +0 3.46288 0.112001 1.87642 +2.41505 4.90383 0 4.64097 +6.81215 6.51241 0 5.4046 +4.40398 5.06305 5.87812 0 +9.59202 6.63672 0 11.5724 +0.367938 2.20664 1.75171 0 +6.57321 4.56913 4.2028 0 +0 10.5325 7.97288 5.32773 +0 4.46326 4.3647 4.53199 +4.60841 5.19301 6.25292 0 +6.99407 3.15642 0 1.14818 +0 2.31117 0.427284 0.328036 +>MA1961.1 PATZ1 lnR0: 1.348 +2.33255 0.419739 0 2.67483 +2.61328 0.900381 0 4.06947 +3.7958 1.5548 0 5.22637 +2.39504 3.1762 0 9.06578 +9.51794 8.99799 0 9.51794 +9.51794 8.99799 0 9.51794 +0.975314 0 7.98145 2.15832 +9.51794 8.99799 0 9.51794 +9.45933 4.46896 0 9.45933 +9.46927 4.72691 0 9.46927 +4.57356 8.9193 0 9.43925 +3.81905 0.409306 0 4.37329 +>MA1962.1 POU2F1::SOX2 lnR0: 4.268 +0 0.132876 1.09757 3.22339 +0 4.3237 4.60319 3.53089 +4.81646 5.63546 8.84175 0 +3.78721 4.29696 7.62035 0 +1.3194 4.36113 7.17159 0 +1.34509 3.64242 0 9.08042 +3.72162 0 7.70179 7.23153 +0 6.50658 4.38886 8.67322 +8.83503 6.1052 7.72149 0 +0 0.00151803 1.09096 4.63967 +0 4.39142 6.08142 4.63449 +5.86002 0 4.48905 3.42019 +0 5.94327 6.90138 5.39023 +0 6.33091 7.43192 6.91631 +1.1975 4.77346 6.70852 0 +0.679739 3.61221 0 2.85355 +2.55341 1.23021 0 3.14971 +>MA1963.1 SATB1 lnR0: 1.932 +0.175733 0.915436 0.955205 0 +0.274935 1.12882 0.867806 0 +0 0.568928 0.000201685 0.248706 +7.42828 0 7.79889 6.02777 +6.02689 6.82464 9.16826 0 +0 7.07783 6.65393 7.55513 +0 7.53979 7.4795 4.62747 +6.79773 7.43009 7.48656 0 +0 5.46233 4.59802 5.19718 +0 4.54941 4.27071 4.20699 +1.1124 0 2.33005 0.955197 +0.143328 0.951975 1.2918 0 +0 0.947598 0.703183 0.291548 +>MA1964.1 SMAD2 lnR0: 0.18 +0.302776 -0.488832 -0.36492 0 +1.91871 0.313316 0 1.33485 +6.84929 0 5.32262 7.87312 +9.39183 0 4.29818 5.62174 +0 3.9585 3.91166 8.49761 +9.28813 6.83312 0 8.05242 +0 11.2357 11.2357 8.20582 +11.2892 0 11.7595 12.2794 +0 0.665773 -0.0781928 0.818262 +1.49363 0.270023 0 1.28599 +>MA1965.1 SP5 lnR0: 0.18 +2.5198 0 1.51072 1.86736 +2.32005 0 0.820813 1.01256 +11.936 0 12.2155 12.4166 +11.7175 0 5.59474 14.6881 +14.1807 13.6608 5.87974 0 +9.18319 0 14.1935 14.7135 +11.1498 0 6.38036 14.6997 +14.7104 0 7.71527 14.7104 +0.974354 0 1.05702 0.982153 +2.02488 0 0.547628 1.5694 +>MA1966.1 TFAP4::ETV1 lnR0: 3.684 +0.626398 2.40463 0 2.29883 +2.80715 0 0.1534 3.61236 +3.04679 0 3.95208 5.31483 +6.84287 6.92271 0 6.92693 +6.58241 5.75735 0 5.95853 +0 5.03297 3.98445 5.29246 +0 4.56941 3.7626 1.10822 +1.87232 2.31655 0 5.97539 +7.57262 0 7.35454 5.10667 +0 4.94078 2.62383 4.82317 +5.64415 2.32929 0 3.06697 +1.54625 0.0380715 0 4.26237 +4.47052 2.65503 3.39383 0 +7.79284 6.86191 0 5.5096 +1.78722 1.80494 0 1.42381 +1.39182 0.585194 0 0.765916 +>MA1967.1 TFAP4::FLI1 lnR0: 3.684 +0 2.67577 1.08169 3.33935 +2.91799 0 1.54186 4.96386 +3.10774 0 4.3573 6.82993 +10.4941 4.24943 0 6.6255 +4.79559 3.32568 0 4.03444 +0 5.03847 5.4934 5.55842 +0 5.90438 9.45424 2.81614 +0 4.91416 2.11739 5.31977 +10.4941 0 9.97419 10.4941 +0 9.45424 8.46403 8.98398 +10.4941 6.8353 0 10.4941 +10.4941 0 6.01335 10.4941 +9.97419 9.45424 9.45424 0 +10.4941 9.97419 0 10.4941 +0 0.920071 -0.103492 0.00823386 +1.00696 0.0998149 0.880125 0 +>MA1968.1 TFCP2 lnR0: 0.18 +0 1.91121 0.853494 2.79678 +0 5.78033 3.96181 4.08514 +0 6.99076 5.42131 2.45911 +8.60989 0 7.51071 9.6001 +7.04045 0 8.08994 2.76083 +2.64648 7.09973 0 6.62947 +8.60989 5.79075 0 8.60989 +1.58441 3.44089 8.5602 0 +3.57994 2.68753 4.21089 0 +1.36954 -0.162542 2.43384 0 +>MA1969.1 THRA lnR0: 8.356 +0.851096 0 0.42749 1.08692 +2.30143 0 1.52102 1.49383 +2.20064 0.833451 1.21958 0 +2.63653 1.67731 0 3.18747 +5.73339 2.82205 6.78289 0 +4.64021 3.96974 0 5.21944 +1.21043 3.66111 1.94114 0 +5.61525 0 5.82505 7.91445 +6.94825 0 7.41851 6.36901 +7.27679 2.40752 6.75684 0 +5.00954 0 2.84291 3.15342 +0 4.74092 2.67389 4.68164 +1.42947 -0.0518257 0.101932 0 +0.968033 1.94425 0 1.83812 +7.37827 4.29866 4.87789 0 +3.33818 3.87814 0 5.70707 +0 3.2704 1.79951 4.5201 +4.38859 0 5.31379 5.2545 +6.35305 0 7.40255 5.94208 +5.5886 1.7324 5.64789 0 +4.60062 0 1.52102 0.958558 +0.139972 1.29857 1.23211 0 +1.78753 0 0.55838 1.14183 +1.64212 0 0.869414 0.959214 +>MA1970.1 TRPS1 lnR0: 1.348 +0.465245 0.470039 0.213036 0 +0 0.218689 0.557608 0.0411734 +3.18359 1.76675 2.30345 0 +4.40198 0 3.28871 3.5969 +4.65127 4.33286 5.13041 0 +4.19547 4.5848 4.62549 0 +0 5.75334 5.14789 5.804 +5.7505 5.46299 6.0209 0 +6.54308 0 5.96233 5.25571 +2.30237 3.58003 3.72396 0 +0.322976 -0.289917 -0.415887 0 +0.355633 0.144887 0.677371 0 +>MA1971.1 ZBED2 lnR0: 2.516 +0.897975 0.178566 0 1.24376 +0.527715 0 0.155255 1.17063 +0 -0.241773 0.661425 1.60103 +0 0.135291 0.862442 2.0695 +5.27072 0 4.75077 6.43752 +6.43076 5.77465 0 8.15072 +0 5.89468 4.80591 7.04582 +0 5.91401 6.5452 6.53983 +0 3.01986 4.18587 5.09429 +6.5408 0 4.74397 6.32058 +4.14755 0 4.28407 2.66863 +0 -0.351226 -0.347055 0.739654 +0.792697 0.127905 0 1.40944 +0.756741 0.302673 0 1.66485 +>MA1972.1 ZFP14 lnR0: 3.1 +3.08059 5.78354 0 6.02047 +3.36676 8.84503 0 7.90791 +0 7.048 8.50506 9.02502 +9.54497 9.02502 0 8.0879 +3.47135 1.62893 0 9.02737 +1.72967 0 1.63654 3.94851 +0 -0.507091 1.89584 0.614466 +2.81743 0 2.81812 3.29055 +0.777029 0.362065 0.547966 0 +3.11726 8.63305 0 3.11726 +7.37714 9.02044 0 9.54039 +0 8.48203 4.97588 9.00198 +0 2.16858 0.413783 6.83839 +1.13891 -0.203081 -0.0796445 0 +4.80685 3.7292 0 3.49088 +>MA1973.1 ZKSCAN3 lnR0: 6.02 +1.66616 1.67153 0 1.02714 +1.09919 1.63025 0 0.539931 +3.34616 1.25676 0 0.982504 +3.13792 0 3.02895 3.26223 +3.57719 0 3.2255 2.99795 +2.15234 0 1.55718 2.89502 +0 5.39881 2.68864 6.498 +5.32332 6.59303 0 6.53374 +8.11726 5.03766 0 6.54782 +5.4102 0 5.15071 3.76352 +6.0067 4.27633 5.48675 0 +0 5.0543 3.89582 5.98522 +6.02774 4.70834 0 4.23808 +2.68992 0 5.02923 6.27893 +8.04546 0 6.5353 3.99801 +7.04787 0 5.94868 4.07724 +0 1.9102 2.46115 1.94948 +1.75825 0 0.107462 0.92404 +0.544796 0.300422 0 0.67595 +0.820373 0 0.0501305 0.648738 +>MA1974.1 ZNF211 lnR0: 3.1 +0 0.242455 1.51476 0.185925 +0 1.92073 1.30925 0.931184 +3.13166 -0.0114505 1.68796 0 +0 4.53668 5.18237 7.49198 +7.51442 4.84579 6.41524 0 +0 6.69779 6.02635 7.94749 +7.20857 5.43795 7.0074 0 +0 6.01351 6.20427 6.53346 +8.0473 0 6.53714 6.88883 +6.53631 0 6.88227 4.72822 +0 4.44925 4.51571 4.04545 +2.39949 0.124755 2.64689 0 +0 1.14002 0.0406109 1.52018 +1.17739 0.149813 1.3558 0 +0 1.32901 2.12847 0.0392609 +>MA1975.1 ZNF214 lnR0: 3.1 +0 0.393206 -0.0568776 1.97557 +0.923698 0.796967 1.5813 0 +1.61563 1.98369 4.3151 0 +2.65016 0 4.28415 3.30751 +0 4.19349 7.90174 6.63964 +3.68928 4.62129 2.37443 0 +4.27285 0 2.90491 2.25478 +0 7.7689 2.23426 8.28885 +0 5.37035 5.37035 8.44107 +2.194 0.699563 0 1.10638 +1.99479 4.82075 0 3.18369 +2.54388 1.84953 1.10031 0 +4.13862 0 2.25627 6.85635 +8.98961 0 8.46966 7.20757 +5.28323 2.91573 7.8111 0 +>MA1976.1 ZNF320 lnR0: 10.108 +0 1.49789 -0.363953 0.811038 +4.39137 3.93588 0 3.82622 +5.0702 3.21204 0 1.14684 +2.73841 3.68933 0 3.0242 +7.24655 6.38212 0 7.24655 +6.39256 6.38212 0 9.68132 +1.1459 3.88108 0 1.58933 +2.66661 0 1.89831 2.32987 +3.46099 0 4.39792 3.32697 +0.828151 0 3.17427 2.33099 +1.2887 3.76571 0 2.44903 +3.84058 6.40049 0 2.93558 +6.92299 9.18229 0 9.70225 +5.46861 9.15433 0 9.67428 +5.53213 5.8116 0 5.66015 +1.70449 0 5.16843 9.1768 +1.58563 0 3.99093 2.73991 +0.660198 2.74151 1.04714 0 +1.60502 2.67599 0 3.40537 +3.09649 1.9051 1.67153 0 +4.68306 3.08156 0 3.60151 +1.06611 0 1.5152 1.42818 +1.27828 0.743479 0 1.86 +0 -0.130987 -0.410167 0.404463 +1.16771 0.274269 0 0.991252 +0.646242 0.41226 0 0 +1.01086 0.211734 0 1.174 +>MA1977.1 ZNF324 lnR0: 6.604 +0.616078 0.597161 0 0.591434 +0.706142 0 0.37175 1.07252 +1.48031 0 0.198217 0.920905 +0 0.624324 0.967448 0.304019 +1.34614 2.44794 0 1.88291 +2.40169 2.02488 0 2.04234 +0 0.062937 1.74056 2.19546 +0 5.45333 1.91009 2.69568 +4.64192 4.80985 0 4.28189 +0 -0.394679 0.607204 0.554791 +1.86527 0 4.95777 1.41754 +0 5.7624 5.7624 3.96795 +0 3.79861 1.21791 3.70573 +3.999 8.65297 0 9.17292 +9.2765 6.37879 0 9.2765 +0 3.16523 6.22218 2.03892 +3.26441 3.85847 3.69899 0 +2.89291 6.88265 0 9.03781 +9.28976 8.76981 0 9.28976 +5.01479 0.703699 7.72077 0 +5.23574 5.56395 1.71623 0 +>MA1978.1 ZNF354A lnR0: 6.604 +0 -0.183239 2.09735 0.615334 +0.970141 1.70061 2.59825 0 +0 2.50353 5.98674 2.09704 +0 1.71582 3.7343 2.23577 +0 0.900189 0.441846 0.469241 +0.965255 0.629013 1.08736 0 +0 2.14879 0.518928 3.18694 +2.64403 2.12408 3.84304 0 +0 6.18216 2.3195 4.55841 +0 4.03846 3.21714 3.73709 +0 2.60458 3.12277 3.64272 +1.53143 3.48831 1.01148 0 +3.3594 4.55841 0 7.22206 +1.12895 1.99195 0 2.5119 +0 0.714138 0.714138 1.69243 +2.36878 0 3.86731 1.28535 +0.656408 1.08736 1.08736 0 +0 1.12917 3.78971 4.30966 +0 3.34736 1.0814 0.897928 +1.14896 0.629013 0.839881 0 +2.74508 3.94409 3.12277 0 +>MA1979.1 ZNF416 lnR0: 0.764 +2.30514 2.32046 2.60714 0 +0 2.38029 0.810847 2.05446 +2.35635 2.58572 3.4353 0 +7.83564 0 5.33527 6.84543 +6.74496 5.01458 6.80424 0 +7.8399 5.33953 0 7.26066 +7.26066 5.7505 0 6.84969 +8.85539 7.34523 0 6.87497 +6.46567 0 6.2645 4.55853 +0 1.90538 2.28018 1.65229 +1.49977 0 1.72344 0.941391 +>MA1980.1 ZNF418 lnR0: 3.1 +0 0.194909 1.05146 3.10042 +0 4.3646 -0.378867 0.769491 +4.37925 6.82258 0 5.73193 +0 2.18024 3.21733 1.3009 +1.92048 6.48363 0 7.00358 +4.24265 6.80572 0 5.42471 +5.25788 0 5.63431 9.10057 +4.14577 1.10462 5.97426 0 +0 4.28833 2.70789 4.18057 +0 1.58745 3.16263 3.98649 +0 8.12367 6.42313 8.64362 +0 7.99477 2.9025 6.05959 +2.89974 6.64427 0 4.81577 +7.40003 0 8.58062 4.87136 +0 5.13831 8.08463 5.65826 +>MA1981.1 ZNF530 lnR0: 4.852 +4.80214 6.655 0 8.94695 +0 0.0201848 1.64821 3.59599 +0 3.74286 5.34864 6.63562 +0 2.45388 -0.187369 1.23445 +5.27088 6.67412 0 8.96607 +9.02195 8.502 0 9.02195 +0 0.33462 2.21918 2.52562 +0 0.507201 -0.0967683 1.74421 +0 7.82789 3.19729 4.41022 +9.02195 8.502 0 9.02195 +3.48184 6.55534 0 8.84729 +9.02195 8.502 0 9.02195 +6.68619 1.14151 0 5.42281 +3.49233 0 3.4018 4.53861 +0.85495 1.00505 0 1.62929 +3.57648 2.03258 0 3.36297 +1.76256 0.653112 0 1.98794 +0 -0.31084 -0.210917 1.31985 +>MA1982.1 ZNF574 lnR0: 3.1 +1.32081 0.514328 0 1.53077 +3.15818 4.48993 0 1.75479 +4.48098 0.396896 0 5.25827 +4.14779 0 3.9552 9.29517 +3.95384 1.07067 4.60209 0 +0 8.43913 8.43913 8.95908 +9.47395 7.44302 0 9.47395 +0 6.18995 6.18995 8.93864 +4.47006 6.15502 0 9.37922 +1.26939 0 1.96473 3.61738 +6.08739 5.85228 0 9.43262 +4.04181 2.51156 0 2.83296 +3.20709 0 5.94432 4.09622 +3.11952 0 1.29726 2.60772 +2.50454 0 0.592016 3.39367 +>MA1983.1 ZNF582 lnR0: 6.604 +2.90744 1.88346 1.96284 0 +3.18988 0 2.77987 1.82894 +2.75329 2.10138 2.9327 0 +2.83689 1.46736 0 2.34986 +5.23366 3.94371 5.19438 0 +5.74539 5.22544 4.55401 0 +0 2.05702 6.37191 5.58288 +5.09741 0 7.01282 4.85876 +5.01115 3.69175 4.4912 0 +6.53038 6.58967 6.58967 0 +6.28568 7.07471 0 5.805 +6.61952 0 7.08978 6.30074 +0 3.57163 4.88061 4.29601 +5.35748 4.55086 0 5.07081 +6.03026 0 6.50052 6.60949 +5.40576 0 6.67547 2.03697 +0 0.515615 0.562458 1.43126 +0 3.67478 2.79891 3.9903 +0 3.31252 2.41451 3.74587 +0 0.874349 1.81064 0.778896 +2.23003 3.30437 0 3.27037 +>MA1984.1 ZNF667 lnR0: 1.348 +5.45731 2.72126 0.687528 0 +5.76981 3.03376 2.2036 0 +0 5.34048 3.12438 3.64433 +0 0.73398 2.46705 1.63521 +1.83936 5.56925 0 6.0892 +0 5.24986 1.68196 5.76981 +6.4656 5.94565 0 4.2495 +6.54602 0 6.02607 6.54602 +2.00135 2.00304 5.0493 0 +6.54602 0 6.02607 6.54602 +0 2.29422 5.34048 5.86044 +1.16377 0.94448 0 3.1975 +>MA1985.1 ZNF669 lnR0: 3.1 +2.50526 2.19577 0 2.50526 +5.68433 7.25915 0 7.7791 +5.68433 7.25915 0 7.7791 +2.71572 1.63939 0 2.96264 +4.24953 0 6.63942 1.45203 +7.80837 7.28842 0 7.80837 +0 3.25322 6.67878 7.19874 +6.3354 -0.462339 5.81545 0 +7.80837 7.28842 0 7.80837 +0 1.23968 4.1965 3.38566 +7.6556 0 7.13565 3.5532 +5.42565 0 3.19677 3.71672 +0 2.33227 -0.190849 2.85222 +2.69534 0 1.09382 1.89204 +3.42556 2.22878 2.22878 0 +>MA1986.1 ZNF692 lnR0: 0.18 +1.89313 0.872709 0 1.1382 +2.78079 2.35439 0 3.00985 +13.7666 6.80257 0 9.99652 +8.82118 10.9531 0 9.06389 +9.01261 0 10.2823 9.29362 +8.40052 0 5.37876 9.61095 +11.7731 0 5.83907 9.33775 +0 12.7123 5.06676 13.2322 +3.046 0 0.428321 2.56676 +1.04003 0 0.261268 1.47583 +>MA1987.1 ZNF701 lnR0: 6.604 +5.57511 5.8543 0 8.35253 +0 7.29474 3.63316 7.81469 +5.55721 5.03726 0 8.33464 +1.52882 0 2.77976 7.71276 +0 5.14444 2.08783 5.66439 +3.80916 0 1.01234 2.00404 +3.02434 0 1.76176 1.43349 +0 0.950888 0.660988 1.09605 +0 1.315 0.495972 1.01592 +0 1.58349 -0.35333 2.28605 +4.05709 7.74078 0 5.48331 +6.40938 7.86771 0 8.38766 +6.31988 4.11663 0 6.31988 +2.54616 7.49291 0 4.05469 +3.46475 7.70234 0 6.24401 +0.596496 2.36259 0 4.51817 +0 3.1939 1.6998 2.61789 +0 0.606378 -0.193045 0.671412 +0.692734 1.08358 0 0.755308 +1.13768 1.89194 0 0.881138 +1.4541 1.01904 0 1.4541 +>MA2003.1 NKX2-4 lnR0: 0.18 +2.12353 0 1.27448 4.73596 +6.76322 0 7.14129 3.67825 +0 2.66049 5.46286 2.48686 +10.6319 0 10.1119 10.6319 +10.1119 4.93754 8.60176 0 +4.44007 0.997456 5.82188 0 +1.89975 0.229158 0 3.9278 +0 3.81618 3.79133 2.91627 +0 -0.291884 -0.132076 2.10363 +0.80249 0 0.951306 1.90083 +>MA0041.2 FOXD3 lnR0: 3.684 +0 1.38064 2.08984 0.0165155 +0 2.20208 0.659333 2.37185 +0 0.47026 0.47026 0.164385 +1.53501 2.66174 0 3.88523 +0.774749 0.118641 3.69472 0 +0 1.63706 5.8434 5.78412 +0 3.69472 6.83361 4.38293 +0 5.8434 3.86298 5.78412 +6.94259 1.01665 6.42264 0 +0 4.53442 5.26417 4.38293 +0 3.28375 3.69472 3.8037 +0 2.70451 2.4843 2.23425 +4.10343 0 3.58348 2.96782 +0 2.03971 1.48333 1.37869 +0 1.46047 0.434985 1.22238 +1.20383 0.151483 0.82928 0 +>MA0067.2 PAX2 lnR0: 4.268 +7.75516 0.00142809 -0.400107 0 +5.70596 0 7.44379 1.84998 +0 5.264 1.33261 5.93771 +0.906118 0.575878 0 1.91852 +5.68366 1.02669 5.89346 0 +3.30293 0.0799186 0 6.44729 +0 10.5219 0.276676 6.28156 +0 4.48805 3.91535 1.07432 +9.58464 1.94917 0 7.28545 +9.23789 0 7.20929 6.77043 +3.67982 8.40165 0 8.09965 +5.72834 4.74898 2.52683 0 +2.4914 9.38798 0 9.32869 +0 6.46028 3.84019 3.87104 +5.94848 0 6.82972 6.38347 +4.87168 2.25696 0 3.99202 +0 1.22607 -0.519152 1.57745 +>MA0079.5 SP1 lnR0: -0.404 +9.28817 8.76822 0 4.77287 +9.35621 8.83626 0 9.35621 +9.35621 8.83626 0 9.35621 +9.35621 8.83626 0 9.35621 +1.95605 0 8.39371 8.91366 +9.35621 8.83626 0 9.35621 +9.22998 3.3682 0 9.22998 +1.87787 3.61184 0 4.68343 +2.86339 8.58602 0 9.10597 +>MA0156.3 FEV lnR0: 1.348 +0 0.432192 -0.353819 1.45686 +0 4.38826 2.64597 4.33974 +6.14724 0 5.41578 8.28834 +6.60979 0 8.97881 13.6279 +13.6279 13.1079 0 13.6279 +7.51834 13.1079 0 8.97344 +0 6.7389 8.62713 10.1373 +0 5.93945 8.71932 3.96945 +2.25831 5.56051 0 8.54909 +6.20386 1.8928 5.15032 0 +1.28119 0.846519 0 2.0489 +0 -0.16733 -0.385089 1.17477 +>MA0160.2 NR4A2 lnR0: 0.18 +1.01768 0.100696 -0.283773 0 +0.847882 0.823461 0.628353 0 +0 7.11877 2.30835 3.15945 +0 7.11877 6.12856 3.43238 +0 4.55912 6.12856 7.63873 +7.7791 7.25915 0 2.1905 +8.15868 7.63873 0 6.58923 +4.85885 2.6395 2.703 0 +8.15868 0 6.64851 4.29003 +0 4.81958 1.81367 7.63873 +>MA0466.3 CEBPB lnR0: 1.348 +1.669 1.08889 -0.155646 0 +0 3.05007 1.13795 10.0355 +12.4052 11.306 12.8755 0 +13.3954 12.8755 6.61542 0 +2.9196 12.1611 0 6.22916 +13.9154 0 11.826 7.18746 +7.30826 10.2565 0 13.9154 +6.2138 0 11.1788 2.97044 +0 6.58015 12.8755 13.3954 +0 11.8852 12.8755 13.3954 +11.4324 1.12003 3.04771 0 +0 -0.181185 1.06057 1.66195 +>MA0493.2 KLF1 lnR0: -0.404 +1.11583 2.36688 0 0.796596 +9.72696 9.20701 0 9.72696 +9.72696 9.20701 0 9.72696 +9.72696 9.20701 0 9.72696 +2.57285 0 8.30029 1.12481 +9.72696 9.20701 0 9.72696 +9.16893 8.64898 0 1.56776 +3.91734 9.053 0 5.80995 +9.72696 9.20701 0 9.72696 +>MA0507.2 POU2F2 lnR0: 2.516 +0 0.840901 0.886829 1.15719 +0 3.19988 1.00887 0.821437 +7.96069 5.92677 10.2206 0 +0 12.5198 12.5198 13.0398 +13.0398 8.74972 10.9504 0 +13.5597 13.0398 0 6.81899 +11.792 0 5.91006 3.23996 +0 12.1842 12.1842 1.89659 +0 9.54917 7.97973 7.23912 +0 9.96015 12.5198 9.90086 +7.26397 9.38091 7.40049 0 +1.95624 2.12745 0.046371 0 +0 2.80317 2.41438 2.61422 +2.14669 2.03029 0 3.26579 +>MA0509.3 RFX1 lnR0: 3.684 +3.37158 0 0.358063 2.22857 +10.1006 12.7968 0 14.307 +13.787 10.4872 11.2867 0 +8.83597 3.86814 11.2867 0 +2.43764 7.58289 0 4.93561 +13.0365 0 8.31016 2.70346 +13.1743 0 12.6543 3.74005 +0 11.2867 8.66868 10.3615 +10.4976 8.91775 10.7074 0 +3.81321 12.0819 0 13.181 +2.80168 8.48607 0 13.0535 +4.79597 0 7.20463 1.65116 +0 12.0691 3.71085 2.64839 +0 10.9679 10.4872 12.2176 +14.307 0 13.787 10.1006 +2.29891 0.424392 0 3.33898 +>MA0516.3 SP2 lnR0: -0.404 +2.81172 8.70389 0 3.73323 +2.79733 8.81925 0 9.3392 +9.60084 9.08089 0 9.60084 +9.60084 9.08089 0 9.60084 +3.4619 0 8.91189 9.43184 +9.60084 9.08089 0 9.60084 +9.56688 9.04693 0 5.74309 +3.34071 8.89765 0 9.4176 +2.06777 1.86361 0 5.4552 +>MA0526.4 USF2 lnR0: 1.348 +1.14421 1.55058 0 1.42056 +1.24348 4.28072 0 8.40032 +5.11473 2.12051 6.0663 0 +14.5742 0 11.2744 11.6036 +0 10.7544 11.2351 11.4946 +14.5742 0 10.7649 9.30439 +9.23469 14.0543 0 14.5742 +10.6287 11.2351 9.87011 0 +10.6134 10.7649 0 14.5742 +0 6.04795 2.11533 5.14606 +8.8636 0 4.30364 1.24543 +1.41885 0 1.57269 1.16251 +>MA0607.2 BHLHA15(MA0607.2) lnR0: 0.18 +0 2.86389 0.774207 2.18939 +2.15583 0 3.44256 8.42894 +8.52147 0 13.341 13.861 +0 8.95245 5.14213 7.90296 +13.341 6.97203 4.28708 0 +0 4.35787 7.04531 13.341 +7.72415 5.09017 10.0412 0 +13.861 13.341 0 8.62734 +8.26324 3.4284 0 2.12836 +2.19245 0.787278 2.83977 0 +>MA0625.2 NFATC3 lnR0: -0.404 +0 0.698133 0.0930439 1.50769 +3.57993 0.0930439 2.42597 0 +12.9158 12.3959 0 12.9158 +12.9158 12.3959 0 12.9158 +0 3.92113 2.28077 9.25696 +0 11.8759 4.41825 12.3959 +0 1.3479 3.06816 2.40452 +0 -0.417657 0.477328 1.24982 +0.0243535 -0.0652114 0.49858 0 +>MA0642.2 EN2 lnR0: -0.988 +0.837773 0 0.454457 1.58726 +3.44523 0 0.911383 2.02265 +9.60506 0 9.08511 1.3557 +0 1.6343 3.75808 3.08127 +0 9.19617 4.24512 9.71612 +9.71612 9.19617 9.19617 0 +4.9057 9.19617 9.19617 0 +0 6.89697 1.86774 9.71612 +>MA0644.2 ESX1 lnR0: -0.988 +3.96956 0 2.48023 1.1532 +4.31265 0.142333 12.9072 0 +0 4.38473 4.01599 6.68985 +0 7.0837 13.6042 14.1241 +14.1241 13.6042 13.6042 0 +8.59386 3.72176 5.86057 0 +0 13.6042 3.8458 5.08935 +0.863795 0.363676 0 1.43053 +>MA0651.2 HOXC11 lnR0: 1.348 +0 1.84324 1.52939 1.65928 +1.81178 3.7748 0 4.29658 +3.90975 4.42999 0 14.1626 +8.33182 5.42644 7.4249 0 +6.72083 0 9.42059 11.3192 +5.2481 13.7188 0 14.2387 +13.7699 13.25 13.25 0 +0 12.9192 9.49361 1.92091 +0 13.25 13.25 8.7749 +0 8.77068 7.78047 8.50008 +0 3.61559 4.46643 3.83881 +0 0.0210431 1.48697 0.397287 +>MA0666.2 MSX1 lnR0: -0.988 +1.94575 0 0.581252 2.02633 +4.94961 0 12.1859 1.57744 +0 4.75695 4.53673 12.1859 +0 6.29278 11.6659 12.1859 +12.1859 11.6659 11.6659 0 +12.1859 3.61113 11.6659 0 +0 11.6659 4.41567 12.1859 +0 0.577945 0.0682554 1.26983 +>MA0685.2 SP4 lnR0: -0.404 +2.62646 8.51801 0 2.23932 +9.63974 9.11979 0 9.63974 +9.63974 9.11979 0 9.63974 +9.63974 9.11979 0 9.63974 +1.89594 0 8.66035 9.1803 +9.63974 9.11979 0 9.63974 +9.52527 9.00532 0 4.03719 +1.69624 8.52993 0 4.17606 +9.63974 9.11979 0 9.63974 +>MA0690.2 TBX21 lnR0: 0.764 +1.21833 1.4597 0.77496 0 +2.85384 3.17759 2.73727 0 +8.30629 5.33923 8.91271 0 +3.78096 0 3.38393 6.63491 +0 6.01535 2.44991 4.83426 +12.2518 0 11.7319 12.2518 +0 5.48714 3.92638 9.75143 +9.11291 0 6.92143 10.6824 +4.83329 0 3.56938 4.0521 +4.61242 1.92649 6.05345 0 +2.30095 1.77808 2.71405 0 +>MA0707.2 MNX1 lnR0: -0.988 +1.00742 0.367982 0 1.72006 +13.3014 -0.0788201 12.7815 0 +0 2.01863 -0.310372 14.088 +0 13.568 13.568 14.088 +14.088 13.568 13.568 0 +14.088 2.60029 4.02214 0 +0 13.568 13.568 14.088 +1.46391 0.497672 0.100986 0 +>MA0708.2 MSX2 lnR0: -0.988 +1.93522 0 0.536747 2.05636 +5.31806 0 12.5098 1.7226 +0 4.60341 4.04599 12.5098 +0 5.23641 11.9898 12.5098 +12.5098 11.9898 11.9898 0 +6.59101 2.84897 11.9898 0 +0 11.9898 4.13672 12.5098 +0 0.42677 0.0221775 1.12398 +>MA0723.2 VAX2 lnR0: -0.988 +1.63455 0.0754502 0 0.902901 +3.15471 -0.0683974 5.46893 0 +0 0.729852 3.25193 2.32418 +0 4.42719 13.0663 2.83841 +5.18548 13.0663 13.0663 0 +3.27666 6.06938 1.63387 0 +0 13.0663 13.0663 3.60412 +0.796494 0.55223 0 1.98093 +>MA0740.2 KLF14 lnR0: -0.404 +4.74839 8.48341 0 1.3393 +9.68376 9.16381 0 9.68376 +9.68376 9.16381 0 9.68376 +9.68376 9.16381 0 9.68376 +3.57754 0 8.87356 3.65148 +9.68376 9.16381 0 9.68376 +9.21358 8.69363 0 1.85769 +3.52689 9.00188 0 9.52183 +2.3911 3.51665 0 9.25426 +>MA0742.2 KLF12 lnR0: -0.404 +3.28007 8.66561 0 2.41474 +3.87285 9.02389 0 9.54384 +9.67199 9.15204 0 9.67199 +9.67199 9.15204 0 9.67199 +4.77613 0 9.08357 9.60352 +9.67199 9.15204 0 9.67199 +7.18367 3.15906 0 2.42618 +4.23435 9.05205 0 9.572 +9.63054 9.11059 0 5.47604 +>MA0754.2 CUX1 lnR0: 0.18 +2.99942 1.96782 2.74494 0 +0 5.27091 2.12332 3.4948 +0 10.9331 2.0637 8.67319 +10.4629 5.2214 5.57668 0 +8.48394 0 6.88353 6.32838 +1.88614 10.4095 0 6.80035 +0 7.79422 6.92831 7.78885 +7.10374 5.37337 6.12269 0 +0 2.81614 3.16443 3.25566 +0 0.387218 1.652 1.50768 +>MA0756.2 ONECUT2 lnR0: -0.404 +1.59918 0 1.0699 2.59155 +2.27368 5.15144 0 6.72982 +0 6.57528 1.99305 5.68293 +13.0365 12.5165 12.5165 0 +13.5564 0 13.0365 13.5564 +1.39757 7.46799 0 12.939 +0 12.5165 12.5165 13.0365 +13.0365 7.04705 12.5165 0 +0 5.16539 2.03592 5.89433 +>MA0759.2 ELK3 lnR0: 0.764 +0 3.2704 0.927222 3.91188 +6.28749 0 3.2985 7.34161 +10.7946 0 10.5934 14.6632 +14.6632 14.1433 0 14.6632 +14.6632 14.1433 0 14.6632 +0 6.94784 6.45577 8.17985 +0 6.24142 6.82065 4.452 +3.79421 4.28175 0 9.44667 +5.66061 1.83562 4.44087 0 +1.08121 1.20036 0 1.63965 +1.0747 0.186307 0 2.10791 +>MA0764.3 ETV4 lnR0: 0.18 +0 2.38444 0.676455 2.27097 +4.64688 0 2.79506 5.91218 +4.96368 0 6.10538 12.4136 +14.394 13.8741 0 14.394 +14.394 13.8741 0 14.394 +0 6.37868 6.14003 6.72557 +0 4.01364 5.15667 1.96834 +2.66536 3.35599 0 6.65692 +4.10028 0.92971 2.6539 0 +1.05613 1.0599 0 1.72489 +>MA0765.3 ETV5 lnR0: 0.18 +0 3.69814 1.94144 3.12559 +6.76922 0 4.73482 7.63161 +7.96332 0 9.24117 14.3595 +14.3595 13.8396 0 14.3595 +14.3595 13.8396 0 14.3595 +0 5.82386 8.77953 7.13763 +0 6.33236 9.04253 3.16268 +3.53417 4.81829 0 8.82297 +5.54951 2.00506 4.74656 0 +0.630079 1.17469 0 1.76225 +>MA0784.2 POU1F1 lnR0: 3.684 +0 1.4927 0.9048 1.1898 +0.707315 0.202949 0 1.42549 +5.25214 0 3.24822 3.33534 +5.13993 4.37518 3.58379 0 +0 -0.217823 3.00879 3.08665 +0 8.40306 6.56327 6.94259 +11.8936 11.3737 10.3835 0 +5.43394 7.60361 9.80424 0 +0.705261 10.6934 10.6934 0 +3.63175 5.71287 0 8.21324 +6.68883 0 10.9034 10.4332 +0 8.08428 8.81403 7.76454 +9.91322 9.39327 11.3737 0 +0 8.81403 8.81403 6.04458 +0 3.25013 4.75234 0.361042 +1.92865 1.67996 2.54012 0 +>MA0798.3 RFX3 lnR0: 3.684 +5.0985 0 1.27933 3.47271 +8.76677 11.0267 0 11.5466 +11.0267 7.72687 8.52632 0 +2.92062 2.36243 8.76403 0 +1.31267 6.02987 0 4.22367 +9.70526 0 6.79392 2.75164 +11.4562 0 9.94606 4.41729 +0 8.52632 8.52632 8.05606 +7.8878 7.94709 7.72687 0 +3.41501 9.85962 0 11.3698 +2.28484 6.79412 0 9.61327 +4.05843 0 6.61092 4.9256 +0 10.5067 3.08032 8.24682 +0 8.9373 7.72687 11.0267 +10.5564 0 11.0267 9.56622 +2.89402 0.594515 0 4.34077 +>MA0799.2 RFX4 lnR0: 4.268 +2.12818 0 0.664647 1.112 +3.04315 0 0.423335 1.97221 +7.63939 8.68888 0 9.20883 +8.68888 6.18851 7.17872 0 +5.90901 3.68966 8.16893 0 +5.00249 6.70846 0 6.90964 +10.199 0 7.69867 8.21862 +5.922 -0.497145 4.63205 0 +0.0521911 1.50603 1.47982 0 +0 4.68285 -0.39281 6.19301 +8.6296 7.69867 0 10.199 +7.06015 0 6.38969 5.04059 +0 8.16893 3.75316 6.12923 +0 7.17872 6.37927 8.68888 +9.20883 0 9.67909 7.63939 +2.11189 0.487387 0 3.0852 +1.14521 0.765884 0 2.24128 +>MA0818.2 BHLHE22(MA0818.2) lnR0: 0.18 +0 3.57767 3.39785 3.46519 +0.857817 0 1.3558 6.57664 +13.4725 0 12.9526 13.4725 +0 12.4326 2.79491 6.67481 +12.9526 6.58358 6.24588 0 +0 6.99455 6.99455 12.9526 +6.50851 2.86722 12.4326 0 +13.4725 12.9526 0 13.4725 +5.94315 1.42129 0 0.89294 +3.48338 0.0213231 3.63296 0 +>MA0819.2 CLOCK lnR0: 0.18 +0 0.125844 0.0465491 0.852116 +0 1.236 0.115827 1.15421 +0 1.2433 1.84469 4.43726 +4.25632 0 10.8656 11.3855 +0 8.36519 4.67376 10.8656 +11.3855 0 8.56636 3.22303 +3.52657 7.31569 0 11.3855 +7.89493 3.94941 7.56573 0 +8.82585 9.87535 0 5.71366 +3.52586 0 0.219769 0.69207 +>MA0821.2 HES5 lnR0: 0.18 +2.32515 1.91765 0 3.03375 +0.995887 1.268 0 4.61754 +6.13513 0 6.50817 7.62628 +0 4.88888 1.77499 5.88394 +8.20552 0 5.74866 4.99541 +5.0106 5.97996 0 7.7454 +5.76415 1.78257 4.92542 0 +7.78742 6.41128 0 6.01307 +4.69635 0 1.26638 0.998594 +3.0497 0 1.89792 2.32591 +>MA0828.2 SREBF2(MA0828.2) lnR0: 2.516 +0.00265189 0.7053 1.63377 0 +0.743101 0.699866 0.523384 0 +0 5.75489 0.559907 12.1239 +7.02905 7.27126 10.8447 0 +14.1838 0 9.0655 14.1838 +0 13.1439 5.53269 12.6737 +10.5196 0 4.63165 11.6242 +11.404 4.63937 0 10.5196 +12.0944 5.44527 13.1439 0 +14.1838 8.95555 0 14.1838 +0 12.1537 7.24803 6.97513 +12.1246 0.562526 5.7918 0 +0 0.500041 0.708473 0.727486 +0 1.62277 0.697037 0.00106213 +>MA0831.3 TFE3 lnR0: 0.18 +1.62699 3.66306 0 7.03252 +5.02425 2.96083 3.38497 0 +14.6635 0 11.8444 14.6635 +0 10.198 10.8437 9.06448 +14.6635 0 11.3637 5.15941 +5.14474 11.3637 0 14.6635 +8.87372 13.6236 9.57615 0 +14.6635 11.5839 0 14.6635 +0 3.36635 2.97565 5.01703 +7.22439 0 3.66275 1.62622 +>MA0837.2 CEBPE lnR0: 1.348 +1.75381 1.28399 -0.338195 0 +0 3.22193 1.2752 7.94822 +13.3851 9.89451 11.2957 0 +13.3851 11.8749 5.66949 0 +3.12198 11.6014 0 5.84357 +12.3356 0 10.0957 5.68255 +5.67354 9.25599 0 10.9344 +5.70679 0 10.8748 3.14447 +0 5.6976 12.8651 13.3851 +0 11.8749 10.5659 13.3851 +8.32208 1.28881 3.20162 0 +0 -0.314926 1.31592 1.77868 +>MA0847.3 FOXD2 lnR0: 1.348 +1.79307 0 0.812831 3.41973 +2.8156 0.272056 3.0254 0 +2.03933 6.06243 10.342 0 +0 6.60121 3.60973 11.1686 +0 2.56867 2.53413 3.20839 +0 6.10858 0.0947905 8.86941 +4.46282 0 8.3091 0.751557 +0 4.35335 10.6487 4.90857 +0 6.10858 6.44232 10.1784 +0 10.6487 8.089 9.59917 +11.6886 0 11.1686 2.19557 +0 6.05027 5.56959 3.38141 +>MA0865.2 E2F8 lnR0: 1.348 +2.67259 1.11736 3.12465 0 +1.92938 2.1724 3.45463 0 +4.78777 0 3.16465 6.98239 +7.36562 0 2.04285 11.0298 +5.59174 0 7.73001 7.25975 +5.76001 7.53925 0 7.25975 +10.0396 0 5.80154 7.06899 +4.38132 0 1.52723 3.00588 +0 3.04734 3.46944 3.95993 +0 0.169649 1.22484 0.555727 +0 1.23726 1.22794 0.889038 +0 1.40578 1.90672 1.07269 +>MA0877.3 BARHL1 lnR0: -0.988 +0 2.45393 1.34848 2.04271 +1.50332 0 2.08709 1.67797 +4.7643 0 9.85422 7.64626 +2.74569 6.75558 0 6.85439 +3.77478 3.58377 6.27704 0 +11.8346 9.0155 11.3147 0 +5.29934 8.02529 11.3147 0 +0 7.26725 6.60636 4.92567 +>MA0878.3 CDX1 lnR0: 0.18 +3.2821 3.05847 0 3.29793 +4.41911 4.46225 0 6.39953 +9.09958 0 12.1295 0.892997 +0 -0.177882 11.596 3.72317 +0 12.4252 4.07728 12.9452 +12.9452 12.4252 12.4252 0 +0 6.64942 12.4252 5.17027 +0 6.29598 5.87525 8.0863 +0 12.4252 12.4252 12.9452 +0 1.80023 2.70165 3.04391 +>MA0879.2 DLX1 lnR0: -0.988 +1.28057 0.122514 0 1.64009 +4.41344 0 11.8699 1.41357 +0 1.81805 2.15968 3.49148 +0 4.23759 11.9621 12.4821 +12.4821 11.9621 11.9621 0 +12.4821 2.73146 4.74804 0 +0 11.9621 4.6337 3.30833 +0.835549 0 0.192123 0.846503 +>MA0884.2 DUXA lnR0: 1.932 +2.22095 0.26583 2.0082 0 +5.65511 6.67839 9.11375 0 +0.767641 12.0517 0 12.5717 +0 12.4032 10.4227 12.9231 +7.93808 0.499904 6.75483 0 +8.49221 1.54661 7.44694 0 +0.00841626 2.51382 2.56816 0 +0 8.96683 1.56964 8.57823 +0 6.75458 0.499141 7.49475 +12.9231 12.4032 12.4032 0 +12.58 0 12.0601 0.786336 +0 8.97759 6.53048 5.63758 +0 2.02653 0.277451 2.22645 +>MA1483.2 ELF2 lnR0: 1.348 +0 1.72489 1.15474 1.31011 +0 2.19412 2.52511 1.09144 +1.33986 0 3.09665 2.54148 +4.05343 0 2.48246 8.96274 +3.12359 0 8.4242 13.061 +12.7644 11.726 0 12.5189 +12.3094 12.1578 0 12.3759 +0 10.0407 12.2597 8.95501 +0 9.86025 10.3458 5.48785 +2.05234 4.01572 0 8.22801 +3.73932 2.1554 3.63545 0 +0 1.16105 -0.0944072 1.39823 +>MA1487.2 FOXE1 lnR0: 2.516 +1.19602 0 0.464356 2.90981 +4.7211 0 4.78038 0.672684 +2.1083 5.27732 10.6833 0 +0 6.16653 2.40704 6.09091 +0 3.91843 3.88132 2.11434 +0 3.69528 0.837991 6.27021 +1.79451 0.428671 6.25507 0 +0 2.55637 10.9769 7.14758 +0 4.53286 10.9769 5.79835 +0 10.9769 6.43687 8.20749 +12.0168 0 11.4969 5.6535 +0 5.98194 6.77061 4.769 +0 1.82362 2.41931 2.14692 +0 0.455318 0.992247 0.27118 +>MA1491.2 GLI3 lnR0: 3.684 +0.658606 1.33889 0 3.95225 +10.1587 10.9477 0 6.91279 +0 3.97586 3.93356 11.9379 +11.1489 0 12.9281 13.4481 +12.4579 0 11.9379 12.4579 +0 4.59668 9.11879 6.51581 +12.4579 0 12.9281 12.4579 +3.9059 0 11.8105 12.3304 +8.58924 0 11.9379 9.31899 +0 10.8387 6.70965 11.3587 +4.33319 0 6.42025 7.0228 +4.13292 3.71093 0 6.2432 +0.483666 3.75164 3.25474 0 +1.20786 0 3.41853 1.18458 +8.01001 5.4249 0 6.46188 +0.666205 0 2.22531 0.865219 +>MA1498.2 HOXA7 lnR0: -0.988 +1.69227 0.528051 0 2.21868 +2.70267 0 3.96514 1.20675 +0 -0.22924 2.52992 2.42256 +0 4.76338 3.1402 4.67115 +11.2829 12.3324 12.3324 0 +2.9913 3.63702 12.3324 0 +0 3.51569 4.42757 3.29047 +0 0.0749429 0.4324 1.38309 +>MA1511.2 KLF10 lnR0: -0.404 +3.91436 8.73886 0 3.45215 +9.53926 9.01931 0 9.53926 +9.53926 9.01931 0 9.53926 +9.53926 9.01931 0 9.53926 +4.67513 0 8.71041 2.88239 +9.53926 9.01931 0 9.53926 +9.02022 3.65951 0 1.95529 +4.2535 8.88341 0 5.50538 +4.2174 8.84732 0 4.61549 +>MA1525.2 NFATC4 lnR0: 0.18 +0 0.695937 0.992953 1.38819 +0 2.76546 0.928148 2.22322 +7.9865 0.287917 6.10801 0 +13.1963 12.6764 0 13.1963 +13.1963 12.6764 0 13.1963 +0 12.1564 12.1564 12.6764 +0 12.1564 12.1564 12.6764 +0 3.39444 6.78329 5.98762 +0 -0.390839 2.08855 2.58999 +0.151411 0.7019 3.87465 0 +>MA1532.2 NR1D2 lnR0: 3.1 +6.09645 4.36633 2.84957 0 +0.560788 4.97992 0 7.35245 +10.2033 9.3267 0 4.12038 +9.5715 11.391 0 11.0637 +10.8794 6.34427 3.20406 0 +10.0574 -0.493899 10.4757 0 +0 15.2185 13.6491 7.54336 +4.17593 2.69598 0 4.58605 +9.70104 6.42848 5.38425 0 +0 6.08715 -0.382847 8.37102 +10.2354 11.0023 0 2.63276 +8.30192 9.44687 0 10.1929 +5.15416 4.04031 2.90781 0 +10.7866 0 5.88292 3.45677 +0 9.67505 2.05076 6.64778 +>MA1547.2 PITX2 lnR0: -0.988 +2.0409 -0.052611 2.53451 0 +12.8424 6.67784 12.3225 0 +0 12.3225 12.3225 12.8424 +0 12.3225 12.3225 12.8424 +12.8424 12.3225 3.02849 0 +13.3624 0 12.8424 13.3624 +13.3624 0 12.8424 5.86662 +2.72544 0 2.36829 1.40484 +>MA1563.2 SOX18 lnR0: -0.988 +0 1.83058 0.780657 3.56677 +0 8.12589 8.12589 8.64584 +9.16579 0 2.18614 7.59635 +0 8.12589 8.12589 8.64584 +0 3.00658 3.99679 8.64584 +8.72113 8.20118 8.20118 0 +0.165146 7.24251 -0.475601 0 +1.04211 0 0.373513 9.5393 +>MA1566.2 TBX3 lnR0: 0.764 +0 0.655527 0.0308952 1.16577 +0 5.1988 2.09911 4.54813 +3.63398 3.19621 0 5.50895 +12.4626 8.07398 0 12.4626 +10.3732 3.30327 11.4227 0 +12.4626 10.3732 0 12.4626 +5.48293 2.46412 7.21633 0 +6.01849 2.2668 0 3.06762 +0 9.12348 6.76825 9.38297 +0 3.09141 2.77348 3.14997 +0 0.0628009 0.155233 1.47907 +>MA1601.2 ZNF75D lnR0: 1.348 +8.52424 9.2518 0 9.77175 +4.49979 4.77641 6.73684 0 +6.55705 7.98576 0 9.75322 +4.66576 7.83515 0 4.23476 +3.02576 5.39164 0 5.16341 +0 6.81637 7.47201 7.33632 +0 5.23242 3.69001 6.18091 +0 8.50995 2.03404 7.12675 +2.97462 1.50956 0 1.84026 +5.54318 0 2.77472 3.47084 +3.99939 0 5.36889 3.29105 +5.16273 2.42216 4.78271 0 +>MA1630.2 ZNF281 lnR0: 1.348 +9.60964 9.08969 0 9.60964 +9.60964 9.08969 0 9.60964 +5.20074 9.03921 0 9.55916 +9.60964 9.08969 0 9.60964 +9.60964 9.08969 0 9.60964 +0 1.43333 8.10485 2.86491 +3.14526 8.72428 0 3.36215 +9.60964 9.08969 0 9.60964 +4.95554 9.00453 0 6.09023 +4.74104 5.00368 0 7.39131 +0 -0.296709 -0.341308 1.29749 +1.11697 0.711893 0 2.4515 +>MA1633.2 BACH1 lnR0: -0.404 +0 3.8825 1.84172 4.89706 +11.863 9.65925 9.65925 0 +15.3536 11.0635 0 5.78286 +0 9.08001 9.71528 10.965 +6.33422 0 14.8336 6.42503 +5.85895 9.36262 2.73811 0 +3.99672 0 9.16177 11.1472 +0 9.04384 8.69678 10.7045 +2.67451 1.34876 2.89373 0 +>MA0597.2 THAP1 lnR0: 1.348 +1.48239 0.279533 0 1.76956 +1.65342 0 0.151799 1.68614 +3.23027 1.70377 0 3.02983 +3.09159 0 1.82548 3.78067 +0 3.86359 3.85711 8.94983 +8.19633 5.22418 0 6.56608 +7.35166 4.6869 0 6.73799 +6.21129 6.12317 0 6.42892 +6.08293 0 5.47892 5.85654 +0 5.0984 4.25705 8.58898 +2.31504 0.682423 0 2.35359 +1.44377 0.217291 0 1.87629 +>M01001 AHR lnR0: -0.404 +0.95621 1.56945 0 1.02591 +2.98543 2.35114 0.896038 0 +1.54859 0.0698283 1.09214 0 +5.66872 6.13898 0 5.34994 +6.69728 0 6.17733 6.11805 +5.69758 6.16784 0 6.68779 +7.16754 4.66717 5.65738 0 +7.72484 7.20489 0 7.72484 +1.14183 0 1.98042 1.7374 +>M01002 AIRE lnR0: 4.852 +0 -0.0223695 0.967841 0.75804 +1.14073 0.620775 0.979795 0 +1.6359 1.11595 0.756932 0 +4.10896 5.15845 0 3.69798 +5.55761 5.03766 0 2.41872 +0.884342 2.56503 3.14426 0 +0.30187 1.53017 2.83916 0 +0 0.661019 0.661019 0.0921979 +0.337698 1.70597 0.906519 0 +0 1.59663 1.11595 0.99021 +0.30187 2.25992 1.84895 0 +1.25067 1.24025 2.03971 0 +5.6784 4.16824 0 3.37921 +5.82505 5.3051 0 4.83484 +0.916934 1.38719 0.260826 0 +2.49886 0.820435 0.820435 0 +0 2.69618 0.71576 0.2455 +0 0.0592853 1.30995 0.839695 +>M01003 ALX1 lnR0: 1.348 +0 0.568821 0.2098 1.88822 +3.13889 2.20797 4.18839 0 +0 3.08823 2.09802 2.61797 +0 2.6709 4.24034 3.19085 +4.81042 2.31005 4.29047 0 +3.28941 0.789036 1.46047 0 +0.606557 4.04745 0 4.5674 +0 0.410974 0 2.55966 +0 4.07844 1.77925 2.61797 +2.77987 4.24034 3.25013 0 +3.19085 3.25013 3.25013 0 +0 2.56503 2.56503 3.08498 +>M01008 ARID5B lnR0: 1.932 +0.579236 0.99021 0 0 +1.73038 0.480675 0 1.3194 +3.13889 0.319745 0.638521 0 +3.13889 1.0495 0.0592853 0 +0 1.56945 0 0.260459 +1.96509 2.43535 0 2.9553 +3.96084 3.44089 3.44089 0 +0 3.25013 1.68069 3.77008 +3.77008 1.68069 3.25013 0 +3.77008 2.25992 2.25992 0 +2.0894 0.839695 0 2.66863 +1.56945 1.62873 0.319745 0 +1.00063 1.21043 0 1.3194 +>M01009 ARNT lnR0: -0.404 +1.99348 0.589191 0 2.17105 +1.94948 2.30225 0.635917 0 +0 3.89582 0.970549 4.82675 +6.76503 0 7.81453 4.97537 +7.40607 7.87633 0 8.39628 +8.87801 8.35806 7.36785 0 +9.38936 6.88899 0 8.39915 +1.07504 0 4.30143 2.9553 +2.19527 0 1.76996 1.82611 +>M01025 ARNTL lnR0: 0.764 +1.69959 1.17964 0 0.786023 +2.08277 0 0.821211 5.63263 +4.24937 0 7.4995 7.44022 +0 5.36439 4.0554 3.90392 +5.2474 0 4.28437 2.2931 +7.06626 5.23732 0 5.90778 +5.77936 8.03928 5.47963 0 +9.08275 6.99336 0 5.94386 +0 0.23809 3.4032 0.824498 +3.69447 0 0.739165 2.08238 +1.48489 -0.209858 0.916509 0 +>M01011 ATF1 lnR0: 0.764 +0.836755 0 1.16639 1.39642 +0.535736 1.63366 0 1.62451 +1.04713 2.22313 0 4.39418 +5.5093 6.29834 4.23131 0 +5.90512 6.25108 0 6.04128 +0 5.72212 5.14288 4.93308 +5.08777 0 3.85497 3.76207 +5.54788 5.55325 0 3.83895 +2.85442 0.354052 4.46541 0 +1.20365 0 1.66409 2.66863 +0 1.67186 0.982073 1.67982 +>M01021 BCL11A lnR0: 4.268 +0 0.493117 -0.131474 1.26434 +0 1.8923 0.755782 2.08788 +0 1.26403 0.582711 1.93009 +0 4.47024 0.843137 1.78244 +2.11916 1.82696 0 3.46624 +0 4.80677 0.759317 3.58901 +3.45993 5.47293 0 4.42344 +2.41288 4.43851 0 6.44625 +0 3.69941 3.58029 4.82999 +0 6.17869 3.34869 3.55975 +1.52154 1.13319 0 4.75492 +2.11058 1.55353 3.72995 0 +3.1606 3.33126 0 4.35524 +0 2.76946 0.855493 4.41577 +0 1.11951 0.0346542 2.3306 +0 2.41451 1.4243 2.09477 +0 0.285432 -0.343775 1.57736 +>M01238 CBFB lnR0: 0.764 +2.674 0.364391 0.845066 0 +2.9553 0 1.44514 0.656108 +3.42556 3.89582 2.90561 0 +4.79957 2.2992 0 3.80936 +4.1291 0.82928 3.60915 0 +3.36628 4.41577 0 4.93573 +4.00902 4.47928 0 4.99923 +4.20634 3.68639 1.12673 0 +2.55966 -0.395649 2.03971 0 +0 1.77925 0.47026 0 +2.66863 0.168261 0 0.688212 +>M01040 CRX lnR0: 1.932 +0.801083 0.866094 0.973287 0 +0 1.79533 0.491742 2.37023 +0 3.02992 0.520745 2.4181 +2.21004 2.56975 0 2.22656 +0 1.05522 0.392419 2.65414 +2.50405 6.53898 0 5.26927 +5.25908 6.22692 0 5.75666 +0 1.26227 4.83835 7.50698 +8.88087 8.36092 8.36092 0 +5.17445 3.34551 4.54015 0 +0 6.60924 4.04958 3.35911 +1.46751 2.92798 0 2.41631 +1.06653 0.0850591 0 2.29319 +>M01045 DLX3 lnR0: 0.18 +2.21936 2.18008 0 3.42978 +0 0 1.08877 3.86864 +5.03766 3.5275 4.51771 0 +0 4.51771 3.5275 5.03766 +0 4.55912 4.55912 5.07907 +5.07907 4.55912 4.55912 0 +4.99501 4.47506 2.90561 0 +0 2.69618 0.0221775 2.22592 +2.16664 0 0.916934 3.15685 +0 0.881234 1.14169 0.535276 +>M01051 E2F5 lnR0: 0.18 +1.2497 0 0 1.2497 +4.06982 2.55966 0 4.06982 +4.18416 0 3.66421 4.18416 +4.18416 3.66421 0 4.18416 +3.94552 0 1.85612 3.94552 +3.29982 0 0 3.29982 +0 3.14426 3.14426 3.66421 +0 3.14426 3.14426 3.66421 +0 3.14426 3.14426 3.66421 +1.09919 0 0.99021 1.51016 +>M01063 EPAS1 lnR0: -0.404 +1.46003 0.788334 0 3.1718 +1.61958 2.31005 0.554815 0 +0 4.73026 2.43107 6.69536 +5.84393 0 4.97947 4.85372 +6.2185 6.27778 0 7.78795 +8.87801 8.35806 7.36785 0 +9.39796 8.87801 0 8.40775 +0.844793 0 2.89978 2.76568 +2.10693 0 1.83689 1.68278 +>M01067 ESRRG lnR0: -0.404 +2.55966 3.02992 1.46047 0 +2.9553 0 2.43535 2.37607 +0 3.02992 1.0495 3.54987 +0 3.34869 3.34869 3.86864 +4.18416 2.674 0 3.19395 +4.29003 2.77987 0 4.29003 +2.77987 3.25013 3.25013 0 +3.07961 0 3.54987 2.50037 +0 2.15405 2.15405 3.66421 +>M01078 FEZF1 lnR0: 1.348 +0.758599 1.53839 0 1.29219 +2.36634 0 2.65655 1.16815 +3.57283 4.12474 4.62232 0 +6.54782 5.38218 0 6.03828 +5.59391 0 2.39995 1.27033 +4.08886 -0.353146 2.63065 0 +3.9934 0 4.65442 2.45403 +1.49264 2.91813 4.85319 0 +6.60008 2.03269 3.40613 0 +5.38517 5.73113 5.00138 0 +4.02906 2.16334 2.86908 0 +0.956986 -0.494515 0.556866 0 +>M01080 FOSB lnR0: -0.404 +0 0.47026 -0.0240855 2.18697 +6.28658 5.54641 7.33607 0 +6.49897 5.78826 0 4.46842 +0 5.4245 4.91496 3.52777 +2.45457 8.55566 0 9.07561 +5.35307 4.16168 2.42398 0 +4.49665 0 4.86835 6.28631 +0 5.75194 6.33118 5.54214 +2.2992 -0.365139 0.146858 0 +>M01090 FOXJ2 lnR0: 0.18 +5.3051 3.79494 4.78515 0 +1.45821 4.70834 0 3.65884 +5.3051 4.78515 3.79494 0 +5.33953 4.81958 4.81958 0 +5.33953 4.81958 4.81958 0 +0 3.95933 -0.320291 4.47928 +5.03766 1.37882 4.51771 0 +2.20064 0.950934 4.24034 0 +4.9057 3.39554 0.960181 0 +0 1.46047 1.20001 0.509536 +>M01091 FOXJ3 lnR0: 1.932 +1.32055 1.20001 1.04031 0 +9.20135 8.6814 8.6814 0 +3.9208 9.07269 0 8.0232 +8.20886 8.67912 8.67912 0 +9.20135 8.6814 8.6814 0 +6.12923 8.38915 1.66125 0 +0 8.39473 3.85465 2.45498 +9.09496 3.10552 8.57501 0 +1.97545 7.56502 -0.432722 0 +3.73084 8.02131 0.417015 0 +4.0425 8.5602 4.35386 0 +6.85349 5.85286 5.08287 0 +0.259405 2.04499 1.08688 0 +>M01093 FOXM1 lnR0: 1.348 +3.8979 4.52416 4.05927 0 +2.00443 4.85488 0 6.36504 +4.94145 4.23074 3.38116 0 +8.68235 3.08333 3.21134 0 +7.77797 7.25802 3.08978 0 +1.38505 3.36396 0 4.36458 +3.78662 0 5.17382 2.68786 +1.15847 1.24685 3.24502 0 +3.35092 0.309926 1.31984 0 +0.663519 3.29038 3.70135 0 +2.52611 1.45314 0 1.15114 +1.54378 0 0.399943 1.05825 +>M01094 FOXO1 lnR0: 1.348 +1.06425 0.756932 0.070149 0 +1.77711 -0.397176 -0.125685 0 +3.36418 0 0.818457 1.45462 +4.00012 0 1.46613 1.12623 +6.85408 5.53468 5.34392 0 +5.2314 4.62979 0 6.13995 +6.98263 1.5417 4.89323 0 +6.16784 4.2467 3.25649 0 +5.64463 3.55524 1.16384 0 +0 0.316933 2.36201 0.331145 +6.89571 0 3.64784 1.96715 +0.553951 -0.186215 0.38766 0 +>M01099 FOXQ1 lnR0: 1.348 +0 0 1.30899 0 +0 1.77925 0.789036 3.28941 +2.43535 1.33617 2.90561 0 +3.77008 3.25013 3.25013 0 +4.29003 3.77008 0 4.29003 +3.77008 3.25013 3.25013 0 +3.77008 3.25013 3.25013 0 +3.77008 3.25013 3.25013 0 +0 3.25013 3.25013 3.77008 +3.66421 3.14426 2.15405 0 +1.56945 2.61894 0.638521 0 +3.28941 0.47026 2.76946 0 +>M01107 GFI1B lnR0: 0.18 +2.54049 3.55427 0 2.65333 +4.12813 0 3.19721 3.16193 +0.720259 0.892709 4.07844 0 +5.32489 0.501708 0 2.81915 +0.421596 3.27145 3.70771 0 +7.3974 6.87745 0 7.80837 +0 3.29174 2.45753 6.32292 +8.84331 5.7637 5.18446 0 +7.30571 8.3552 8.3552 0 +4.04745 1.83793 1.15502 0 +>M01112 HIC1 lnR0: -0.404 +1.73038 2.05012 0 1.89864 +4.38859 2.55966 0 2.81915 +5.6784 5.15845 0 3.69798 +3.60818 4.07844 0.2098 0 +5.26983 4.74988 4.74988 0 +4.7634 5.23366 0 5.75361 +4.7634 0 5.23366 5.75361 +5.78978 0 5.26983 5.78978 +1.92114 0 2.24088 2.76083 +>M01142 ISL1 lnR0: -0.404 +1.48693 0.23723 0 1.83285 +4.26429 0 3.68602 1.90678 +1.15847 2.92783 4.95838 0 +0 3.01796 1.1234 6.41634 +0 5.54933 5.76954 8.84915 +5.16701 5.80553 0.57187 0 +4.06523 8.1997 0 1.41682 +2.70451 4.14788 0 4.9697 +0 -0.313592 -0.323212 2.22592 +>M01155 KLF8 lnR0: -0.404 +2.81915 0 2.2992 1.82894 +0 -0.108976 1.46047 1.98042 +2.81915 2.2992 0 1.82894 +2.50037 1.98042 0 0.930925 +3.07961 2.55966 0 3.07961 +2.50037 1.98042 0 0.930925 +3.07961 2.55966 0 3.07961 +2.2992 0.789036 1.77925 0 +2.81915 1.30899 0 2.81915 +>M01159 LHX3 lnR0: 1.932 +0 1.97001 0.979795 1.40118 +0 2.73329 0.752868 1.18621 +0 2.31005 2.31005 4.81042 +0 3.28375 1.30333 1.24404 +5.05851 4.53856 3.95933 0 +6.10952 5.58957 4.59936 0 +0 5.60928 5.60928 6.12923 +0 5.58957 4.59936 6.10952 +6.12923 5.60928 5.60928 0 +4.47928 4.53856 4.53856 0 +0 5.50792 3.93847 4.04745 +0 1.54708 -0.0806867 1.89877 +1.24148 0.106128 0.835879 0 +>M01160 LYL1 lnR0: 2.516 +1.60568 0 1.10101 2.04738 +2.73574 0 4.55828 2.86976 +0 3.04472 3.16902 1.26547 +3.53614 1.9239 0 1.09599 +2.96394 0 3.94373 3.40702 +3.01017 8.04996 6.06954 0 +7.96986 2.16233 0 6.40041 +5.8129 0.255287 0.960736 0 +2.97063 0.755564 0.668074 0 +1.07061 0.46317 1.20714 0 +3.95783 0 2.06244 1.16827 +3.07961 0 2.34875 1.93564 +1.76112 0.841227 0.891951 0 +2.15703 0.464254 0 1.24695 +>M01161 MAFB lnR0: 0.764 +2.98175 4.44222 3.13323 0 +7.19208 3.89226 0 5.0434 +4.22479 0 5.68526 6.03695 +3.43882 6.17211 8.15253 0 +4.96783 5.15142 0 3.72379 +0 4.45325 3.29478 2.99278 +2.53431 0 0.520114 2.23768 +1.45593 1.40775 1.98699 0 +1.76919 0 1.35643 1.26655 +0 1.11117 0.710739 0.996933 +1.3652 1.99436 0 1.46915 +>M01168 MBD2 lnR0: 0.764 +1.82894 0 0 3.17817 +3.19395 0.238649 0 2.73902 +6.84969 1.51932 0 6.84969 +5.33037 5.80063 0 0.622035 +7.26066 0 6.74071 7.26066 +7.26066 0 6.74071 7.26066 +7.26066 6.74071 0 7.26066 +7.26066 6.74071 0 7.26066 +0 0.0592853 1.6649 4.85885 +2.84096 2.32101 0 2.02589 +1.06005 1.82991 0 3.07961 +>M01076 MECOM lnR0: 3.684 +0 0.825826 0.544811 0.745985 +0 3.36448 2.25992 1.36502 +5.48212 4.64339 0 4.68267 +0 5.52877 5.52877 5.46949 +3.30967 -0.393818 4.57938 0 +0 4.91814 4.91814 5.02711 +0 5.44346 4.86422 3.66421 +5.2493 6.03833 0 7.54849 +0 6.50859 6.50859 4.46889 +6.87455 2.14826 5.36439 0 +0 3.85186 6.41152 3.64206 +0 5.20481 1.71574 3.42556 +1.20286 0.880266 0 0.950101 +0 2.37202 2.59224 2.99784 +1.52102 0.801405 -0.125303 0 +0 1.42023 1.07005 1.03162 +>M01169 MECP2 lnR0: -1.572 +4.3103 0 0.7164 4.62907 +7.35922 0 6.83927 7.35922 +7.35922 0 6.83927 7.35922 +7.35922 6.83927 0 7.35922 +7.35922 6.83927 0 7.35922 +0 4.53856 -0.0881207 6.04872 +0.854809 5.01649 0 6.52665 +>M01186 NANOG lnR0: 4.268 +1.34801 -0.162151 -0.278188 0 +3.89377 0 1.4248 1.25361 +3.00354 0 2.80237 1.13879 +0.928604 3.12502 2.6986 0 +5.92523 3.27945 3.76937 0 +3.62603 5.88595 3.90553 0 +2.8937 1.22666 0 3.93586 +0.525321 3.07781 3.28724 0 +0.450449 -0.243226 0.18604 0 +0 3.9244 3.70418 2.72439 +3.62925 5.21774 4.22753 0 +5.33037 5.2911 0 2.97123 +4.88281 0 2.40645 2.02355 +0 3.76386 4.67242 1.31318 +0 3.11868 0.92197 3.75297 +0 3.45156 2.97089 3.30008 +1.82655 1.20938 0.803111 0 +>M01191 NFATC1 lnR0: 3.1 +0 0.530546 0.506125 3.08105 +0.327408 2.7077 2.45643 0 +3.8838 6.43779 0 7.68749 +6.32673 4.23733 0 6.7377 +0 5.5019 4.07543 6.8213 +0 2.98149 2.38871 5.2911 +0 3.00244 2.70837 4.83138 +0 1.04382 0.366018 2.85585 +0 2.64804 1.24685 0.653118 +0 0.0513267 -0.479478 2.50486 +0 1.9009 2.85971 0.355693 +1.5577 4.06312 0 2.28387 +0 1.58189 0.737082 2.14868 +0 -0.0912297 0.65348 2.68396 +0 1.35099 1.15439 0.614432 +>M01189 NFE2L1 lnR0: -1.572 +0 0.22937 1.75039 0.799451 +2.19934 3.71813 0 4.81731 +6.74071 6.22076 5.23055 0 +5.13256 0 6.59303 3.82357 +0 4.58607 5.16531 4.69505 +5.38966 1.65358 2.88929 0 +0.839695 -0.0550614 -0.438296 0 +>M01203 NKX2-1 lnR0: 0.18 +3.13456 0 0.886268 1.07248 +2.46793 2.45447 4.29047 0 +2.84133 4.00517 0.235085 0 +5.21054 6.83927 0 8.34943 +0 7.36499 8.3552 7.88494 +6.81526 6.55577 0 9.37492 +1.10146 6.67105 1.98941 0 +3.49058 7.70518 0 6.43547 +4.19703 0.439008 0 1.66567 +1.63818 0 1.1362 0.561361 +>M01209 NOBOX lnR0: -0.404 +0.19966 0 2.49886 0 +6.0067 5.48675 5.48675 0 +0 5.44346 5.44346 4.39396 +0 3.87401 5.44346 5.96341 +4.30323 3.78328 3.78328 0 +4.23119 5.28068 2.31005 0 +1.2947 5.37314 0 5.89309 +1.60872 0.509536 0 3.07961 +2.43535 0.268719 0.925194 0 +>M01211 NR1H3 lnR0: 5.436 +2.01465 0 1.19282 2.25177 +0 0.385627 1.22027 0.880514 +0.684831 1.70425 0 2.86036 +0 3.7235 -0.00966716 3.35911 +3.21157 6.6071 0 4.24862 +4.72253 4.00292 0 2.70683 +3.21841 1.43343 1.48803 0 +2.06306 0 2.2992 0.830445 +0 4.80591 3.33502 3.02666 +2.85322 0 2.02438 2.44842 +1.17384 0.979001 2.00132 0 +0.788259 0.340964 0 0.776501 +1.01826 0 0.187008 1.48411 +0 2.2993 1.38892 3.01891 +3.84038 4.85545 0 4.28663 +3.23012 4.0594 0 2.87995 +1.65932 1.27553 0.616909 0 +3.69798 0 3.28941 3.19202 +0 3.68639 3.56727 4.47928 +>M01217 NR2E3 lnR0: 2.516 +0 0.730719 0.730719 1.25067 +0 2.11694 2.11694 3.21613 +0 2.69618 1.70597 3.21613 +2.99795 2.478 0 2.58698 +2.71017 3.75967 2.19022 0 +3.29982 0 3.35911 4.86927 +0 3.89582 2.90561 3.42556 +0 1.70597 2.11694 4.20634 +0 3.95933 3.95933 3.48907 +0 3.75967 1.77925 3.28941 +1.51016 2.20064 0 2.72059 +2.97063 1.87144 0.881234 0 +2.58698 0 2.478 2.99795 +0 1.62873 2.03971 3.13889 +>M01220 NR5A2 lnR0: 0.764 +1.72593 1.25334 0 1.48371 +2.5157 -0.118862 -0.00615686 0 +3.56761 -0.397251 3.19818 0 +7.75524 0 4.20634 9.32469 +0 5.77826 6.3575 8.85787 +0 7.28249 4.31186 4.92401 +8.40203 7.88208 0 8.40203 +8.39628 7.29709 0 7.81704 +2.26687 0 3.38606 0.567461 +5.58191 0 6.05217 3.04223 +0 4.07463 1.89455 2.99373 +>M01251 PGR lnR0: 3.684 +0 3.50633 -0.454508 1.43717 +3.55068 6.00136 0 4.54089 +0 1.09543 0.863264 1.64367 +0 3.49753 4.40608 4.77552 +6.57384 0 6.05389 3.5166 +0 3.5275 1.91891 1.61209 +4.25076 1.21958 1.29545 0 +2.81093 0.876123 1.78695 0 +3.24305 0 1.63866 1.05172 +3.05162 3.04121 3.62045 0 +5.96858 3.248 0 4.86403 +3.8228 3.95933 3.95933 0 +1.02781 1.33617 1.14541 0 +4.09231 0 5.94126 3.24508 +2.85353 0.712175 3.90302 0 +1.54659 0.142296 0.198326 0 +>M01246 PPARA lnR0: 4.268 +0 0.648679 1.40934 1.54082 +0 3.80296 2.02908 0.584576 +2.83269 0 0.194615 2.20881 +3.35911 1.96515 1.58477 0 +0.594827 3.83857 0 3.46051 +3.6186 7.63873 0 4.11123 +2.91847 5.78649 0 4.80669 +2.1569 1.07316 0 0.847914 +2.81915 0 0.9684 2.61472 +0 4.95882 3.48794 7.19874 +0 3.33565 0.808832 3.61695 +0 8.06407 1.55853 8.58402 +3.12507 7.04238 0 4.92544 +4.23101 6.27071 0 3.10464 +3.77977 1.76007 0.688867 0 +3.50926 0 1.98042 2.42802 +0 2.5611 2.31202 2.86083 +>M01248 PRDM14 lnR0: 2.516 +0 1.41285 0.226034 1.79877 +0.688212 3.13889 0 2.55869 +3.72016 2.13673 0 4.10629 +2.12847 4.69898 3.63907 0 +6.05463 5.75489 5.75489 0 +0 6.76557 6.3546 6.55577 +3.83965 3.75353 0 8.18896 +0 5.01529 0.117294 3.55482 +3.91523 3.63392 0 5.59902 +0 1.6971 3.59586 1.70961 +2.62117 0 3.4102 5.09917 +4.70737 0 2.41831 3.71716 +1.81754 -0.499095 2.01915 0 +0 0.723259 0.0078659 0.910218 +>M01250 PRDM6 lnR0: 1.932 +0 0.937509 0.381131 1.86843 +0 2.33716 0.448937 1.96972 +0 0.607728 -0.130654 3.34282 +0 3.39092 1.06343 2.06126 +0 4.73191 -0.458365 2.77386 +8.32542 4.25561 0 6.75598 +0 5.19031 8.3292 6.86873 +0 6.76847 8.33792 6.078 +0 5.97047 5.97047 4.24954 +0 1.96306 2.89069 4.1404 +0 0.827261 1.86674 3.50805 +0 0.815303 1.40934 1.35006 +0 1.14282 0.777788 1.83556 +>M01253 PTF1A lnR0: 4.852 +2.04544 0 0.296628 3.90156 +6.36305 0 6.03386 5.90812 +0 5.71305 6.29228 4.31338 +7.04045 4.02164 0 2.54573 +3.96536 0 5.1292 5.06991 +5.88143 6.76267 7.3419 0 +6.74382 5.64463 0 4.95416 +4.81892 0 0.685597 1.26905 +3.36852 0 1.78631 0.602789 +1.58439 0 0.393005 0.584687 +2.79167 0 0.702278 1.17758 +2.11714 0 1.53551 0.921797 +1.4132 0.238808 0.275916 0 +3.02691 -0.102832 1.21852 0 +2.59775 -0.354037 2.11694 0 +3.68269 0 2.15105 2.0706 +1.36872 0 2.674 1.31134 +1.9231 0 1.43489 2.0894 +>M01268 RXRA lnR0: 6.02 +1.19278 0.850889 0 2.32362 +0.968033 2.12484 0 1.6097 +2.44506 2.72909 0 2.50037 +1.13833 1.95744 0 0.80063 +1.13361 0.625323 0 1.93888 +0 2.86368 0.029209 1.41954 +1.74827 1.7062 0 1.95918 +0.748644 0.884342 0 1.26956 +1.06271 0 0.0416523 2.5505 +0 3.62396 0.620229 2.11953 +1.18627 2.96552 0 4.6959 +0 4.89009 0.821784 6.08147 +4.22871 6.18676 0 6.29574 +6.0269 4.29652 0 3.60605 +3.59671 3.54605 0.50761 0 +4.58555 0 2.74424 4.35649 +0 4.01699 3.94371 5.45387 +1.34469 1.34387 0 2.45111 +0 1.12315 -0.190365 1.23213 +1.63253 1.8579 0 3.23725 +>M01271 SALL4 lnR0: 0.18 +2.00866 1.86352 0 2.10611 +2.32157 0.875864 0 2.36421 +0 4.92605 -0.455371 0.306986 +6.58046 7.85017 0 6.3897 +8.38471 7.28552 0 6.59505 +5.6643 2.2746 0 6.11923 +0.638768 3.63861 5.03979 0 +7.40318 7.87344 0 7.81416 +3.22009 5.14985 0 2.04269 +3.25841 4.92331 0 4.6282 +>M01276 SMAD4 lnR0: 1.932 +1.5359 0 1.12382 2.28746 +0.796798 1.8556 2.76416 0 +6.0232 6.233 0 5.54252 +3.88443 3.36448 1.49222 0 +8.37597 0 6.54704 7.06699 +7.86766 6.3575 7.34771 0 +2.52943 1.47665 0 4.11858 +1.4423 1.30899 0 0.867982 +5.43483 0 5.64463 6.16458 +0 3.16045 2.36858 2.27922 +4.16779 0 1.85064 3.92508 +2.57207 0 3.08498 1.83394 +1.99586 0.876123 1.99435 0 +>M01282 SOX17 lnR0: 0.764 +2.385 0.575902 0 1.77329 +5.04595 0 3.07324 3.97409 +4.73343 0 6.99336 2.84068 +0 5.05269 6.62214 3.21132 +7.2621 4.88603 5.75194 0 +6.19426 2.12444 2.19772 0 +5.05544 3.16205 0 1.60022 +4.91488 4.71371 5.12468 0 +1.70121 1.18125 0.18073 0 +2.36365 -0.0420743 0.298889 0 +1.69197 0.351404 0.614266 0 +>M01284 SOX3 lnR0: 0.764 +3.84076 0.507319 0 0.608014 +6.53939 0 2.37738 2.30329 +6.2185 0 6.498 2.2199 +0.985875 5.20048 5.77971 0 +8.86077 5.78116 6.77137 0 +8.87801 8.35806 7.36785 0 +7.26385 3.19403 0 7.67482 +6.56446 7.35349 7.35349 0 +4.60062 0 0.1378 0.622035 +2.76212 0 2.76061 0.627312 +2.14771 0 0.599791 0.665938 +>M01286 SOX5 lnR0: -0.988 +1.47088 -0.238936 0.690475 0 +0 5.35273 3.05353 3.31302 +5.91876 3.82937 2.83916 0 +5.03766 4.51771 5.50792 0 +4.45829 4.34932 0 4.86927 +4.9732 3.14426 5.44346 0 +3.59671 3.39554 4.38575 0 +0 0.638521 0.898981 0.168261 +>M01301 STAT2 lnR0: 5.436 +0 1.37506 -0.228002 1.6821 +0.877166 1.71575 0 3.22591 +1.59789 5.67633 0 3.94552 +0 6.07308 0.177173 4.61261 +0 6.77426 6.77426 7.29421 +0 5.13986 4.98935 5.24884 +0 0.968829 1.33025 1.09471 +0.715393 0.256242 0.945174 0 +4.00591 7.76558 0 7.70629 +0 6.34001 4.89486 7.85017 +0 8.34081 5.37018 8.86077 +0 8.35234 6.78289 7.88208 +3.42564 0 1.65501 6.08385 +2.70882 1.44838 4.72183 0 +2.07378 2.2129 0 2.2557 +0 3.22439 2.2089 3.46698 +0 2.11252 1.56157 2.49886 +0 1.93925 1.13226 2.48591 +1.37192 0.343823 0 1.98626 +>M01303 STAT4 lnR0: 0.764 +3.34136 0.135249 3.25013 0 +8.86077 5.56094 7.3506 0 +7.85894 5.76954 5.76954 0 +5.89007 0 7.22624 5.18653 +6.25506 0 5.25444 0.881921 +4.97006 -0.188532 0.801679 0 +1.17379 2.01886 0 2.00353 +3.58704 2.4062 0 1.72711 +0 0.426569 5.74899 4.69949 +0 6.31634 5.15787 5.26685 +0.662507 0.905013 0 1.90263 +>M01298 STAT5A lnR0: 0.18 +6.50854 4.00817 6.71834 0 +3.65792 4.66717 6.23662 0 +6.82106 0 7.87055 8.39051 +3.22765 -0.355986 4.58225 0 +0 7.76447 0.410904 8.28442 +1.11134 6.5548 0 5.21864 +7.81127 7.87055 0 7.08152 +0 8.28177 4.99237 4.59538 +0 6.32526 4.34484 7.83542 +0 0.752447 0.341472 1.23993 +>M01299 STAT5B lnR0: 1.348 +1.50155 0.384397 0.981603 0 +6.5205 4.52966 6.00055 0 +3.89382 5.09383 5.45285 0 +6.77701 0 6.83629 5.46802 +2.90505 0.377463 4.64812 0 +8.0949 7.57494 -0.0840441 0 +0 3.99612 -0.332646 2.18858 +5.884 7.22017 0 5.02995 +0 4.00015 4.70368 3.08946 +0 7.32728 4.54741 7.84723 +0 1.06231 0.661019 1.04216 +1.11141 0.180484 1.02241 0 +>M01304 STAT6 lnR0: 0.764 +5.58503 2.18664 2.87725 0 +4.55978 3.88932 3.40864 0 +3.82587 0 5.54017 5.15157 +1.53315 0.637209 3.35924 0 +3.08555 0 0.558638 2.50631 +0 1.00161 6.45548 0.836452 +1.9007 5.57631 0 4.74703 +5.25297 6.80005 0 5.33958 +0 4.22829 4.98633 6.49649 +0 5.69166 3.49102 6.21161 +0 0.490523 -0.137748 3.17971 +>M01307 TAF1 lnR0: 3.684 +0 2.53167 -0.206787 3.94964 +0 3.41461 1.71262 3.93456 +0.788213 3.11683 0 6.14801 +0 1.89673 0.0300484 5.00579 +0.338125 0.824712 3.07548 0 +3.6794 4.58149 0 4.79957 +6.05024 5.84906 0 6.77999 +1.51454 0 5.97217 5.65243 +1.92114 3.39387 0 3.25475 +4.01933 3.62368 0 5.00954 +1.44322 0 3.09733 2.67391 +2.32965 3.25878 0 2.99795 +2.48692 1.89726 0 4.26768 +0.961148 0 1.11263 2.54952 +1.96509 1.81698 0 2.41631 +1.46245 1.90176 0 3.53994 +>M01308 TAL1 lnR0: 5.436 +2.96029 0 1.80719 2.27519 +3.10318 1.5347 1.4971 0 +4.80353 4.20634 0 2.27058 +3.50833 0.829152 0 1.86164 +1.30632 0.510788 0 0.810523 +1.17123 0.676125 0 1.51799 +1.3567 0.836753 0 1.55504 +1.58196 0.935258 0 1.58196 +1.54633 0.0453553 0 1.0423 +0.896261 1.1324 0 1.72039 +2.48842 0 0.523322 3.03238 +0 3.67752 5.42577 0.985767 +8.40489 7.88494 0 9.3951 +0 8.36092 8.36092 8.88087 +7.30284 8.35234 7.36213 0 +0 7.29758 5.50792 4.6014 +0 4.94262 1.91367 5.63083 +2.62222 1.91887 0 3.8926 +1.02557 0.910082 0 2.87518 +>M01309 TBP lnR0: 0.18 +1.44212 0 1.75524 4.83484 +3.83247 2.51307 2.51307 0 +0 6.34294 3.37231 2.44711 +3.98299 3.46304 3.6538 0 +0 3.13323 3.64277 4.16272 +0 3.59586 3.85632 1.5964 +0 4.29047 1.41204 5.2214 +0 4.91814 1.36827 1.26985 +0.838727 3.60818 0 3.13792 +3.33344 0.863142 0 3.91267 +>M01334 WT1 lnR0: 6.02 +1.22954 2.28817 0 3.2943 +1.91269 1.77701 0 3.45543 +3.57532 2.71767 0 4.73379 +0.667357 0 0.137091 1.55763 +3.50126 3.19677 0 6.11923 +1.544 3.43515 0 3.71239 +2.00044 4.63068 0 6.62151 +7.35625 5.04663 0 6.55679 +6.58046 5.70149 0 9.36033 +0 1.92059 6.51898 5.05851 +6.57752 6.53824 0 6.79774 +5.05689 5.96341 0 4.78396 +0 1.68668 -0.221943 3.5439 +2.08144 4.19442 0 6.14084 +1.59539 1.4479 0 3.64785 +0.85716 0.844098 0 2.5526 +3.12191 3.39557 0 4.08889 +2.28863 2.78835 0 4.55897 +0.866113 2.08675 0 3.67704 +2.16245 3.02616 0 5.08113 +>M01338 ZBTB17 lnR0: 5.436 +1.74348 0.8594 0 2.1091 +0 0.770838 -0.154637 1.29079 +1.45332 3.24273 0 2.58172 +2.02103 2.87145 0 3.1079 +2.0119 2.03625 0 3.10471 +0.509536 1.28532 1.71845 0 +3.01443 4.2347 0 6.80477 +2.23017 4.56118 0 3.38172 +2.02029 4.21051 0 4.38029 +2.85939 6.56446 0 4.35649 +4.0107 3.45265 0 7.5997 +0 1.25141 6.85423 2.71975 +1.93888 3.9503 0 1.71459 +4.51993 5.56943 0 4.68819 +2.14135 4.87464 0 5.51889 +1.97012 6.09356 0 5.14263 +0 0.401844 1.40237 3.06535 +0 2.17451 -0.185859 1.15509 +1.48242 2.11546 0 2.56336 +>M01340 ZBTB48 lnR0: 1.348 +3.79978 -0.175968 1.65543 0 +0.396322 -0.161982 3.45569 0 +0 8.32336 5.35273 6.06344 +9.40082 8.88087 0 9.40082 +7.08729 7.87633 0 9.38649 +6.80653 5.8756 0 9.36618 +0 3.70418 1.94398 5.79358 +2.78579 0 1.20855 2.01809 +2.62722 0 3.27085 2.1612 +1.39489 1.52222 0 2.61272 +1.75524 1.78507 0.316265 0 +1.60769 0.315155 0 2.2916 +>M01344 ZFP28 lnR0: 6.02 +2.63515 1.2283 2.83391 0 +6.02787 5.76838 7.07736 0 +7.95425 0 8.42451 3.24591 +2.97532 1.62406 4.36252 0 +0 2.55614 1.06564 2.90272 +6.1448 2.48596 6.93383 0 +5.90738 2.90943 5.38743 0 +7.59029 4.63499 7.07034 0 +7.01417 0 5.91498 3.95693 +2.71827 1.34426 6.61409 0 +4.66173 4.58486 6.44098 0 +6.85393 0 5.53453 2.70513 +2.59652 2.38837 3.82482 0 +3.24098 3.01359 0.701464 0 +2.35841 3.57135 0 2.73129 +0.333736 3.70135 0.984053 0 +3.68072 4.07374 0 3.64158 +4.05543 3.75569 3.40552 0 +3.4706 0 2.08474 3.51085 +0 4.11869 4.02013 3.45767 +>M01346 ZFP82 lnR0: 8.356 +4.50103 2.2279 3.16968 0 +5.77579 3.62807 4.56225 0 +6.54431 0 5.61339 2.82618 +3.36628 0 5.57425 3.65884 +0 2.7804 3.10837 3.30035 +0.95545 2.21149 -0.223864 0 +2.94715 2.1209 2.73823 0 +4.06065 0.884159 2.66798 0 +3.46051 0 1.76455 1.97271 +0 2.1998 2.84943 2.33652 +3.37009 0 2.48182 1.03767 +2.05887 1.51606 0.656353 0 +0 1.52737 1.18146 3.3177 +0 1.74308 3.08595 1.61126 +1.96044 2.28018 0.887957 0 +1.87834 1.9132 2.7872 0 +4.60062 0 2.87025 0.966018 +4.40812 1.24685 5.63642 0 +3.00861 0 4.44334 1.90605 +3.10583 0.564051 2.81312 0 +2.12894 0 4.34445 2.05567 +5.07225 2.27711 4.43795 0 +4.42339 1.43039 4.28668 0 +5.27171 0 4.02201 1.8035 +>M01347 ZFX lnR0: 0.18 +2.78842 0 0.272936 3.52834 +2.49441 0 1.56348 1.55263 +0 7.33315 8.32336 6.86289 +7.37697 7.84723 0 7.78795 +7.36516 6.26598 0 7.77614 +8.37597 0 7.27679 9.36618 +7.03747 0 7.8265 6.19777 +3.08779 0 0.136974 0.922785 +2.04498 0 1.83292 3.59992 +1.37173 3.31469 0 3.99654 +>M01352 ZNF121 lnR0: 6.02 +5.46781 0 4.8493 5.46781 +3.2143 3.87035 2.65992 0 +6.52055 6.0006 0 6.16153 +5.05689 5.07907 0 7.69379 +3.63097 3.54285 0 7.12003 +5.11517 0 4.59522 6.94507 +0 2.58047 3.14426 5.2805 +0 3.11923 2.46518 4.7748 +4.53651 0 2.99424 3.1765 +0 3.86822 2.60507 4.72587 +3.39272 0.463631 0.0232001 0 +0 4.17777 3.56713 2.97776 +5.68802 4.58884 0 5.57368 +4.51709 0 3.83825 1.18627 +0 1.9089 -0.486957 3.65123 +0 4.46168 3.04682 4.59839 +5.72587 5.33022 0 6.30511 +0 3.6331 3.03331 5.20677 +5.18168 0 4.25076 3.13156 +4.94714 0 3.99536 2.86536 +>M01353 ZNF134 lnR0: 7.188 +3.20957 2.3306 0 2.70003 +2.26719 0 2.1411 2.39306 +1.74488 0 1.72357 2.92585 +1.84471 1.80901 1.39804 0 +1.80923 0 0.159361 1.51016 +0 0.613614 -0.106581 1.57664 +1.21353 0 1.91596 1.01387 +2.49094 0 2.78461 2.36507 +3.59209 0.560917 3.07214 0 +0 0.0675192 2.3503 2.87025 +0 5.48065 3.78124 6.0006 +5.47336 4.0554 1.18333 0 +6.7377 0 4.81657 5.33652 +0 5.49586 4.14663 6.01581 +6.69413 6.43463 0 3.94868 +3.05076 1.81209 -0.487108 0 +3.46821 2.57346 1.30158 0 +3.11124 5.81812 0 4.9116 +0 1.29745 3.09413 5.28561 +0 1.68809 1.34357 1.08167 +4.96281 3.3441 0 5.04005 +3.12887 2.37801 0 4.25024 +>M01227 ZNF146 lnR0: 8.356 +8.73383 8.21388 8.21388 0 +8.67578 5.1852 4.60596 0 +8.7275 7.21734 7.21734 0 +6.73752 8.19799 6.62854 0 +4.69781 0 3.59863 1.85555 +0 3.88897 4.95642 5.1897 +3.70675 2.78863 4.07844 0 +5.08583 8.52673 0 3.54646 +5.93241 7.71166 0 9.22182 +9.17584 0 5.68526 5.04674 +5.68859 4.09183 8.13927 0 +5.42235 6.37329 0 7.62299 +0.912726 0 6.63484 1.76514 +0 4.47072 0.981657 8.28008 +8.73383 8.21388 8.21388 0 +0 6.2015 5.88272 6.72145 +1.42447 3.21354 0 6.24471 +8.72432 6.22395 8.20437 0 +0 8.17868 4.88928 7.12919 +8.5805 2.65457 6.08013 0 +8.73383 8.21388 8.21388 0 +9.24108 0 8.72113 6.94189 +7.19542 0 8.65589 4.76007 +0 4.14178 2.97277 4.76029 +>M01395 ZNF18 lnR0: 1.348 +1.56693 5.21523 0 3.43598 +7.81416 6.56446 0 9.3836 +5.55097 8.32043 5.76077 0 +5.80752 6.85702 0 8.36718 +3.84547 7.14573 2.69785 0 +7.39159 5.88143 0 9.37201 +0 4.42214 6.31037 5.84011 +0 4.8788 2.03247 3.45858 +4.8644 0 1.76789 1.89377 +0.743292 0.32921 1.57257 0 +2.8918 0.833804 0 2.08351 +1.48961 1.18987 0 1.53102 +>M01358 ZNF250 lnR0: 6.02 +5.47833 3.53191 3.96817 0 +0 6.5598 1.52214 4.78056 +5.42145 0 6.75762 5.55761 +8.90869 0 7.39853 6.34903 +0 6.82528 4.38993 5.19655 +6.45451 1.22622 5.20481 0 +0.95423 6.62104 0 6.15078 +7.85681 0 7.33685 4.5674 +5.20072 5.26001 5.26001 0 +4.99092 6.35919 0 7.86936 +7.37418 4.41887 6.85423 0 +6.78261 4.40654 5.85168 0 +6.79494 4.41887 7.84444 0 +6.78261 5.85168 4.40654 0 +4.20164 5.72043 0 6.81961 +0 4.18839 -0.189791 3.35911 +6.79494 4.41887 7.84444 0 +4.66809 4.0338 3.15793 0 +0 4.85734 5.52877 5.78826 +7.16847 0 4.7924 3.65884 +>M01360 ZNF260 lnR0: 8.356 +3.33874 3.84814 4.83835 0 +4.59839 4.2692 3.99184 0 +4.87343 4.46783 3.2574 0 +0.382685 2.19022 1.10781 0 +3.10567 0.655428 1.77925 0 +0 4.16348 4.36791 4.20276 +5.67185 0.920708 4.93168 0 +1.95423 4.98415 0 2.19694 +3.67718 5.97072 0 6.49067 +7.70629 0 6.6071 1.67842 +5.34293 4.68682 5.81319 0 +5.29197 2.73768 0 5.29197 +2.83291 0 6.63942 2.68009 +0 5.06457 1.44824 6.79494 +8.68235 5.38252 6.59295 0 +0 6.35846 3.88046 2.67207 +2.75692 1.763 0 5.49071 +6.01379 4.76409 3.34516 0 +0 8.12925 4.99036 5.22363 +6.92775 2.3054 5.00661 0 +6.70846 6.59949 7.17872 0 +9.15567 0 8.63572 4.67639 +5.85607 0 7.63532 5.18464 +0 3.46017 3.59013 3.60054 +>M01362 ZNF264 lnR0: 8.356 +2.32806 0.2098 1.64309 0 +1.10325 0 2.04688 0.57793 +2.54661 1.56466 2.28193 0 +2.89029 0.221656 0.958036 0 +0 0.946442 0.82607 2.06141 +0.605093 0.980711 1.42879 0 +0 1.99286 2.24414 3.54987 +0 3.31093 2.55655 1.6481 +2.9211 4.66173 0 4.51025 +5.1679 5.26983 0 4.09603 +1.41472 1.91444 0 5.2545 +2.98523 0 4.82443 6.33459 +0 3.39134 2.53729 1.71996 +7.11651 0 2.35311 5.04948 +3.04125 2.09115 1.0177 0 +0 3.00076 2.29722 3.7053 +0 2.68589 4.13103 3.8014 +5.56338 1.70143 3.73445 0 +4.63498 0 1.71839 2.20728 +2.73949 0 1.71485 2.26923 +1.69625 0 3.30035 1.8817 +0 1.70706 2.2863 2.40306 +3.59937 1.14081 2.03529 0 +2.49726 -0.343695 1.83783 0 +>M01367 ZNF322 lnR0: 6.02 +3.04579 2.80142 0 3.91588 +0 1.88661 0.967841 0.769072 +3.55446 3.68519 0 3.03451 +2.4956 0 3.72772 2.53421 +4.73651 0 5.85246 4.94594 +3.45671 2.49368 3.65215 0 +1.58576 3.68897 0 4.4956 +2.8791 0.439525 0 2.71841 +2.80288 1.77015 2.12917 0 +0 1.80388 3.64626 3.5137 +7.29532 0 6.77537 8.28553 +0 1.97891 0.874349 0.479295 +5.78978 0.712845 0 5.01978 +0 1.77243 1.67387 0.270061 +5.28364 5.6617 0 4.55389 +4.48451 0 4.02536 3.86613 +3.52748 0 4.17433 3.20207 +2.58327 2.3124 1.5424 0 +3.5549 2.38244 0 3.07961 +1.05799 1.13399 0 1.99388 +>M01368 ZNF329 lnR0: 6.02 +6.345 0 6.81526 7.91445 +5.71172 2.89257 6.76121 0 +3.48034 8.03946 0 2.94252 +6.61752 7.40656 0 8.91672 +0 6.24605 4.26563 5.36481 +5.30945 5.46093 3.28085 0 +4.88729 0 3.95637 5.33037 +1.36624 0 4.39616 4.07642 +0 3.29578 3.94147 4.80594 +2.82969 3.35387 0 4.86403 +7.33117 0 7.39046 6.12075 +5.02386 0 5.23366 1.53479 +0 1.99575 0.455456 2.13756 +3.4147 1.76298 2.7804 0 +0.888278 4.097 0 2.53321 +5.90138 0 7.36185 5.73311 +7.34326 0 7.40255 6.93229 +8.40872 6.89856 6.89856 0 +6.60949 6.40832 0 8.90869 +0 2.99984 5.46093 6.71064 +>M01370 ZNF335 lnR0: 7.188 +1.48693 4.30323 0 2.84276 +3.98215 3.10318 0 3.21215 +3.34447 0 1.83431 2.61472 +4.65442 1.22464 4.13447 0 +5.92594 4.097 0 3.36628 +3.13889 0.0592853 1.75303 0 +6.03528 0 4.52512 4.46583 +5.40242 0 4.30323 1.08752 +0.729751 0.279501 -0.346578 0 +1.71756 0 0.618377 0.819551 +0.867982 0.679177 0 1.5493 +2.61472 0.834211 0 2.3945 +1.69734 0 2.99592 2.16664 +1.82894 2.44971 0 1.34826 +1.20974 0 1.45276 2.25008 +4.39945 1.99128 5.85992 0 +5.29715 4.04745 0 3.09651 +5.39459 0 5.45387 3.53847 +4.74125 0 6.5205 4.74125 +4.1291 3.34869 3.34869 0 +3.22361 2.57936 0 3.22361 +0 1.02121 2.76946 0.509536 +>M01372 ZNF350 lnR0: 4.852 +1.69332 0 1.30012 2.50631 +0 2.89428 0.582711 1.12751 +3.63886 1.82789 0 1.88799 +2.17016 -0.354352 0.796161 0 +3.57224 0 3.27952 1.42355 +3.90868 0 3.22683 1.06495 +3.26726 1.89142 4.69156 0 +7.83838 5.01924 5.16975 0 +6.82431 4.41614 4.99538 0 +3.86498 2.22366 3.0484 0 +0 0.908867 1.5803 1.56945 +1.47698 3.55379 2.52647 0 +1.33754 2.69713 0 1.25847 +0 0.849836 1.90355 0.898012 +4.257 0 2.6369 2.54277 +4.48079 0 3.49974 2.01485 +0.205018 0.388605 1.20256 0 +0 1.14569 0.289502 1.09353 +>M01375 ZNF394 lnR0: 6.02 +0 -0.293167 -0.452869 0.829249 +0.794246 1.60429 0 4.53338 +0 5.36206 4.37185 2.74312 +0 3.32814 0.319745 2.71247 +0.727078 2.34252 1.08196 0 +1.26927 7.54016 0 2.36157 +2.44284 1.55001 0 4.17118 +0 1.17946 4.41426 3.09442 +0 1.35283 2.38988 2.3306 +0.610054 2.63647 0.541703 0 +0 -0.0881207 -0.34858 0.815064 +2.0197 1.32897 0 2.26661 +0 1.94363 3.20129 1.52662 +0 0.336928 2.45068 1.62485 +0.353574 4.39341 2.19277 0 +2.30656 4.36775 0 2.5885 +1.44008 2.75613 0 1.90263 +0 3.05556 2.03463 4.09395 +0 4.21979 1.86456 3.21872 +1.75004 1.49664 -0.120832 0 +>M01396 ZNF41 lnR0: 8.356 +1.47806 0 1.94832 2.56683 +0 2.24854 1.86764 3.60818 +3.22824 0 3.25042 3.30548 +0 2.95009 1.84076 3.74297 +0 5.3817 0.96593 4.33221 +4.09343 5.20124 0 4.82318 +3.27927 4.36493 0 4.00902 +1.11292 5.65149 0 7.16165 +0 5.79268 4.34753 5.73339 +0.591394 2.57719 0 5.24582 +0.999111 0.66992 1.39967 0 +0 0.451585 0.547499 1.53234 +0 1.59817 0.509401 2.33834 +1.00063 3.60818 0 2.66456 +1.23337 0.922858 0 2.22358 +4.18965 0 2.60979 3.61041 +0 6.23346 5.02304 6.34244 +4.98586 0 4.18854 7.18649 +2.07187 0 4.70834 4.16084 +0 5.2856 2.17881 4.44053 +2.55966 3.25013 2.07413 0 +3.19081 1.87725 0 3.41103 +0 3.30893 1.98323 2.43824 +2.55765 2.90361 0 3.04875 +>M01377 ZNF436 lnR0: 8.356 +3.66421 2.6709 2.10392 0 +5.70965 0 4.40892 3.76207 +0 0.213482 3.64829 2.06565 +1.14069 2.21964 0 2.26318 +3.78591 5.3497 0 5.49484 +5.64839 7.80244 0 7.74316 +0 3.48658 3.08996 4.47582 +0 4.59368 -0.350977 4.92287 +4.93263 6.78158 0 7.7125 +2.66087 3.57738 0 5.66677 +9.35739 0 8.83744 9.35739 +5.33022 4.57162 5.67618 0 +6.04527 3.32468 2.74545 0 +9.33069 0 7.82053 6.1918 +3.99515 0 6.03485 3.95601 +4.55054 2.43341 4.93915 0 +4.53275 8.72113 0 5.57687 +5.11834 5.75687 0 5.58323 +0 6.67878 5.10934 4.9981 +3.37854 8.65922 0 9.17917 +6.77701 7.8265 0 8.34646 +0 4.05605 5.40528 4.35578 +2.8871 8.59102 0 9.11097 +5.42565 7.78413 0 6.51442 +>M01379 ZNF467 lnR0: 7.188 +1.63406 4.59839 0 4.82172 +3.57719 7.0764 0 4.5674 +4.51233 5.2028 0 6.97342 +8.37305 5.5539 0 7.79381 +0 4.62057 6.71534 5.25487 +2.58969 6.24568 0 5.92594 +5.24684 5.48493 0 5.86873 +1.67206 5.17127 0 5.85948 +2.52788 3.44122 0 5.29197 +0 1.44011 -0.492344 2.51259 +0.55421 1.74961 0 3.62539 +1.51985 2.97063 0 4.16976 +1.89919 3.02013 0 4.64464 +1.08065 3.27879 0 3.79874 +1.62988 3.38928 0 4.44004 +1.50034 3.14878 0 3.54071 +1.08044 3.37265 0 3.45334 +1.85589 3.20726 0 4.34909 +1.78239 2.9219 0 4.97687 +1.33311 3.13889 0 4.33028 +1.0502 2.55966 0 3.91267 +1.41336 2.33118 0 3.48532 +>M01380 ZNF490 lnR0: 8.356 +4.52135 3.36385 4.19216 0 +2.83636 5.16274 0 4.22319 +0.769027 4.81861 0 1.23616 +4.88706 6.01379 0 6.7942 +7.02158 5.10044 4.30099 0 +5.38935 0 5.70909 1.38936 +7.65227 5.82333 6.55308 0 +7.18873 0 7.07975 9.16915 +7.59731 3.5883 8.06757 0 +7.64212 6.13196 5.33251 0 +6.85986 7.06966 0 7.58961 +0 3.59586 4.58607 0.0824405 +0 6.5293 4.95985 6.3195 +3.64718 6.13314 0 4.53651 +0.586408 6.71497 0 7.23492 +7.60973 0 8.65922 9.17917 +0 8.13927 6.56983 8.65922 +2.34817 8.31864 0 8.83859 +7.60639 0 7.66568 9.17584 +0 8.14592 8.14592 8.66587 +3.53848 2.28878 0.436379 0 +0 7.11537 4.68001 7.63532 +3.3943 -0.218452 5.24325 0 +1.04112 0 4.62357 3.12396 +>M01381 ZNF502 lnR0: 6.02 +3.91267 4.64339 0 6.47233 +0 3.71826 5.50792 5.44863 +0 4.89682 4.16707 4.20634 +4.66537 3.15521 5.45441 0 +5.60919 7.06966 0 6.5994 +4.93573 4.0048 0 6.50517 +0 6.5293 4.95985 4.75005 +0 1.26971 4.65132 6.74071 +3.67516 3.88496 6.44462 0 +4.60881 0 0.128017 3.29982 +3.86767 4.59839 0 4.85789 +0 4.89682 5.47605 3.69681 +0 5.48675 3.18756 6.0067 +5.38417 2.8838 4.86422 0 +3.40397 6.93147 0 6.46121 +6.00999 5.49004 0 6.58923 +0 5.53909 6.5293 4.48959 +0 6.5598 4.99036 6.08954 +4.67623 4.47506 3.67561 0 +4.21522 0 1.13561 4.43544 +>M01383 ZNF547 lnR0: 6.02 +2.08717 1.80811 1.72322 0 +3.95015 2.88538 0 3.80474 +4.91116 0 7.36185 3.43392 +1.04078 2.21108 2.21108 0 +0 1.52717 2.32137 4.02754 +0 4.2637 3.72157 5.66799 +1.94543 0.89309 3.45275 0 +6.70671 3.27693 0 1.07127 +8.09254 0 7.57259 7.10233 +0 0.784765 2.08313 0.172545 +1.87223 4.43726 0 3.90868 +6.1918 0 5.31282 4.55589 +0 2.45068 4.94064 2.90093 +1.186 2.31274 0 3.75644 +1.90375 2.95324 0 3.10906 +3.38534 0 4.40273 4.31204 +0 2.35848 1.2283 2.478 +1.34426 0.215619 0.452943 0 +0 2.15812 -0.383793 1.91692 +4.442 0 3.23371 4.08298 +>M01385 ZNF554 lnR0: 6.02 +1.82184 2.62273 0 3.63531 +4.21918 0 6.6245 3.37437 +0.171011 1.21227 0.789036 0 +4.68315 3.64747 0 4.62235 +0 5.26417 0.734045 4.91821 +3.00145 4.3114 0 7.54153 +5.46105 0 3.53991 1.14229 +9.38072 0 8.86077 6.41008 +0 3.09742 2.53363 3.36461 +0.836083 -0.316216 -0.138801 0 +1.77722 1.07846 0 1.69998 +2.16163 1.23658 1.16772 0 +0.59357 3.34936 0 2.46812 +2.80702 2.52755 0 4.54725 +1.29319 1.89961 0 0.803268 +2.21313 1.88978 0 1.18268 +1.44033 1.2794 0.159226 0 +0.668232 1.96044 0 2.74085 +2.85442 0 2.80625 2.81046 +1.46869 1.20001 1.29465 0 +>M01386 ZNF563 lnR0: 6.604 +1.38693 1.7547 0 1.73252 +3.22117 2.55966 0 2.42171 +2.0128 1.51016 0 1.71832 +0 -0.467997 -0.369436 0.452385 +4.91717 2.60756 1.79842 0 +7.25106 0 6.41234 3.67174 +0.986642 0 4.30323 2.28351 +2.45307 1.10593 1.34458 0 +1.48312 0 0.194664 0.80057 +0 0.813318 -0.275453 0.754033 +2.98741 0 1.85461 3.26842 +0.604081 -0.0877067 3.0229 0 +2.30507 4.44334 0 2.38672 +4.72629 2.48638 0 2.54277 +5.01738 0 2.19823 6.76563 +0 1.33484 5.5856 3.09964 +1.51016 2.07898 0 3.43863 +5.95168 0 5.43173 4.16202 +1.51787 1.12498 1.87144 0 +4.06129 1.85754 0 3.23298 +1.87932 0 2.54558 0.61498 +>M01388 ZNF586 lnR0: 6.02 +0 8.24823 4.95882 7.77797 +6.51749 8.77741 0 8.30715 +6.30511 6.45659 0 7.29532 +5.46756 0 6.05217 3.79225 +6.36901 0 6.64851 3.7108 +5.59573 2.27062 4.90752 0 +0 6.64444 4.16643 6.75341 +4.98047 8.74014 0 9.26009 +5.99872 7.77797 0 9.28813 +0 8.26052 5.96132 7.21102 +7.32 8.78047 0 7.32 +5.84706 8.75267 0 6.71296 +0 5.08489 1.14979 6.08551 +0 2.2635 5.74009 4.78915 +0 6.20795 5.88917 4.22904 +0 5.68549 1.81684 5.07907 +0 8.27876 8.27876 8.79871 +0 6.55308 2.59224 8.64248 +6.43463 4.34524 6.23346 0 +6.32366 8.77434 0 8.30408 +>M01393 ZNF770 lnR0: 7.188 +1.72307 2.41354 0 2.31512 +3.19918 4.93378 0 6.33807 +4.72629 5.19655 0 8.27616 +0 6.26472 3.82937 6.20544 +5.26212 8.78962 0 6.74991 +5.42565 5.99447 0 6.51442 +4.83318 0 3.85213 5.41242 +2.08588 0.38208 2.98256 0 +3.22024 3.19581 0 5.5953 +0 2.5787 0.846881 3.80219 +2.85776 3.60818 0 5.02615 +2.2369 2.7844 0 3.54589 +1.74488 0 0.961638 1.34672 +1.05743 2.68616 0 2.47636 +3.29982 2.92143 0 4.55589 +2.62839 2.86827 0 4.84098 +0 3.17596 0.975324 3.00233 +3.66229 4.13255 0 5.84237 +2.1205 2.674 0 5.11834 +0 1.02909 1.18977 2.84291 +2.47239 1.3418 0.481553 0 +2.75615 0 1.13813 1.96071 +>M01400 ZSCAN22 lnR0: 3.684 +1.03242 2.07216 0 1.96509 +2.25708 2.45645 0 3.99282 +1.71556 1.02979 0.250044 0 +2.82864 0 1.77788 3.77201 +0.346517 0.633037 1.57482 0 +4.36297 6.40267 0 7.65238 +0 5.10741 2.5183 5.04812 +2.48404 3.04362 0 1.60638 +3.88072 7.09642 0 6.88662 +5.60528 6.45035 0 6.9703 +0 0.269881 2.04523 3.1279 +3.31383 6.29531 0 6.33459 +5.98009 7.1801 0 5.98009 +0 1.0579 4.38575 4.46262 +4.25452 6.7052 0 6.4257 +4.05574 4.03337 0 4.9643 +>M01400 SREBF1 lnR0: 3.1 +6.82395 9.85386 0 10.3738 +9.85386 5.78405 9.33391 0 +9.78741 3.49167 9.26746 0 +10.2722 3.97642 0 5.79288 +10.2201 0 9.70014 3.46668 +10.1254 0 9.60547 2.78857 +0 2.6406 1.88256 3.6448 +3.1803 4.20894 0.628353 0 +3.63055 9.71771 0 10.2377 +3.776 5.22086 0 10.2201 +2.63318 0 2.3779 2.41898 +1.05234 5.43809 0 3.24787 +0 3.38499 3.69129 5.20145 +6.68779 0 5.23843 4.20979 +3.15779 0.44231 0 3.94834 +>M01400 TRIM28 lnR0: 0.18 +9.86965 9.3497 9.3497 0 +10.3896 9.86965 0 10.3896 +0 9.3497 9.3497 9.86965 +3.87489 0.248811 0 6.00907 +9.86965 9.3497 9.3497 0 +10.3896 0 9.86965 10.3896 +0 9.3497 9.3497 9.86965 +8.6492 -0.133359 0.230064 0 +1.04918 0 8.58402 0.886008 +0 -0.147074 -0.238096 0.311555 +>M01400 SIN3A lnR0: 3.1 +4.87413 4.91056 5.83431 0 +5.2317 2.87673 0 5.78808 +5.38417 3.31764 5.78798 0 +10.3313 0 9.81139 5.02624 +10.3313 0 9.81139 5.02624 +1.45013 2.0367 0 1.85524 +1.78678 0.499356 1.4837 0 +4.94834 5.38417 0 5.34775 +10.3896 9.86965 0 10.3896 +9.86965 9.3497 9.3497 0 +4.38676 2.64856 0 4.38676 +10.3753 0 9.85531 6.94969 +9.85531 5.90979 9.33536 0 +6.92057 9.82618 0 5.99681 +0 4.89528 3.9395 6.33898 +>M01400 SIX5 lnR0: 0.18 +7.08152 7.55178 0 10.3709 +0 5.43243 3.96885 4.19217 +0 2.09724 -0.125588 1.80383 +1.19086 2.20674 2.20674 0 +9.78135 3.73111 5.49131 0 +10.3896 9.86965 0 10.3896 +4.50297 4.8009 4.31098 0 +0 6.96977 3.62433 9.78892 +10.3896 9.86965 0 10.3896 +9.85098 9.33102 5.56094 0 diff --git a/assets/PWMs/Jaspar_Hocomoco_Kellis_mouse_PSEMs.txt b/assets/PWMs/Jaspar_Hocomoco_Kellis_mouse_PSEMs.txt new file mode 100644 index 0000000..21d26dc --- /dev/null +++ b/assets/PWMs/Jaspar_Hocomoco_Kellis_mouse_PSEMs.txt @@ -0,0 +1,6211 @@ +#/Lambda=0.7 /Regression_slope=0.584 /Regression_intercept=-5.66 /GC_content=0.42 +>MA0004.1 ARNT lnR0: -2.156 +2.20936 0 4.04745 4.50855 +0 3.81851 2.8283 4.27962 +4.81042 0 4.34932 4.81042 +4.81042 4.34932 0 4.81042 +4.34932 3.88821 3.88821 0 +4.81042 4.34932 0 4.81042 +>MA0006.1 AHR::ARNT lnR0: -2.156 +1.56945 -0.0501305 1.51932 0 +5.00118 4.54008 0 4.01097 +5.00118 0 4.54008 4.01097 +5.00118 4.54008 0 4.01097 +4.59839 4.13729 4.13729 0 +5.0595 4.59839 0 5.0595 +>MA0009.1 TBXT lnR0: 0.764 +3.70208 0 1.67153 3.70208 +4.24345 3.78234 4.77255 0 +0 4.844 4.844 5.3051 +5.76621 5.3051 0 5.76621 +5.76621 5.3051 0 5.76621 +5.3051 4.844 4.844 0 +5.76621 5.3051 0 5.76621 +5.23366 3.20311 4.77255 0 +4.28132 1.83979 0 2.97233 +0 4.844 4.844 5.3051 +0 1.93029 4.48995 2.65185 +>MA0014.1 PAX5 lnR0: 6.02 +0 1.30899 0 0.318777 +1.3008 3.13889 0 3.6 +0 -0.142328 -0.142328 0.729751 +2.03055 0.99021 0 0.721564 +1.86229 0 1.98042 1.86229 +0 0.94008 1.51932 1.40118 +1.45132 0 0.579236 1.45132 +2.97063 0.529105 0.94008 0 +2.60979 1.56945 0 2.60979 +0 1.32856 0.338346 1.21043 +0 2.31877 0.749321 0.480675 +4.12532 3.66421 0 4.12532 +2.03055 0 2.14868 2.60979 +1.77009 3.28941 0 3.75051 +1.98042 2.50953 0.210329 0 +0 1.32856 -0.24089 2.77987 +0 1.56945 0 1.56945 +2.31722 0 3.42556 3.88667 +1.45132 0 0 3.02076 +0.68132 2.77987 0 2.25077 +>MA0027.1 EN1 lnR0: 0.764 +0 0.847882 0.268646 0.318777 +0 0.529105 0.529105 1.56945 +1.45132 2.97063 0 3.43174 +3.13889 2.67779 1.10834 0 +0 1.83809 -0.142328 0.318777 +1.45132 2.97063 0 3.43174 +0.99021 2.50953 2.50953 0 +1.19086 1.30899 0 0.779881 +0.99021 0 0 0 +1.30899 0 1.30899 0 +2.25077 0 1.78966 1.67153 +>MA0029.1 MECOM lnR0: 2.516 +0 1.83809 0.627667 1.30899 +0 2.898 2.31877 2.05012 +5.11553 3.66421 0 4.12532 +0 4.29919 4.29919 4.76029 +3.05724 0.160778 3.58634 0 +0 4.29919 4.29919 4.76029 +0 4.24723 3.25702 4.70834 +5.2214 4.76029 0 5.2214 +0 4.29919 4.29919 4.76029 +4.59839 2.15687 4.13729 0 +0 3.14708 4.13729 3.02895 +0 4.07897 1.77978 4.54008 +0.190759 0 0 0 +0 0.719865 1.51932 1.98042 +>MA0060.1 NFYA lnR0: 3.684 +0.578588 0 0.436259 1.45132 +1.29208 -0.159235 0.170085 0 +3.13511 0 0.99021 1.06808 +0 1.49531 0.0244206 3.84463 +0.592258 3.47659 0 3.67724 +7.26421 0 6.80311 7.26421 +5.65766 0 5.77579 7.2271 +0 6.29231 5.3021 4.77299 +0 6.342 6.342 6.80311 +6.79084 5.33953 6.32974 0 +2.57768 0 0.947563 4.14713 +0 2.76573 0.172456 4.43726 +2.83969 1.79935 0 3.1842 +0.597262 0 0.926708 2.20288 +0.832938 2.24088 0 1.393 +0.925994 0 0.260459 0.820125 +>MA0105.1 NFKB1 lnR0: 0.18 +5.69476 5.23366 0 5.69476 +5.69476 5.23366 0 5.69476 +4.66745 5.19655 0 5.65766 +0 4.19332 0.423237 4.65442 +0 0.0484308 2.8283 1.71996 +1.78966 3.30898 2.31877 0 +4.04745 3.00711 3.00711 0 +2.71017 -0.31059 3.81851 0 +4.01097 0 5.11931 4.59021 +5.61956 0 5.15845 4.05011 +>MA0063.1 NKX2-5 lnR0: -1.572 +0.318777 2.8283 1.83809 0 +3.77008 1.00978 3.30898 0 +0 3.668 3.668 4.1291 +0 3.668 3.668 4.1291 +3.42556 2.96446 -0.00617094 0 +1.25067 1.51932 3.08876 0 +2.44153 2.55966 0 2.03055 +>MA0067.1 PAX2 lnR0: -0.988 +0 -0.00617094 0.404803 0.136157 +1.90625 3.42556 0 3.30743 +2.72792 2.67779 4.24723 0 +5.27153 0 3.82021 3.70208 +0 3.25702 2.26681 3.71813 +3.02076 0 3.13889 1.04034 +3.17128 4.27962 0 1.31516 +3.02076 0 0 0.872079 +>MA0068.1 PAX4 lnR0: 11.86 +1.04034 1.98042 0 3.02076 +0 3.88821 2.898 4.34932 +0 2.0169 2.59613 2.478 +0 2.09855 2.09855 0.410974 +0 2.31877 1.32856 1.47088 +0 1.10834 2.09855 0.769995 +0.884342 2.2129 1.63366 0 +0.136157 1.97425 1.97425 0 +0.410974 0.529105 -0.270346 0 +1.45132 0 2.55966 1.71177 +1.2311 0 1.25067 4.01097 +0 0 0.410974 1.40118 +0 -0.292843 1.10834 0.839695 +0.509536 0.268646 1.83809 0 +0 0.404803 0.665263 1.85612 +1.3008 0 0.839695 1.04034 +1.15847 -0.102084 0.37859 0 +0.629366 0 1.15847 1.61958 +1.45132 0 1.30899 1.19086 +0 0.0484308 1.25886 0.99021 +0.872079 0 0.410974 1.13254 +0.579236 -0.102084 1.10834 0 +1.04034 0 3.54987 2.03055 +0.97064 0 2.2992 1.19086 +2.1449 0 2.09477 1.82612 +0.779881 0 1.71996 1.77009 +2.1449 0 2.09477 1.82612 +3.02076 0 1.56945 1.2311 +1.2311 0 2.55966 2.03055 +2.25077 0 2.20064 2.25077 +>MA0092.1 HAND1::TCF3 lnR0: 0.18 +1.58747 0.286672 0 0.916039 +0.996381 3.96084 0 2.12275 +3.02895 2.56784 3.14708 0 +5.27153 0 4.81042 4.28132 +4.85885 4.39775 4.39775 0 +5.31996 4.85885 0 5.31996 +5.11553 2.674 0 4.12532 +1.04034 0 2.87843 1.77009 +0 3.58634 1.60592 0.621883 +1.48779 1.28715 1.28715 0 +>MA0111.1 SPZ1 lnR0: 0.764 +0 2.8283 0.847882 3.28941 +3.75051 1.71996 0 2.7603 +2.31722 3.42556 0 3.88667 +4.01097 3.54987 0 3.02076 +2.43535 2.96446 1.97425 0 +0 2.67779 2.67779 0.839695 +0 2.31877 0.749321 0.480675 +2.7603 0 1.71996 3.75051 +0 2.96446 1.39501 3.42556 +3.75051 2.2992 0 2.18107 +2.03055 0 1.56945 3.6 +>MA0112.1 ESR1 lnR0: 4.852 +2.03055 0 1.56945 1.45132 +2.03055 0 1.56945 1.45132 +0 1.51932 1.51932 2.97063 +1.86229 2.97063 0 3.43174 +3.75051 3.28941 0 3.75051 +3.28941 2.8283 2.8283 0 +3.43174 0 1.40118 3.43174 +0 2.31877 0.749321 1.78966 +2.44153 0 1.98042 3.43174 +1.45132 0 1.56945 2.03055 +0.779881 0.729751 0 2.7603 +1.78966 1.32856 1.32856 0 +2.60979 3.13889 0 3.6 +0 1.10834 0.118131 2.55966 +3.6 0 3.13889 2.60979 +3.75051 0 3.28941 3.75051 +1.19086 0 2.2992 0.779881 +0.779881 0 1.30899 1.77009 +>MA0125.1 NOBOX lnR0: -0.988 +5.19655 3.74524 4.73545 0 +0 4.69735 4.69735 3.58901 +0 4.77255 4.77255 5.23366 +4.08886 3.62775 3.04852 0 +3.42556 4.53391 2.23471 0 +0.979541 4.47928 0 3.95017 +2.36825 0.542128 0 2.36825 +2.55966 -0.102084 0.888126 0 +>MA0132.1 PDX1 lnR0: -2.156 +3.75051 0 1.71996 1.96085 +4.95105 4.48995 4.48995 0 +0 4.48995 4.48995 4.95105 +0 4.48995 4.48995 4.95105 +4.9057 4.44459 3.45438 0 +3.28941 2.8283 0.392948 0 +>MA0135.1 LHX3 lnR0: 1.932 +0 2.8283 0.847882 0.150515 +0 2.0169 2.0169 4.04745 +0 3.81851 3.81851 3.28941 +4.34932 3.88821 3.88821 0 +4.34932 3.88821 3.88821 0 +0 3.81851 3.81851 3.28941 +0 3.88821 3.88821 4.34932 +2.478 2.0169 3.58634 0 +4.27962 2.8283 3.81851 0 +0 2.59613 3.58634 2.06703 +0 2.8283 0.847882 0.150515 +1.85612 -0.174432 2.96446 0 +2.18107 0 1.30899 0.97064 +>MA0140.1 GATA1::TAL1 lnR0: 4.852 +2.17392 0 1.09261 1.60781 +2.68653 1.46867 1.24342 0 +4.28728 3.35948 0 1.88175 +2.64748 0.711273 0 1.251 +0.36823 -0.0184757 -0.302696 0 +0.822385 0.390058 0 0.921382 +0.954003 0.3287 0 1.10094 +0.779081 0.346265 0 0.92427 +0.690454 0.376628 0 0.776574 +0 0.8153 -0.378523 0.715967 +1.60142 0 0.375293 2.20522 +0 5.41741 5.17191 1.07891 +9.88803 8.43672 0 11.8685 +0 7.97172 9.3729 7.97789 +7.32892 6.20693 6.00957 0 +0 8.08326 6.32305 4.21461 +0 5.003 2.173 4.1012 +1.99358 1.52468 0 3.15531 +>MA0142.1 POU5F1::SOX2 lnR0: 3.1 +4.15084 0 3.6243 1.56904 +0.272722 3.0766 4.09123 0 +6.66093 4.1328 4.59124 0 +4.63599 6.04096 3.44513 0 +3.22892 1.17063 0 4.11498 +1.11508 5.0629 4.41039 0 +1.55092 0.275655 1.23498 0 +0 4.80411 5.11141 3.89312 +6.14974 7.25808 5.85689 0 +7.21106 6.12808 0 3.98811 +6.50291 0 2.95683 2.82412 +0 5.43073 4.57248 1.94154 +0 3.1887 1.01494 3.22339 +0 4.63111 3.482 4.43132 +2.05388 2.31536 1.52958 0 +>MA0144.1 STAT3 lnR0: 0.18 +4.66485 4.27345 3.89864 0 +4.99501 4.87842 1.35037 0 +4.24939 0 5.73253 5.6144 +6.67447 0 8.00303 3.46912 +0 3.37248 0.63976 1.36324 +6.4749 9.15269 0 9.61379 +6.80294 7.55226 0 5.81273 +0 4.22786 5.67301 9.10474 +0 7.70373 6.13428 8.16483 +1.48804 4.5768 0 5.13011 +>MA0062.2 GABPA lnR0: 0.764 +4.95908 0 2.00478 8.96388 +4.11288 0 7.44212 9.21221 +10.3164 9.85531 0 9.3262 +10.3179 9.85675 0 10.3179 +0 8.40543 8.40543 9.85675 +0 7.82331 9.39276 8.28442 +3.61991 4.66933 0 10.1254 +3.45041 0.810315 3.56854 0 +2.40417 2.10903 0 3.07377 +1.10533 0.655045 0 3.48777 +1.06855 0 0.663475 1.46737 +>MA0039.2 KLF4 lnR0: 0.18 +0.26305 3.92426 0.318863 0 +5.97998 8.6418 0 9.61244 +8.54608 8.18354 0 8.64464 +8.53843 6.78751 0 8.35962 +2.91563 -0.308363 6.94412 0 +7.92512 7.98245 0 7.32533 +6.0695 4.70376 0 0.553827 +4.30363 6.31336 0 5.3657 +5.34659 4.80703 0 4.13288 +3.91391 0 3.3141 2.06085 +>MA0002.2 RUNX1 lnR0: 0.764 +1.72371 0.483136 0 0.87413 +1.77658 0.277437 0.331352 0 +3.54387 0 2.81083 1.16186 +5.01208 10.3516 7.38097 0 +11.2258 4.57795 0 5.52727 +4.24428 3.2479 4.08983 0 +11.3109 10.8498 0 7.54086 +7.07829 5.37314 0 4.71697 +6.86076 1.26241 1.92603 0 +3.29589 1.03895 3.5149 0 +1.06249 2.24096 1.38242 0 +>MA0047.2 FOXA2 lnR0: 1.348 +8.56991 8.1088 8.1088 0 +1.8404 7.11699 0 7.57809 +8.57168 8.11058 8.11058 0 +8.50463 7.05332 3.87528 0 +8.22925 7.76815 1.37195 0 +0 6.67197 2.9433 7.45185 +8.30244 0 7.84134 3.57658 +0.207517 1.8454 6.08885 0 +3.06873 0.248091 2.39946 0 +0 5.38114 3.56262 0.209434 +2.31427 3.13005 0 2.22004 +1.61223 0.564584 0 1.0701 +>MA0065.2 PPARG::RXRA lnR0: 3.1 +2.20048 0.0134139 0 1.78575 +2.16724 1.00181 1.38176 0 +0 3.52554 -0.378375 2.26669 +3.16844 7.31995 0 3.36528 +2.70835 5.34589 0 4.68877 +1.88654 1.59126 0 1.48047 +3.36055 0 1.59045 3.46337 +0 4.70784 5.16277 6.44583 +0 2.92141 0.478128 4.40218 +0 6.36621 1.88694 6.09757 +3.6396 7.92168 0 6.28802 +4.46797 6.05698 0 2.95636 +4.34042 1.77978 0.392948 0 +3.76601 0 1.92005 2.7758 +0 3.0248 3.31957 3.01565 +>MA0151.1 ARID3A lnR0: -2.156 +0 4.29919 4.29919 4.76029 +4.76029 4.29919 4.29919 0 +3.13889 0.37859 3.668 0 +0 4.29919 4.29919 4.76029 +0 4.29919 4.29919 4.76029 +0 3.88821 2.898 1.56945 +>MA0153.1 HNF1B lnR0: 1.348 +2.77987 0.338346 2.31877 0 +2.77987 0.338346 2.31877 0 +0 1.68758 2.67779 3.13889 +0 1.51932 1.51932 2.97063 +3.28941 2.8283 2.8283 0 +0 2.09855 -0.200645 2.55966 +0.579236 2.09855 1.10834 0 +3.13889 2.67779 1.68758 0 +3.28941 2.8283 2.8283 0 +0 2.67779 1.68758 3.13889 +0 2.8283 2.8283 3.28941 +3.6 0 3.13889 2.60979 +>MA0154.1 EBF1 lnR0: 0.18 +0 -0.200645 1.51932 1.56945 +4.94038 0 4.47928 2.95996 +3.51834 0 3.05724 1.53792 +3.24098 0 4.34932 2.83 +0 -0.200645 3.08876 0.99021 +0 2.59613 1.02669 2.06703 +5.11553 4.65442 0 5.11553 +3.43174 4.54008 0 5.00118 +5.11553 4.65442 0 5.11553 +0 3.95467 1.65547 4.41577 +>MA0158.1 HOXA5 lnR0: -0.988 +2.66174 0 3.77008 4.23119 +0 2.50953 -0.0501305 0.671434 +3.43174 0 0.410974 1.13254 +0.509536 2.8283 1.83809 0 +0 3.40754 3.40754 2.2992 +0 3.40754 1.83809 3.86864 +4.04745 3.58634 3.58634 0 +3.28941 1.83809 0.0484308 0 +>MA0160.1 NR4A2 lnR0: -0.988 +0 1.68758 0.697367 2.14868 +0 3.30898 2.31877 3.77008 +4.23119 3.77008 0 3.24098 +2.03055 3.54987 0 4.01097 +1.85612 1.39501 2.96446 0 +4.23119 0 3.77008 3.24098 +0 3.40754 3.40754 3.86864 +1.61958 0 1.56945 3.6 +>MA0162.1 EGR1 lnR0: 0.764 +0.99021 0.210329 1.51932 0 +2.55587 2.674 0 4.12532 +4.23119 0 3.77008 2.66174 +4.42195 3.96084 0 4.42195 +3.66421 3.20311 1.22269 0 +2.1449 3.66421 0 4.12532 +3.33954 3.86864 0 4.32975 +4.42195 3.96084 0 4.42195 +2.31722 0 3.42556 1.90625 +4.42195 3.96084 0 4.42195 +1.98042 2.97063 0 0 +>MA0164.1 NR2E3 lnR0: -1.572 +1.82612 0 2.09477 1.56566 +0 4.07897 4.07897 4.54008 +0 4.07897 4.07897 4.54008 +4.94038 3.48907 0 4.94038 +5.00118 0 4.54008 5.00118 +4.54008 4.07897 4.07897 0 +4.54008 4.07897 4.07897 0 +>MA0018.2 CREB1 lnR0: -0.988 +3.28941 1.83809 1.83809 0 +3.88667 2.43535 0 3.88667 +0 3.08876 3.08876 3.54987 +3.75051 0 1.71996 3.75051 +2.89646 3.42556 0 3.88667 +3.13889 0.697367 2.67779 0 +1.86229 0 1.98042 2.44153 +0 2.67779 1.68758 1.56945 +>MA0099.2 FOS::JUN(MA0099.2) lnR0: -1.572 +4.1291 2.67779 3.668 0 +4.42195 3.96084 0 2.44153 +0 2.0169 3.58634 4.04745 +1.56566 0 2.674 4.12532 +1.88822 3.40754 2.41733 0 +4.42195 0 1.98042 4.42195 +0 3.58634 2.59613 3.05724 +>MA0079.2 SP1 lnR0: 0.18 +5.45612 0 4.0048 3.88667 +5.3668 0 3.91549 3.0676 +5.58042 0 5.11931 5.58042 +2.9222 0 4.76029 2.9222 +2.8525 1.40118 0 0.651864 +5.27153 0 3.82021 2.49166 +4.42195 0 4.95105 3.43174 +5.0595 0 2.61797 1.92061 +2.33566 0 4.65442 2.81633 +3.18902 0 2.72792 3.18902 +>MA0102.2 CEBPA lnR0: -0.404 +1.98042 3.49974 3.49974 0 +2.674 2.2129 0.903912 0 +0.671434 1.51932 -0.270346 0 +2.18107 0 1.71996 1.19086 +1.58747 1.85612 0 2.31722 +2.8525 0 3.96084 3.43174 +0 3.74524 3.74524 4.20634 +0 3.74524 3.74524 4.20634 +3.42556 0.184588 1.39501 0 +>MA0259.1 ARNT::HIF1A lnR0: -0.988 +1.28942 0.778182 0 6.04971 +2.11461 0.220215 0 0.589122 +0 4.21152 1.24089 5.25186 +7.09595 0 6.63484 6.10574 +7.10962 6.64851 0 7.10962 +6.64851 6.18741 6.18741 0 +7.10962 6.64851 0 7.10962 +1.8994 0 1.29532 2.1449 +>MA0442.1 SOX10 lnR0: -2.156 +4.74072 0 4.27962 2.7603 +0.286672 1.39501 1.39501 0 +4.1291 2.67779 1.3688 0 +4.47928 4.01817 4.01817 0 +4.74072 2.2992 0 4.74072 +4.41577 3.95467 2.96446 0 +>MA0141.2 ESRRB lnR0: 1.348 +0 -0.0680551 -0.361674 0.443817 +1.4566 0.692923 0 1.27009 +2.03173 0 0 1.04152 +2.67947 0.0025588 1.44018 0 +3.51485 0 2.05217 6.07908 +0 6.13834 3.25127 6.83416 +0 9.664 5.36077 8.91468 +7.12078 10.1279 0 7.29958 +8.50412 8.15736 0 8.12088 +4.10031 5.65965 3.21254 0 +8.78607 0 4.29442 5.71212 +0 6.77241 4.24559 6.94095 +>MA0145.2 TFCP2L1 lnR0: 2.516 +9.08588 0 3.84198 6.91967 +3.9571 0 7.09671 3.25969 +0 6.26445 0.652662 2.24065 +7.69338 5.26622 0 8.62756 +1.39741 -0.0121078 3.68242 0 +2.45488 0.454177 2.65321 0 +1.65325 0 1.38869 0.979049 +0 0.196917 0.0443911 1.09031 +0 2.67945 1.24931 2.52365 +0 2.43112 -0.112798 0.677291 +8.19353 0 4.04895 7.16191 +4.13523 0 7.92039 3.19074 +0 5.62779 0.366048 1.8255 +6.67837 4.97855 0 8.13787 +>MA0146.2 ZFX lnR0: 2.516 +2.26272 0.00795864 0 1.79007 +1.98212 0.0248453 0 1.64442 +1.57043 0.392053 0 2.83358 +2.47058 2.5501 0 2.7039 +5.17425 0 1.02909 3.69411 +6.09787 0 6.84719 2.12433 +3.00532 0.552317 0 0.801393 +0 -0.146044 0.175054 3.54987 +6.11487 7.22321 0 8.26355 +9.27483 6.83331 0 8.28462 +9.28674 0 8.82563 9.28674 +9.28377 0 8.82267 8.29356 +8.82267 7.37135 8.36156 0 +1.81313 0.824125 0 2.38399 +>MA0463.1 BCL6 lnR0: 2.516 +0.857768 0.553808 0.0426118 0 +4.55324 4.73217 4.40103 0 +7.06289 2.88365 4.25574 0 +5.23613 0 5.08233 5.43349 +10.0458 0 9.58472 3.00689 +9.80543 9.34433 9.34433 0 +0 1.87697 -0.320146 4.36862 +2.94731 9.57598 0 10.0371 +0 9.32176 5.77189 7.48367 +0 2.16914 1.38984 4.00369 +0 5.74433 1.04928 2.31318 +3.06444 2.73529 0 2.67463 +1.82901 0 2.06055 2.09248 +0 0.498547 0.675337 0.654546 +>MA0464.1 BHLHE40 lnR0: 0.764 +2.51865 0 0.120809 3.21399 +0.571589 3.29256 0.734261 0 +14.2727 0 13.8115 14.2727 +0 13.3504 13.3504 13.8115 +14.1489 0 13.6878 3.89279 +2.4806 3.38213 0 13.858 +13.8115 13.3504 13.3504 0 +14.2727 13.8115 0 14.2727 +2.07189 0 8.70019 13.8696 +0 0.172145 3.75735 0.529685 +2.07832 0 0.765915 1.18083 +>MA0469.1 E2F3 lnR0: 3.1 +10.811 0 10.3499 0.74314 +11.2055 10.7444 10.7444 0 +11.6666 0 11.2055 11.6666 +11.6211 0 4.88218 11.6211 +11.6666 0 11.2055 11.6666 +11.4821 11.021 0 3.28697 +11.6666 0 11.2055 11.6666 +11.0907 0 1.47223 3.26124 +2.30224 0 1.7214 1.97258 +2.156 0 0.28019 0.976976 +3.35731 0 1.41141 2.74227 +0 0.825192 0.19493 1.54676 +3.719 0 0.875455 3.17482 +0.542128 -0.450005 1.20674 0 +1.6815 0 0.155159 1.91422 +>MA0472.1 EGR2 lnR0: 3.1 +2.19694 0 0.963046 1.86146 +0.904465 0 1.33557 1.22536 +2.20537 0 1.38713 1.42905 +1.35025 0 3.41965 3.73675 +5.86589 0 10.1131 5.49516 +0.882382 9.1456 0 2.05927 +10.6447 0 10.1836 10.6447 +3.27264 0 9.99787 10.459 +10.5536 0 10.0925 4.32975 +0 2.00973 9.49036 9.95146 +10.6447 0 10.1836 10.6447 +0.789148 9.09004 0 1.92609 +10.3881 0 3.14852 3.9284 +0 0.413776 1.00723 1.55673 +2.71033 0 1.28151 1.74262 +>MA0482.1 GATA4 lnR0: 0.764 +6.8436 -0.116195 1.34102 0 +11.4334 0 2.79113 3.4043 +11.2648 4.37535 10.8037 0 +11.3118 10.8507 10.8507 0 +0 5.56045 10.8303 11.2914 +11.3118 10.8507 10.8507 0 +11.7729 0 11.3118 11.7729 +1.98562 10.5335 10.5335 0 +10.6378 0 0.395328 1.58012 +1.19323 0 2.64307 0.489821 +1.71362 0 0.440985 0.768407 +>MA0483.1 GFI1B lnR0: 0.764 +0 0.883236 2.92686 3.51599 +0 10.2163 10.2163 10.6774 +0 10.2147 8.64526 10.6758 +10.3448 1.56085 5.07328 0 +11.1385 0 10.6774 11.1385 +0 5.03911 9.45488 0.541066 +4.82244 0 1.73784 10.7183 +0 9.56518 8.57497 0.784502 +5.26727 9.61659 0 6.30762 +3.64587 0 4.06911 3.05668 +0 0.303118 2.01433 0.684215 +>MA0485.1 HOXC9 lnR0: 1.932 +1.22199 1.83846 0 1.96798 +2.68769 1.62643 0 3.4344 +3.20145 0 3.84758 2.42745 +1.51039 0 7.79637 1.72955 +0 6.83743 1.20659 5.2315 +9.68072 5.93021 9.21962 0 +0 2.64186 3.86919 5.03383 +0 9.22774 9.22774 7.38965 +0 6.44463 9.2245 9.6856 +5.45965 9.20488 9.20488 0 +4.29233 0 6.83132 3.03681 +0 2.46984 5.8192 1.22475 +1.66577 0 1.02527 0.823841 +>MA0493.1 KLF1 lnR0: 0.764 +0.883856 1.38486 0 1.48694 +1.31771 2.87145 0 4.76901 +2.98172 0 3.55347 4.05853 +5.45612 0 8.76509 3.55435 +0 1.28856 8.11588 6.27778 +9.41425 0 8.95314 9.41425 +0 8.1017 1.55174 3.70395 +9.41425 0 8.95314 9.41425 +9.41425 0 8.95314 9.41425 +9.3646 0 8.9035 5.15826 +0 2.47437 7.59369 0.402526 +>MA0494.1 NR1H3::RXRA lnR0: 5.436 +10.1191 4.04113 4.8476 0 +3.38278 5.08564 0 7.02687 +0 1.12194 1.9361 2.25917 +2.4182 0 9.82765 4.61691 +4.61554 0 7.99907 3.498 +3.21708 0.784628 2.05546 0 +0 -0.292346 -0.400132 0.511242 +0 0.0731329 -0.308472 0.304562 +0 9.07938 0.830025 2.3356 +2.14056 5.44442 0 4.11587 +3.89166 9.65442 7.35522 0 +0 2.35494 -0.119831 1.5144 +0 1.85564 1.74006 9.71929 +2.35378 0 5.46504 5.28046 +3.57147 0 9.92562 3.63332 +5.83911 0.0413128 3.55473 0 +2.34652 0 1.35606 0.698733 +0.699028 0.750356 -0.00383985 0 +1.33897 0.590645 0 0.989315 +>MA0498.1 MEIS1(MA0498.1) lnR0: 3.1 +0 2.9528 0.949335 1.04445 +3.47166 0.887952 0 2.85958 +4.72423 0 9.1456 5.45789 +11.2376 10.7765 10.7765 0 +11.6987 11.2376 0 11.6987 +4.79834 5.0837 10.7006 0 +11.6987 0 11.2376 11.6987 +0 10.6925 10.6925 3.99554 +2.53134 0 0.0521434 3.26291 +2.11658 0.978719 1.99573 0 +3.49621 0 1.55786 2.10214 +0 0.481394 2.37092 0.303695 +1.09289 0 0.202242 0.889381 +1.542 0 0.899608 1.219 +0.696482 -0.235638 0.373963 0 +>MA0499.1 MYOD1 lnR0: 1.932 +0.0406315 -0.12738 0.0308224 0 +1.8562 0.748618 0 2.38563 +14.8997 0 14.4386 14.8997 +0 13.9681 13.9681 7.16122 +14.4642 1.47768 0 10.1846 +14.8997 0 14.4386 14.8997 +14.4386 13.9775 13.9775 0 +14.8997 14.4386 0 14.8997 +10.4249 0.232188 3.98944 0 +9.70887 0 1.90302 0.517607 +0.830539 0 0.349109 1.02444 +3.03795 0 1.4139 1.25641 +0.998144 -0.345066 0.438801 0 +>MA0500.1 MYOG lnR0: 0.764 +0.60158 1.5754 0 13.4114 +0 4.61217 0.167358 13.3663 +14.5623 0 14.1012 14.5623 +0 13.6401 13.6401 14.1012 +14.5623 14.1012 0 14.5623 +8.2855 0 2.40086 14.3134 +14.1012 13.6401 13.6401 0 +14.5623 14.1012 0 14.5623 +2.03491 0 0.530152 2.44909 +0 0.0392188 -0.41354 0.0718136 +1.33814 0.650015 0 1.77437 +>MA0509.1 RFX1 lnR0: 2.516 +2.8349 3.24627 0 3.6894 +4.60516 2.24458 1.49069 0 +2.79101 -0.159561 2.47391 0 +1.30718 0.806019 0 1.00064 +5.93141 0 4.13155 3.19516 +11.3541 0 10.893 4.91003 +0 1.16169 3.58293 1.59819 +3.65071 3.44801 3.70355 0 +1.79119 10.4804 0 10.9415 +3.81255 10.8245 0 11.2856 +3.00664 0 6.97126 4.14296 +0 10.242 2.3831 4.09604 +0 10.4554 4.67963 10.9165 +11.4155 0 10.9544 11.4155 +>MA0515.1 SOX6 lnR0: 0.18 +5.2214 0 1.4426 1.74481 +8.17922 0 7.71811 3.36879 +0 6.80689 6.80689 0.855657 +7.8878 7.4267 7.4267 0 +7.8878 7.4267 7.4267 0 +8.34891 7.8878 0 8.34891 +7.8878 7.4267 7.4267 0 +6.95362 -0.298327 3.93286 0 +4.69772 -0.217602 6.53581 0 +3.07395 0.276048 1.53043 0 +>MA0518.1 STAT4 lnR0: 2.516 +2.42798 -0.277366 0.784647 0 +7.70518 9.33884 10.9083 0 +6.36151 10.6087 1.64749 0 +2.26009 0 7.34973 11.475 +2.71507 0 4.31059 1.027 +0 5.12848 -0.218064 3.03817 +1.98641 10.9517 0 8.63298 +6.34544 11.3538 0 11.8149 +0 10.9153 10.9153 11.3764 +0 10.9153 10.9153 11.3764 +0 2.00545 0.446241 3.02804 +0.905619 -0.239333 -0.0449338 0 +1.15521 0.506168 0 1.5123 +0.786927 1.31925 0 1.84283 +>MA0519.1 STAT5A::STAT5B lnR0: 0.764 +0 0.932617 0.0141647 0.776324 +1.9174 0.669697 0.976411 0 +13.8737 13.4126 13.4126 0 +13.7281 2.72642 13.267 0 +14.3204 0 13.8593 7.00896 +6.0053 0 13.5098 2.33362 +0 -0.26422 12.1961 1.07178 +0 12.9016 1.00351 3.76934 +14.3348 13.8737 0 14.3348 +0 6.77473 13.2651 3.25331 +0 13.265 2.70579 13.7261 +>MA0520.1 STAT6 lnR0: 3.1 +1.81157 0 0.454665 1.0137 +0 0.546369 0.367054 0.444249 +2.1703 -0.162117 0.20992 0 +10.7494 10.2883 10.2883 0 +6.96923 10.2782 10.2782 0 +4.19676 0 10.6102 5.45442 +4.50618 0 10.1346 1.50815 +0.508031 4.91656 1.62715 0 +1.89714 0.741452 0 3.70208 +0 7.63132 0.993043 2.01805 +6.4583 10.7055 0 6.26094 +0 10.2883 10.2883 10.7494 +0 10.286 8.30553 10.7471 +0 -0.261789 0.17315 1.07051 +1.16671 0.205593 1.25218 0 +>MA0522.1 TCF3 lnR0: 0.764 +2.08824 0 0.847795 3.07006 +0 -0.131975 1.72229 3.02766 +14.3986 0 13.9375 14.3986 +0 13.4764 13.4764 13.9375 +13.9265 1.58078 0 4.45409 +14.3642 0 5.30163 14.3642 +13.9375 13.4764 13.4764 0 +14.3986 13.9375 0 14.3986 +13.9409 0 1.8642 3.65888 +0 0.258349 5.64309 0.210428 +1.94073 0.680171 0 1.12231 +>MA0098.2 ETS1 lnR0: 3.1 +1.0859 0 0.661645 1.38661 +3.42315 0 2.22254 2.30213 +2.35509 0 2.37899 1.67153 +0 2.8283 0.909734 3.24178 +10.9162 0 8.15586 2.5154 +2.20064 10.0239 10.0239 0 +10.7617 10.3006 10.3006 0 +11.2228 0 10.7617 11.2228 +11.2228 0 10.7617 11.2228 +10.6371 10.176 2.95283 0 +10.8333 2.08776 0 4.01802 +4.09872 0.532795 3.70407 0 +2.64709 0 0.626289 0.618885 +1.20176 -0.0740069 0.72676 0 +1.69285 0 0.409463 0.782719 +>MA0035.3 GATA1 lnR0: 0.764 +2.13426 0.597829 1.36226 0 +3.98529 -0.0995842 1.08652 0 +14.1855 0 5.03555 2.92509 +13.9373 4.12157 13.4762 0 +13.9938 13.5327 13.5327 0 +0 13.5327 13.5327 13.9938 +13.9938 13.5327 13.5327 0 +14.4549 0 13.9938 14.4549 +2.83719 13.3491 13.3491 0 +1.86514 0.115861 0 1.81027 +2.29389 0.420006 2.06937 0 +>MA0100.2 MYB lnR0: 0.18 +2.49984 0 0.963789 0.65677 +1.44189 0 8.73699 1.04508 +0 9.37826 9.37826 9.83936 +0 9.27396 3.20468 9.73506 +10.3005 0 9.83936 10.3005 +4.06139 9.29883 9.29883 0 +10.3005 9.83936 0 10.3005 +1.91226 0 5.32929 0.502818 +5.35035 0 9.79495 10.2561 +0 5.81079 8.94968 1.54023 +>MA0147.2 MYC lnR0: 0.18 +2.07224 0 2.826 12.1793 +12.7214 0 12.2603 12.7214 +0 11.7992 11.7992 12.2603 +11.4571 -0.0596507 10.996 0 +12.7214 12.2603 0 12.7214 +12.2603 11.7992 11.7992 0 +12.7214 12.2603 0 12.7214 +5.92935 0 0.141015 1.78603 +1.72751 0.912069 1.86854 0 +4.90736 -0.00963281 1.20587 0 +>MA0104.3 MYCN lnR0: -0.988 +0.560206 1.92847 0 2.23324 +10.5115 0 2.05794 10.5115 +10.8141 0 10.353 10.8141 +0 9.89187 9.89187 10.353 +10.8141 0 10.353 10.8141 +3.30359 10.1709 0 10.632 +10.353 9.89187 9.89187 0 +10.8141 10.353 0 10.8141 +>MA0150.2 NFE2L2 lnR0: 3.1 +1.47254 0 1.60789 2.01796 +0 1.86319 0.855007 2.15402 +1.66293 0.19966 0 1.98471 +0.740117 0 0.689987 1.43984 +0 3.5747 0.773876 6.28658 +9.41275 8.95165 8.95165 0 +9.84407 9.38297 0 5.88323 +0 8.95165 8.95165 9.41275 +5.08378 0 2.14467 3.6826 +2.8084 4.34462 4.64649 0 +3.49005 0 3.51396 3.46857 +0 6.64358 2.17992 3.30932 +6.39218 5.80678 0 6.84712 +7.52059 0 5.07907 7.52059 +0 4.02506 3.78234 3.69429 +>MA0143.3 SOX2 lnR0: -0.988 +10.8865 0 10.4254 10.8865 +10.8865 0 10.4254 10.8865 +0.267549 9.10256 9.10256 0 +10.4254 9.96428 9.96428 0 +10.4254 9.96428 9.96428 0 +10.8865 10.4254 0 10.8865 +10.4254 9.96428 9.96428 0 +9.47805 0.388008 0.878238 0 +>MA0591.1 BACH1::MAFK lnR0: 3.1 +0 1.13974 -0.331145 1.60084 +2.09267 0.341757 0 1.75497 +2.22503 0.385234 0 3.88667 +0 1.49815 0.550588 6.0067 +5.17127 5.2894 6.27961 0 +7.14986 6.68876 0 4.17923 +0 6.30489 6.30489 5.77579 +6.96664 0 2.15622 6.96664 +5.72476 6.25387 3.95467 0 +4.59021 0 5.11931 7.14986 +0 5.25061 4.2604 5.13248 +7.2271 5.77579 0 7.2271 +7.23958 0 6.77847 7.23958 +0 3.80416 3.32348 3.78459 +2.17003 0 0.139484 1.35497 +>MA0594.1 HOXA9 lnR0: 0.764 +1.67735 0.596765 0 4.45722 +3.52479 0 4.16824 1.71952 +2.04271 0 6.81526 3.14727 +0 4.82647 3.668 7.26799 +7.36185 6.90074 6.90074 0 +0 0.320946 3.00711 4.04745 +0 3.9913 6.77117 3.94287 +0 5.90225 6.89246 7.35356 +4.75176 6.85031 5.8601 0 +4.69537 0 7.20489 4.11613 +0 2.96446 6.51433 2.06974 +>MA0113.2 NR3C1 lnR0: 3.1 +0 7.42097 0.253428 1.85421 +2.82328 8.45172 0 4.2584 +0 0.658411 0.448978 1.87455 +0 8.10526 2.9468 3.75594 +9.23851 0 8.77741 9.23851 +0 8.04723 4.17859 2.50164 +0.677313 0.374004 0 7.86365 +0 1.22878 1.04299 1.53937 +0 0.737938 0.711725 7.8878 +1.62093 7.86175 3.58213 0 +9.23851 8.77741 0 9.23851 +3.0677 4.99799 8.13689 0 +0.598779 -0.287983 6.9888 0 +9.04863 0 8.58752 3.22358 +2.04901 0.293035 7.46058 0 +>MA0601.1 ARID3B lnR0: 0.764 +0 0.922923 0.922923 1.38403 +1.0389 2.31877 2.31877 0 +0 1.86171 3.62191 1.33856 +3.06283 9.25024 9.25024 0 +9.86965 9.40854 9.40854 0 +0 9.40854 9.40854 9.86965 +0 9.27552 9.27552 3.30833 +3.30833 9.27552 9.27552 0 +0.914932 1.08562 2.26538 0 +0 1.04572 1.04572 1.50683 +0 0.229943 0.229943 0.691048 +>MA0602.1 ARID5A lnR0: 2.516 +1.66075 0 0.865908 1.73799 +1.5123 0.103628 3.11822 0 +0 3.92183 2.93162 3.8037 +0 6.0742 5.08399 4.96586 +3.71055 6.02932 5.03911 0 +0 5.03911 5.03911 3.71055 +4.96586 5.08399 5.08399 0 +4.03054 2.57923 3.56944 0 +1.59287 3.69143 0 1.65367 +0.501349 0 0.912971 1.9162 +0.0921979 0.719865 -0.270346 0 +0 2.20064 1.05991 1.75319 +0 0.191407 -0.31059 0.0985612 +0 0.0778869 0.657123 0.318777 +>MA0603.1 ARNTL lnR0: 0.18 +0.516698 0.186093 0 0.472052 +1.62791 2.12838 0 3.38894 +3.54419 3.56376 1.90211 0 +8.34605 0 9.86536 10.3265 +0 5.2924 5.91428 5.38517 +8.71046 0 6.5294 5.68152 +4.69179 7.81001 0 8.27111 +3.89098 3.32958 3.51 0 +6.95001 7.47911 0 4.67967 +0.832473 0 1.16386 0.76171 +>MA0604.1 ATF1 lnR0: -0.988 +0 1.92721 -0.208645 2.78296 +5.213 5.30284 9.35029 0 +10.0177 5.07729 0 2.63127 +0 9.40854 9.40854 9.86965 +10.3308 0 9.86965 10.3308 +7.3501 9.85962 0 10.3207 +2.94089 1.362 8.92387 0 +0 1.6305 1.39422 2.54782 +>MA0605.1 ATF3(MA0605.1) lnR0: -0.988 +3.41541 2.37507 0 3.41541 +0 9.13921 1.77736 9.60031 +9.86822 9.40712 9.40712 0 +10.2606 9.79945 0 4.70081 +0 9.40712 9.40712 9.86822 +10.3293 0 9.86822 10.3293 +3.32813 9.56895 0 3.73475 +2.76311 1.31911 3.8143 0 +>MA0607.1 BHLHA15(MA0607.1) lnR0: -0.988 +2.43157 0 0.985224 8.54109 +10.3293 0 9.86822 10.3293 +0 9.40712 9.40712 9.86822 +9.54945 9.08834 1.51219 0 +0 1.51219 9.08834 9.54945 +9.86822 9.40712 9.40712 0 +10.3293 9.86822 0 10.3293 +8.18354 0.931588 1.50775 0 +>MA0608.1 CREB3L2 lnR0: -0.404 +8.34127 7.88016 0 2.01721 +1.7621 0 8.20429 2.73534 +9.14509 0 2.75393 9.14509 +0 8.41261 8.41261 8.87372 +9.33482 0 8.87372 9.33482 +9.33482 8.87372 0 9.33482 +8.87372 8.41261 8.41261 0 +9.11533 2.5447 0 9.11533 +0.981647 6.8446 0.520543 0 +>MA0609.1 CREM lnR0: 0.18 +0.974597 0.513492 -0.044888 0 +0 2.3867 1.35647 2.8478 +9.86822 9.40712 9.40712 0 +9.87189 9.41079 0 1.84275 +0 9.40712 9.40712 9.86822 +10.3293 0 9.86822 10.3293 +10.3293 9.86822 0 10.3293 +9.86822 9.40712 9.40712 0 +0 0.314477 2.5226 2.9837 +0 1.16526 1.16526 1.62637 +>MA0614.1 FOXJ2 lnR0: -0.988 +0.68132 8.98531 0 9.44641 +4.13995 4.64132 9.29574 0 +0 1.46993 9.08118 9.54228 +0 9.37534 9.37534 5.35716 +0 9.40712 9.40712 9.86822 +10.2635 0 9.80244 4.76334 +0 9.40712 9.40712 9.86822 +0 1.75403 1.75403 1.90091 +>MA0615.1 GMEB1 lnR0: 4.268 +1.45132 0.410974 0 1.10114 +0 -0.333087 0.657123 0.729751 +2.03055 0.579236 0 0.629366 +1.38837 0.218072 -0.161504 0 +1.53502 2.33447 0 0 +3.28941 3.08876 0.350301 0 +0 4.65821 0.837996 6.10952 +7.03992 0 6.57881 6.04971 +6.04971 6.57881 0 7.03992 +6.10952 0.837996 4.65821 0 +0 0.350301 3.08876 3.28941 +0 0 2.33447 1.53502 +1.24188 0.656475 0 1.37804 +0 1.01614 0.770643 0.839695 +0.831316 -0.131785 0.0364761 0 +0.651864 0.535276 0 1.06284 +0.623003 0.105869 0 0.623003 +>MA1099.1 HES1 lnR0: 0.18 +1.45889 0.540094 0 1.52897 +1.37086 0.40022 0 2.47428 +4.8351 0 5.81045 4.03068 +0 3.94701 1.90492 3.13314 +5.21116 0 3.83312 3.75738 +2.65311 4.15532 0 5.24761 +2.45065 0 2.76479 0.889371 +3.915 2.51295 0 2.41163 +0.499431 -0.374221 0.611282 0 +1.2736 0 0.942769 1.38959 +>MA0616.1 HES2 lnR0: 1.932 +0.728421 0.267317 0.267317 0 +0 0.319672 0.319672 0.364401 +0 0.319672 0.319672 0.364401 +0.897975 0 0.436871 1.36019 +3.45493 2.13722 0 3.45493 +0 8.68686 0.134784 9.14796 +1.79313 0 9.39694 9.85805 +0 9.30498 3.21544 9.76608 +2.54958 0 4.30829 4.76939 +3.07354 3.8 0 4.26111 +3.92399 3.46289 3.46289 0 +2.74434 3.2343 0 3.69541 +1.29681 0 1.33928 1.80038 +>MA0620.1 MITF lnR0: 0.18 +0.646008 0.68335 0 0.958306 +0.673627 2.47287 0 3.38022 +3.19281 2.43507 2.36254 0 +7.34434 0 7.87344 8.74552 +0 3.55751 5.18191 4.07357 +6.733 0 3.26212 2.33903 +2.78556 4.51 0 6.23868 +0.941573 0.79328 1.58902 0 +5.34438 4.88327 0 4.28212 +0.931789 0.656475 0 1.22752 +>MA0622.1 MLXIP lnR0: -0.988 +3.39828 0.67008 0 1.13119 +10.3293 0 9.86822 10.3293 +0 9.40712 9.40712 9.86822 +10.3293 0 9.86822 10.3293 +10.3293 9.86822 0 10.3293 +9.86822 9.40712 9.40712 0 +10.3293 9.86822 0 10.3293 +1.3898 2.47565 0.523403 0 +>MA0623.1 NEUROG1 lnR0: 0.18 +0 1.4221 0.38262 0.89927 +2.23758 0 1.76814 3.55494 +1.78888 0 4.57577 5.92852 +0 3.70714 1.34582 2.52156 +8.54488 3.11057 1.97425 0 +0 1.99963 3.3036 6.25108 +3.27823 1.84559 5.4727 0 +6.46781 8.68071 0 3.3047 +3.83038 1.46213 0 0.577141 +2.09831 0.109318 0.306871 0 +>MA0626.1 NPAS2 lnR0: 0.18 +0.56175 0.716852 0 0.647705 +1.88854 0.153912 0 3.53369 +10.3293 0 9.86822 10.3293 +0 9.40712 9.40712 9.86822 +3.91334 0 9.74755 10.2087 +3.91334 9.74755 0 10.2087 +9.86822 9.40712 9.40712 0 +3.91334 9.74755 0 10.2087 +2.88982 1.23471 1.10834 0 +0.470661 0 0.557966 1.01907 +>MA0627.1 POU2F3 lnR0: 3.684 +1.39064 0.627667 0.627667 0 +0.671434 0.329445 0.847882 0 +1.48659 1.53502 0 0.955785 +2.89735 2.06144 3.42646 0 +0 6.11771 6.11771 5.5886 +6.56446 5.11314 6.10335 0 +6.96664 6.50554 0 4.18677 +6.9208 0 6.4597 3.78191 +0 5.70674 5.70674 1.4595 +0 5.99859 5.00838 3.32081 +0 6.11771 6.11771 5.5886 +4.96586 6.0742 4.50475 0 +1.34426 0.79655 -0.0148553 0 +0 0.440712 1.48924 1.22059 +0.721564 1.07187 0 1.3008 +0 0.280029 0.672082 1.29208 +>MA0629.1 RHOX11 lnR0: 4.268 +0 1.49357 1.30282 1.51842 +0 -0.23387 0.0364761 0.908555 +1.56566 1.68379 0 0.657106 +0 -0.365831 -0.0954857 0.626078 +2.46681 0 2.99592 1.58247 +5.00118 5.53029 0 5.99139 +3.37713 0 2.2446 6.66654 +5.5886 6.11771 5.1275 0 +4.66745 6.50554 0 5.3972 +5.5886 5.1275 6.11771 0 +0 5.31468 5.31468 0.369802 +0 3.48177 3.80054 2.28123 +0 1.78518 4.22053 0.513391 +0.547711 1.48779 0 0.900369 +1.02116 0 0.348032 1.95535 +0.916039 1.35854 0 2.44153 +0 1.10834 1.45286 0.220215 +>MA0631.1 SIX3 lnR0: 4.268 +0.581901 1.86905 0 1.20378 +0 2.52923 2.52923 2.46501 +1.21043 2.72974 1.1603 0 +0 1.64362 0.0741715 2.10472 +3.8031 3.342 0 4.47454 +5.33574 4.87464 0 3.93456 +2.7434 5.33953 0 6.79084 +6.5205 6.05939 3.7602 0 +0 6.08885 4.10843 6.54995 +6.57881 6.11771 6.11771 0 +6.02085 0 6.54995 6.02085 +0 4.03362 4.03362 4.9057 +1.65098 0 2.18008 1.1703 +0.340587 -0.00617094 0.184588 0 +0 1.70511 1.29413 0 +0 0.138686 0.411622 0.318777 +2.68616 1.81408 0.765555 0 +>MA0632.1 TCFL5 lnR0: 0.18 +0.685951 0.593173 0 0.901664 +2.12353 0.672217 0 0.755627 +4.31351 0 5.54836 4.49393 +0 2.03488 -0.316111 0.70319 +7.40685 0 5.446 4.0772 +4.0772 5.446 0 7.40685 +0.70319 -0.316111 2.03488 0 +4.49393 5.54836 0 4.31351 +0.755627 0 0.672217 2.12353 +0.901664 0 0.593173 0.685951 +>MA0007.3 AR lnR0: 4.268 +0.963054 3.17987 0 2.87595 +1.69008 6.8797 0 7.19029 +9.11179 11.7896 0 9.47081 +0 1.55555 2.20754 0.218626 +0 7.9529 8.53213 8.99324 +9.14999 0 8.42842 9.87974 +0 6.04658 2.37714 7.30714 +3.05487 0 1.88271 1.23893 +1.27285 0.689987 0 1.41155 +1.59672 2.71074 0 3.4403 +6.15659 2.69369 7.59425 0 +12.1668 9.40645 0 11.1765 +6.84392 8.5629 10.8621 0 +0 2.9094 1.88792 0.12604 +8.46347 0 10.973 8.29521 +5.95393 0 8.91839 1.3469 +1.7905 0 1.65149 0.716606 +>MA0643.1 ESRRG lnR0: 0.18 +2.07447 0.845249 1.92755 0 +4.24928 0 1.01992 4.7681 +0 13.2672 4.1192 6.1881 +0 9.60295 8.18809 11.1686 +10.5252 10.7576 0 6.04588 +14.1894 9.59917 0 10.3207 +4.92956 7.92763 3.63954 0 +11.2187 0 5.71998 3.96738 +0 8.18809 2.76185 7.85559 +0.524683 0.484095 1.91044 0 +>MA0676.1 NR2E1 lnR0: -0.404 +0 1.7088 2.05703 1.46248 +0 3.13944 0.843421 1.58098 +0 8.57753 2.96064 5.74923 +0 9.56774 3.3999 7.46919 +5.18485 10.0288 0 7.35106 +10.0288 3.74269 9.56774 0 +6.94008 0 6.36463 3.73654 +0 9.56774 9.56774 10.0288 +0 2.59231 2.75248 2.15252 +>MA0677.1 NR2F6(MA0677.1) lnR0: 2.516 +0.560288 1.2368 0 1.99613 +0 3.6746 -0.0168289 4.9057 +5.2444 5.23823 0 4.25419 +5.08779 5.03766 0 4.03926 +5.72847 3.84089 3.39281 0 +5.85623 0 4.73865 3.63031 +0 5.50231 5.14328 5.60439 +0 4.63823 2.81495 3.52989 +0 6.70012 3.15025 8.73067 +7.13657 6.67547 0 6.14636 +6.37987 7.22775 0 4.63162 +7.05949 4.74227 4.20699 0 +8.64464 0 4.75797 3.78579 +0 5.29576 2.8283 5.75687 +>MA0681.1 PHOX2B lnR0: 0.764 +2.66958 3.27311 4.74182 0 +0 5.90555 2.64436 4.29932 +0 9.25416 7.96732 12.0705 +3.67372 0.860165 4.18138 0 +3.66088 -0.285132 0.731383 0 +2.02837 -0.144887 2.10606 0 +0 3.88999 1.97367 5.21936 +0 6.23624 5.36732 7.74864 +14.3697 10.6192 13.9086 0 +3.90801 3.8645 8.29169 0 +0 6.31829 3.90031 2.97406 +>MA0682.1 PITX1 lnR0: -0.988 +1.1412 0.196707 1.49809 0 +4.21554 6.49114 11.0312 0 +0 3.81714 3.38571 5.90372 +0 11.0312 11.0312 7.36322 +5.40278 5.18215 2.24769 0 +4.2289 0 6.11918 4.14795 +4.65922 0 4.44307 2.78434 +1.29454 0 1.55054 1.31679 +>MA0075.2 PRRX2 lnR0: -0.988 +1.68851 0 1.07822 1.10559 +2.76938 0 3.00229 0.650572 +0 2.9163 2.72801 3.65055 +0 3.54574 4.43534 5.7045 +8.02396 6.85366 7.78307 0 +3.01357 2.44071 3.50345 0 +0 3.77107 6.06311 3.23124 +0 0.0246685 -0.210099 0.804956 +>MA0512.2 RXRA lnR0: 2.516 +1.74206 2.5887 0 4.30844 +0.966546 7.17018 0 9.02067 +8.80888 8.8518 0 8.28653 +8.4788 8.87468 0 3.48901 +9.62893 7.98314 6.23871 0 +9.19645 0 6.20019 4.46615 +0 9.23832 8.03183 10.9283 +0 8.42564 5.25018 6.87105 +0 8.70496 4.53567 11.0351 +10.3221 9.02133 0 9.94732 +9.59159 8.7084 0 3.94353 +9.69524 7.89375 6.6851 0 +9.78385 0 6.89962 5.03637 +0 7.58487 3.67898 10.0907 +>MA0704.1 LHX4 lnR0: -0.988 +1.44361 0.0403746 0.755069 0 +3.69562 1.18846 10.9267 0 +0 2.26743 2.73155 3.46608 +0 10.9267 10.9267 4.17368 +11.3878 10.9267 10.9267 0 +11.3878 2.20871 5.12602 0 +0 5.65683 2.69965 4.36968 +0 1.07082 0.148878 2.23027 +>MA0705.1 LHX8 lnR0: -0.988 +2.88958 0 1.46879 1.67227 +12.1937 0.876354 11.7326 0 +0 4.47349 1.13096 12.1937 +0 11.7326 11.7326 12.1937 +12.1937 11.7326 11.7326 0 +12.1937 0.815435 5.3203 0 +0 11.7326 0.925105 12.1937 +1.11268 0.88984 0 2.81567 +>MA0709.1 MSX3 lnR0: -0.988 +1.68183 0 0.375642 1.81726 +4.63144 0 7.52035 1.61644 +0 5.18506 4.62668 6.39978 +0 6.01591 7.21055 10.3457 +12.9053 12.4442 12.4442 0 +6.04243 4.76524 5.78216 0 +0 6.59515 6.03188 5.23964 +0 0.162904 -0.410291 0.973316 +>MA0124.2 NKX3-1 lnR0: -0.404 +0 0.824067 0.371229 2.1408 +2.87916 0 1.57079 4.69229 +12.7214 0 8.83477 4.40703 +0 6.9888 8.37366 5.84799 +6.87237 0 8.97092 9.43203 +12.2603 10.809 11.7992 0 +12.2603 3.88314 11.7992 0 +0 3.78047 4.42915 3.31534 +0 1.44219 0.848819 1.80338 +>MA0720.1 SHOX2 lnR0: -0.988 +2.13109 0 1.21272 1.13462 +3.19183 -0.441461 4.80763 0 +0 4.34908 4.89789 4.52227 +0 6.50119 11.57 7.7515 +9.15269 9.88622 13.5504 0 +4.87784 4.54669 3.87952 0 +0 6.02492 8.39198 4.3002 +0 0.642434 -0.41563 1.50666 +>MA0592.2 ESRRA lnR0: 0.764 +5.37404 2.28829 1.20966 0 +5.12651 3.31377 5.8402 0 +7.52539 0 3.52496 10.2638 +0 11.6408 9.34164 12.1019 +0 11.6408 9.34164 12.1019 +11.5728 10.1215 0 9.27364 +12.563 10.5325 0 10.5826 +9.32207 8.09097 5.96899 0 +12.563 0 4.44967 7.1899 +0 8.86096 3.52144 10.5325 +2.2723 2.87672 5.49877 0 +>MA0114.3 HNF4A(MA0114.3) lnR0: 3.684 +1.26871 2.46118 0 3.24837 +1.57301 7.13364 0 9.57516 +9.89448 12.2132 0 11.6841 +5.02209 8.3446 0 3.29138 +5.06475 5.74544 2.69953 0 +11.6841 0 9.65359 5.7998 +0 10.1827 4.50189 12.2132 +0 11.7521 5.68286 8.66338 +0 11.7521 6.0803 12.2132 +12.6744 11.223 0 10.6939 +12.2132 9.19249 8.78151 0 +5.72073 0 5.23782 2.85999 +12.6744 0 9.91405 5.16364 +0 6.42149 2.16185 4.98383 +0 0.48267 0.467309 1.43868 +1.08175 0.558972 0.788383 0 +>MA0728.1 NR2F6(MA0728.1) lnR0: 3.1 +1.22992 3.3144 0 7.82295 +0 7.51532 1.81677 5.996 +8.10662 7.64551 0 8.10662 +6.9208 7.44991 0 7.91101 +8.48219 8.02109 7.03088 0 +9.75295 0 8.30163 4.10831 +0 3.49685 8.40255 7.87344 +0 5.82372 5.15228 5.29461 +0 6.84173 0.336196 1.45378 +0 7.47722 7.47722 7.93833 +8.72371 8.26261 0 8.72371 +7.67518 7.21408 0 5.11553 +6.87842 7.98676 7.98676 0 +9.77628 0 9.31517 7.79586 +0 8.25684 4.96743 8.71794 +>MA0739.1 HIC1 lnR0: -0.404 +0 2.64613 -0.025119 3.21647 +7.37606 4.19462 6.68506 0 +3.95948 4.18279 0 6.30602 +8.13904 0 6.43194 13.7559 +7.34359 0 8.34377 7.70721 +0 1.68901 10.567 4.77704 +0 1.15084 0.96188 3.28732 +3.60246 0 2.72863 3.31899 +2.02759 0 1.3421 1.29359 +>MA0742.1 KLF12 lnR0: 3.1 +3.22017 4.95971 0 2.7965 +0 5.01355 -0.403217 9.02452 +5.47546 0 6.15508 6.46567 +7.19969 0 5.63403 7.77893 +0 4.42136 7.61221 9.64276 +6.48054 0 9.30885 7.47076 +3.07802 9.30567 0 6.70954 +9.79509 0 9.33398 7.49589 +9.83401 0 6.08349 6.06392 +9.85208 0 9.39097 6.08199 +0.23356 1.51932 8.37045 0 +0.74993 0.407163 1.53353 0 +0 -0.100101 1.38274 0.08574 +0.839031 0.728433 1.38618 0 +0.280452 0.182124 0.747883 0 +>MA0769.1 TCF7 lnR0: 1.348 +0 2.51211 1.74557 2.47199 +0 4.12293 1.96436 2.79438 +0 6.96847 4.50738 4.77772 +7.34914 1.40823 0 7.12892 +0 7.70764 6.97789 4.36505 +9.67746 6.6567 5.01002 0 +5.94044 0 5.08469 5.94044 +0 9.288 6.72834 6.96923 +0 6.51123 5.86554 7.77179 +0 9.28178 9.28178 7.44368 +5.0971 9.631 0 10.0921 +2.35171 2.01166 0 3.17366 +>MA0816.1 ASCL2 lnR0: 0.18 +0 2.19797 1.41516 3.77008 +0.880361 2.02232 0 6.83274 +6.6337 0 8.15301 7.62391 +0 7.69191 7.69191 4.19217 +5.64349 3.61294 0 4.40778 +6.6337 0 6.58357 7.62391 +5.85382 7.69191 7.69191 0 +8.61412 7.1628 0 7.04467 +5.2994 0 3.65733 1.57374 +2.48996 0.500816 2.2975 0 +>MA0461.2 ATOH1(MA0461.2) lnR0: 0.18 +0 2.10291 0.345441 3.41688 +0 0.177983 1.32583 4.52921 +4.99563 0 6.76878 10.3688 +0 5.09725 4.3675 9.90767 +5.77857 6.021 2.41802 0 +0 3.27873 9.44657 9.90767 +5.42839 7.14737 6.88691 0 +8.79933 8.91746 0 5.41773 +3.42556 0.244121 -0.431107 0 +2.0294 -0.352765 1.59062 0 +>MA0829.1 SREBF1(MA0829.1) lnR0: 0.18 +0 2.64689 0.671766 6.06808 +3.05765 4.515 6.3182 0 +8.32918 0 10.6479 11.1091 +0 10.1868 5.42655 7.22238 +11.1091 0 4.92318 6.82943 +7.68349 2.86075 0 11.1091 +6.6005 3.9268 7.62718 0 +10.1188 7.67731 0 11.1091 +0 5.70756 7.04795 4.33532 +5.87195 0 3.81779 0.525637 +>MA0832.1 TCF21(MA0832.1) lnR0: 2.516 +0.800145 1.23069 0 2.42155 +1.85612 0 1.72616 1.16633 +0 5.90225 2.35238 5.37314 +0 3.46689 6.89246 7.35356 +7.81467 0 7.35356 7.81467 +0 5.90225 6.89246 7.35356 +7.81467 7.35356 0 6.24522 +7.81467 0 6.36335 6.82446 +7.35356 6.89246 6.89246 0 +7.81467 7.35356 0 7.81467 +7.35356 4.59326 2.54314 0 +4.79391 2.35238 6.89246 0 +1.122 1.73771 0 2.45927 +0.966981 -0.177032 0.416561 0 +>MA0840.1 CREB5 lnR0: 1.348 +0 0.231142 -0.289723 0.781749 +0 3.52189 3.35084 6.43409 +8.95933 7.23065 11.2781 0 +8.43022 8.95933 0 2.45275 +0 11.2781 10.2879 8.31363 +12.2003 0 11.7392 6.39967 +5.02333 11.7392 0 12.2003 +7.53286 8.49822 11.2781 0 +2.45431 0 11.7392 9.90111 +0 11.2781 11.2781 10.1698 +6.56298 0 4.53243 0.474982 +1.43678 0 1.95628 0.837762 +>MA0117.2 MAFB lnR0: 1.348 +0 2.33385 1.44074 1.45528 +0 2.87892 2.49156 0.972241 +0 1.83282 2.07626 0.610634 +0 0.430928 0.324037 0.280931 +3.01247 1.3394 5.57135 0 +9.87517 7.11486 0 8.88496 +3.31553 0 8.42385 8.47398 +6.03246 5.36395 8.95296 0 +5.97512 7.21343 0 4.09938 +0 6.75232 6.3933 7.21343 +4.00249 0 2.13144 3.42586 +0.482074 2.06913 -0.127829 0 +>MA0851.1 FOXJ3 lnR0: 4.268 +0 -0.409151 -0.116588 0.0519538 +0 0.847882 -0.333087 0.599791 +0 0.819021 1.05119 1.43064 +0 1.41345 1.05443 1.36502 +0 0.888126 -0.37945 0.769995 +1.60413 5.05851 0 6.50983 +5.55974 4.5194 6.08885 0 +0 2.8597 5.99859 6.4597 +0 4.50475 6.0742 4.55488 +0 6.11771 6.11771 5.5886 +6.75642 0 6.29531 2.55008 +0 6.11771 6.11771 5.5886 +0 2.8283 3.01906 2.97063 +0 2.05012 2.3689 1.04034 +1.0609 0 0.37073 1.33383 +0 0 0.161898 0.281015 +1.13254 0 1.14073 1.45132 +>MA0852.1 FOXK1 lnR0: 4.268 +0 0.338346 0.202189 0.37073 +0 1.21421 0.0680006 0.99021 +0 2.44094 1.74736 1.4569 +0 3.34922 3.08876 1.76021 +2.16084 1.69974 1.15761 0 +2.37183 5.26983 0 6.72114 +4.98051 6.08885 6.08885 0 +0 2.87515 6.01404 6.47514 +0 5.09864 6.08885 4.98051 +0 6.11771 6.11771 6.57881 +6.8894 0 6.4283 3.33954 +0 6.11771 6.11771 6.57881 +0 3.03681 4.24723 2.72792 +0 2.02528 1.88912 1.17739 +0.606509 0 0.0468426 1.49816 +0 0.138686 -0.0364598 0.799451 +1.49527 0.234719 0 0.801692 +>MA0853.1 ALX4 lnR0: 4.268 +2.26272 0 1.88822 2.7603 +2.81133 1.17739 0 2.81133 +1.61958 0 1.39064 1.48342 +0 0.883157 -0.0148553 1.25766 +4.34932 0.37859 4.46745 0 +5.48493 2.87515 6.01404 0 +0 5.1275 5.1275 6.57881 +0 6.10335 5.11314 5.57425 +5.57425 5.11314 6.10335 0 +6.57881 5.1275 5.1275 0 +0 6.01404 2.87515 5.48493 +0 4.46745 0.37859 4.34932 +1.24404 0.371961 0.705697 0 +0.0468426 -0.365831 0.674509 0 +0 0.157272 0.417732 0.679177 +0.779881 0 0.20443 0.779881 +2.20288 0 0.99021 1.2687 +>MA0854.1 ALX1 lnR0: 4.268 +1.61958 0 1.30899 1.54988 +3.4757 1.56945 0 3.4757 +0 -0.265103 0.903912 1.27282 +0 1.65547 -0.00617094 1.27688 +3.13889 -0.0676592 3.668 0 +5.48493 3.04341 6.01404 0 +0 6.10335 5.11314 6.56446 +0 6.10335 5.11314 5.57425 +5.57425 5.11314 6.10335 0 +6.56446 5.11314 6.10335 0 +0 6.01404 3.04341 5.48493 +0 3.668 -0.0676592 3.13889 +1.73771 0.821669 1.68758 0 +0.916039 0 0.947563 0.597262 +0 -0.142328 1.14451 1.14073 +0.721564 0 0.318777 0.721564 +1.80537 0 1.43646 0.815157 +>MA0857.1 RARB(MA0857.1) lnR0: 3.684 +0 1.60918 2.10768 1.3947 +0 4.79712 2.0053 3.83619 +0 8.22342 1.93977 10.254 +11.2943 10.8332 0 10.3041 +11.2775 9.82618 0 6.32644 +7.91048 7.93005 6.2684 0 +9.73248 0 6.97218 7.5838 +0 10.0954 6.22677 10.5565 +0 6.49252 8.06196 4.15684 +0 7.6328 2.56192 5.79471 +0 10.0258 5.12011 10.4869 +10.3099 10.839 0 11.3001 +11.149 9.69773 0 3.13551 +9.6511 7.04131 7.88101 0 +9.82996 0 8.78962 7.68128 +0 10.046 8.06562 8.9377 +>MA0858.1 RARB(MA0858.1) lnR0: 4.268 +0 6.7229 3.43349 9.16442 +9.84808 8.39677 0 9.84808 +8.17492 8.29305 0 5.26509 +9.34845 7.31789 8.88734 0 +8.8028 0 7.76246 8.8028 +0 8.95557 6.65637 9.41668 +0 0.0127832 3.69745 0.5151 +0.478146 0 0.835185 2.40254 +2.82621 -0.230722 0.795657 0 +0 3.15197 2.89151 1.45085 +0 5.79536 0.39588 6.25646 +0 8.76956 3.57301 8.24046 +8.79446 8.33335 0 9.78467 +9.74437 7.71381 0 5.03603 +9.30673 6.86521 6.54643 0 +9.94851 0 9.4874 7.64931 +0 8.88528 7.31584 8.35618 +>MA0859.1 RARG(MA0859.1) lnR0: 3.684 +0 2.43209 -0.310071 3.22802 +0 5.09252 0.75845 10.1328 +11.9872 13.5065 0 13.9676 +13.8756 11.4341 0 3.14643 +8.81273 7.58163 6.73754 0 +11.9746 0 8.26024 7.69496 +0 10.9517 8.56035 12.9823 +0 6.98414 5.79427 5.10105 +0 8.75434 3.34141 4.60081 +0 10.2801 4.038 13.0404 +13.0325 12.5714 0 12.0423 +13.5149 11.4844 0 2.26582 +10.3452 7.35891 7.01938 0 +13.8468 0 7.35783 7.18475 +0 10.2701 6.25668 12.0402 +0 0.718443 1.67797 0.978745 +>MA0860.1 RARG(MA0860.1) lnR0: 4.268 +0 7.98851 1.85218 6.92413 +0 8.59907 3.58258 12.0308 +12.8623 10.102 0 11.2929 +12.7838 12.3227 0 5.20762 +11.9553 7.9443 7.82996 0 +11.3795 0 12.4878 12.9489 +0 9.4231 7.73931 11.8646 +1.39278 0 2.76343 2.22146 +3.3874 0.453108 0 2.47645 +0 2.26187 2.05311 2.73188 +0 5.02513 -0.100895 5.51065 +0 6.2436 1.62117 10.1303 +12.863 12.4019 0 11.8728 +12.6402 9.04019 0 4.39973 +8.16122 9.99931 11.5688 0 +9.75214 0 10.6922 8.2435 +0 9.07789 8.85767 12.0986 +>MA0870.1 SOX1 lnR0: 3.1 +0 1.30837 1.46008 2.77779 +0 4.96287 5.44905 4.70526 +11.5297 0 11.0686 11.5297 +0 6.94329 10.6075 8.09798 +0 2.34051 10.6075 11.0686 +7.29853 10.6075 10.6075 0 +0 7.59114 1.74208 1.39244 +0 0.154159 0.107226 0.632204 +9.23052 0 5.42398 6.49206 +0 10.6075 10.6075 11.0686 +11.0686 10.6075 2.74857 0 +11.0686 6.73886 10.6075 0 +11.5297 11.0686 0 11.5297 +4.80857 2.65819 4.78245 0 +2.72293 1.70193 2.00993 0 +>MA0874.1 ARX lnR0: 4.268 +1.16781 0.825826 0 1.89756 +1.90176 1.16329 0.931123 0 +1.61021 0 0.337698 1.37804 +1.75761 0 2.00571 2.81133 +0 2.37592 -0.0778706 2.64626 +4.88247 0.177913 4.42136 0 +5.38966 2.14868 5.91876 0 +0 6.10335 6.10335 5.57425 +0 6.11771 5.1275 5.5886 +5.5886 5.1275 6.11771 0 +5.57425 6.10335 6.10335 0 +0 5.91876 2.14868 5.38966 +0 4.42136 0.177913 4.88247 +1.67731 1.21621 1.39501 0 +1.69285 1.88822 0 1.1389 +2.36825 0.0380975 0 1.45132 +0 1.81188 2.26681 0.792853 +>MA0877.1 BARHL1 lnR0: 0.18 +1.25904 0.383441 0 1.15696 +1.38919 0 0.935708 0.67549 +3.37297 6.68921 12.0287 0 +0 12.0287 6.33019 5.05555 +0 12.0287 6.75892 10.5094 +0.941354 3.40321 1.20575 0 +1.71829 1.15751 1.2153 0 +2.2719 4.17121 0 3.63789 +1.30596 0 0.157176 1.18553 +1.22607 -0.0635788 0.489134 0 +>MA0879.1 DLX1 lnR0: 0.18 +0.869049 0 0.632538 1.34704 +0.573197 0 0.803673 1.54202 +1.25548 0.534542 4.69193 0 +0 2.77116 3.80854 4.52805 +0 5.76518 7.05409 3.91101 +3.01584 7.08771 6.83863 0 +5.65606 4.01852 3.51535 0 +0 5.79239 7.26878 2.09494 +0.51026 -0.0442999 -0.175996 0 +1.4059 0 0.716262 1.37525 +>MA0880.1 DLX3 lnR0: -0.988 +0.918637 0 0.167651 1.40386 +3.28413 0 4.60151 0.830978 +0 2.38913 3.14202 3.47316 +0 3.27163 6.33286 4.56447 +5.34265 6.24492 6.37895 0 +4.1535 3.27429 3.51464 0 +0 4.66133 5.64452 3.37047 +0.532548 0 0.645406 0.69501 +>MA0881.1 DLX4 lnR0: -0.988 +1.0302 0 0.0935317 1.56675 +3.66777 0 5.49604 0.849295 +0 2.51511 3.52544 3.73254 +0 3.51582 7.21301 4.54661 +7.01228 6.60016 7.72986 0 +4.72599 3.29588 3.96765 0 +0 4.73651 5.95598 3.38433 +0.731161 0 0.688818 0.762249 +>MA0883.1 DMBX1 lnR0: 4.268 +0.260459 1.10834 1.21421 0 +0.847234 2.05766 0 0.897364 +0 1.98861 0.176448 1.92439 +0 1.98861 1.35742 0.682908 +0.965135 0 0.952113 1.20378 +1.26758 0 1.26758 4.09758 +4.17165 5.50021 0 6.95153 +7.03992 5.5886 0 7.03992 +0 3.26456 6.04443 6.50554 +6.57881 6.11771 6.11771 0 +5.57425 5.11314 6.10335 0 +0 6.08885 6.08885 4.56953 +0 2.28434 -0.275315 0.955785 +2.08374 1.36217 -0.284513 0 +1.40596 0.0952734 0 0.606509 +0 0.0952734 0.164974 0 +0 1.07123 0.774606 0.0380975 +>MA0896.1 HMX1 lnR0: 4.268 +0 -0.24089 0.0195698 1.30899 +1.73799 0 0.645693 2.09701 +0 -0.161504 -0.0109891 1.86905 +0 2.8283 1.56073 2.77987 +2.82025 2.99034 0 3.6197 +5.99139 0 6.5205 4.68241 +0 5.93509 2.27088 5.40599 +0 2.40137 5.95123 5.42213 +6.57881 6.11771 6.11771 0 +4.92097 3.24944 6.02932 0 +0 6.05939 5.06918 4.54008 +0 4.96102 3.65204 3.63247 +0.751562 0.984039 0.815778 0 +2.20936 1.13762 0 2.30792 +0 -0.0862988 -0.037868 2.93446 +0 0.806471 -0.021841 0.0866066 +1.09876 0.49468 0.364721 0 +>MA0897.1 HMX2 lnR0: 4.268 +0 0.806471 0.615712 2.64626 +1.61958 0 0.898012 2.03055 +0 1.00978 1.1603 2.4611 +0 2.98289 2.09855 3.444 +2.13264 1.83979 0 2.71187 +6.02085 0 6.54995 6.02085 +0 5.90225 1.94141 6.36335 +0 2.13217 4.91204 5.37314 +5.5886 6.11771 6.11771 0 +4.92097 3.24944 6.02932 0 +0 6.02932 5.03911 3.93076 +0 4.97698 4.39775 3.28941 +0 0.417732 1.14748 0.0793855 +1.14621 0.923753 0 1.93199 +0 0.118131 0.118131 2.77987 +0 1.64362 0.414759 1.32395 +2.87843 2.7361 2.41733 0 +>MA0898.1 HMX3 lnR0: 4.268 +0 0.711725 0.711725 2.2992 +2.3855 0 0.934181 2.27963 +0 0.558562 0.819021 2.13418 +0 2.7737 2.19446 3.42556 +2.34933 2.4235 0 2.34933 +5.3972 0 6.50554 4.66745 +0 5.88554 1.83809 5.35643 +0 2.27088 5.93509 5.40599 +5.5886 6.11771 6.11771 0 +5.51533 3.74524 6.04443 0 +0 6.01404 4.44459 3.91549 +0 4.36564 3.95467 3.42556 +0 0.847882 1.14451 0.150515 +0.986426 1.02732 0 1.48842 +0 0.653407 0.360844 2.75042 +0 1.66087 1.0044 1.39223 +2.19333 2.07674 1.73222 0 +>MA0904.1 HOXB5 lnR0: 3.684 +0 0.670664 1.3421 2.12198 +0.820125 0 0.839695 1.3008 +2.31722 2.69581 0 3.02076 +2.03055 1.27282 0 0.575452 +5.48493 3.04341 6.01404 0 +0 2.69357 5.98298 6.44409 +0 5.11314 6.10335 5.57425 +5.57425 6.10335 5.11314 0 +6.44409 5.98298 2.69357 0 +0 6.01404 3.04341 5.48493 +1.52102 0.480675 0 2.25077 +3.02076 0 2.69581 2.31722 +0.348032 0.0429257 1.27178 0 +1.08877 0 1.88822 1.77009 +0 3.02796 1.71898 2.18008 +1.08047 1.05119 1.23 0 +>MA0910.1 HOXD8 lnR0: 4.268 +1.98042 1.62518 0.94008 0 +0 1.74736 1.86171 1.82523 +0 2.27268 1.06225 2.32281 +0 2.0169 -0.2823 0 +3.09865 1.0681 4.61796 0 +0 2.00391 3.6877 2.46501 +0 4.44459 4.44459 4.17595 +4.20634 5.05422 5.05422 0 +3.94588 5.05422 6.04443 0 +0 6.05939 5.06918 4.54008 +0 3.23928 4.22949 2.48996 +3.28941 2.50953 3.23928 0 +0.872079 3.23109 0 2.12275 +1.6385 2.80516 0 2.46681 +1.79838 0 2.478 1.4796 +1.56945 2.09855 1.51932 0 +0 0.281574 0.491008 0.504031 +>MA0911.1 HOXA11 lnR0: 1.348 +1.23641 1.48393 0 1.90625 +1.69606 1.44717 0 7.84954 +8.37864 4.09733 4.8603 0 +4.92426 0 9.36885 4.6715 +1.93645 7.79941 0 6.85933 +5.50021 7.91754 6.92733 0 +0 6.40763 4.61796 1.17018 +0 8.90775 7.3383 4.4178 +0 4.14746 6.92733 4.06375 +0 1.6575 2.09249 1.81419 +0.233756 -0.103047 0.0236186 0 +1.28428 1.15477 1.12926 0 +>MA0912.1 HOXD3 lnR0: 3.684 +0.99021 -0.387829 2.24907 0 +1.7056 2.38522 2.38522 0 +2.46514 2.44711 0 2.28633 +0 1.30988 -0.302211 0.780777 +1.3008 2.14868 0 1.3008 +1.16901 -0.021841 -0.2823 0 +5.35643 2.0169 5.88554 0 +0 2.27088 5.93509 6.3962 +0 5.11314 6.10335 5.57425 +5.57425 6.10335 5.11314 0 +6.3962 5.93509 2.27088 0 +0 5.88554 2.0169 5.35643 +0 0 1.32791 1.64669 +1.3008 0 2.14868 1.3008 +1.99344 0 0.2455 1.24188 +2.27034 0.619361 0.682864 0 +>MA0913.1 HOXD9 lnR0: 0.18 +1.8072 2.09477 0 4.70455 +3.89185 0 4.36493 0.957392 +0 0.847882 1.9133 7.53286 +0 5.50231 2.1207 4.9732 +3.76277 4.10112 4.10112 0 +0 4.13729 6.11771 0.0583171 +0 5.50231 7.07175 3.40375 +0 4.10112 7.07175 4.56223 +0 2.36341 1.76665 2.09477 +0 1.05821 1.58902 0.344517 +>MA1153.1 SMAD4 lnR0: -0.988 +2.67856 0.740059 2.34031 0 +10.3308 9.86965 0 10.3308 +9.86965 9.40854 9.40854 0 +10.3308 0 9.86965 10.3308 +9.86965 9.40854 9.40854 0 +0 8.66922 0.090785 9.13032 +10.3308 9.86965 0 10.3308 +0 0.384799 1.48966 2.12806 +>MA1603.1 DMRT1 lnR0: 1.932 +2.68801 3.4344 0 2.88429 +0 0.354445 2.09702 0.476285 +1.62747 2.82189 3.23714 0 +0 7.46169 7.21834 6.33981 +6.77682 0 6.90849 6.22022 +0 6.76726 6.84664 4.83456 +0 4.50035 4.5794 3.09009 +0 5.39649 4.75395 1.20851 +4.96483 6.45309 0 6.00293 +4.93894 6.21881 5.91065 0 +0 2.57956 1.55843 1.29944 +0.225798 1.89107 0.275611 0 +2.57507 0 3.05663 2.73156 +>MA1604.1 EBF2 lnR0: 1.932 +0.776021 -0.0114232 -0.394944 0 +1.95665 0.343017 1.49199 0 +7.40846 0 6.02016 7.43777 +5.96692 0 6.47945 4.71117 +6.25324 0 6.62725 6.21445 +0 1.87656 3.25391 3.34051 +0 3.33032 1.9128 3.14121 +5.49945 6.64306 0 7.49153 +4.67473 6.71949 0 6.4063 +5.04917 5.32322 0 5.76965 +0 3.42289 3.1821 4.00415 +0.575871 0 0.151364 1.18478 +0.187649 -0.374956 0.186038 0 +>MA1606.1 FOXF1 lnR0: 0.764 +0 0.634822 0.424127 0.806733 +0.606807 1.32615 1.195 0 +1.31091 3.13063 0 3.63068 +6.59054 6.47418 5.1131 0 +0 5.47255 6.47551 5.92732 +0 4.07746 5.53344 4.36594 +0 6.37937 5.2249 6.04274 +7.3494 0 6.63492 4.12403 +0 5.71912 6.4604 4.83195 +0 0.0959657 -0.0793586 0.418594 +0 0.325819 0.194392 0.466783 +>MA1607.1 FOXL2 lnR0: 2.516 +0 0.569062 -0.0332314 0.559556 +0 0.550522 0.279314 0.0386852 +0.396805 1.94437 1.92369 0 +0 1.95808 1.91962 1.98234 +2.08487 3.34181 2.73472 0 +2.92652 5.26292 0 5.34445 +3.85251 5.23543 4.76425 0 +0 4.43624 6.72019 6.3304 +0 5.15795 5.99172 5.49723 +0 5.7813 4.8654 5.64789 +6.19811 0 6.62496 3.42547 +0 3.77033 4.76763 3.58429 +0 -0.163679 -0.0216225 0.127633 +0 -0.215014 -0.27952 0.323714 +>MA1608.1 ISL1 lnR0: 0.764 +0 0.324 -0.0852852 0.446483 +0.728955 0.00341682 -0.180436 0 +4.1467 0 4.56424 4.05751 +3.92309 0 6.40971 4.61379 +0 6.93079 5.25767 7.30258 +6.27129 6.11329 6.75898 0 +6.32213 5.17592 6.55461 0 +0 6.36334 7.48351 5.56603 +2.2082 3.14044 0 3.51391 +1.13418 0 0.400648 0.691447 +0 -0.445671 -0.365898 0.209383 +>MA1615.1 PLAGL1 lnR0: 1.932 +1.1537 0 0.0830325 1.25039 +1.06275 0 0.125778 1.0897 +2.21668 0 1.25953 2.5609 +2.27307 2.19154 2.32682 0 +6.50291 5.74338 0 7.23026 +3.7648 5.05218 0 5.65184 +6.56873 5.60647 0 6.59945 +6.62061 5.27152 0 6.95725 +4.44569 0 5.28993 5.7151 +6.57596 0 4.91005 5.4546 +0 3.63279 3.0501 4.97024 +1.66185 0.0705983 0 1.35761 +0.876673 0.334262 0 1.2889 +>MA1616.1 PRDM15 lnR0: 3.1 +0 -0.0730472 -0.275128 0.203914 +1.01497 1.46624 0 1.78334 +2.83617 2.01291 0 2.46528 +0 4.5332 3.38779 5.91593 +0 5.40285 4.65686 6.34463 +0 4.82573 2.77987 5.25738 +0 3.19915 3.06206 3.58031 +5.24963 0 4.20929 4.33491 +3.51192 0 4.08659 6.75718 +2.85366 1.68758 5.29379 0 +7.17608 8.02396 0 7.79148 +5.44408 6.40631 0 6.80909 +0 1.79855 2.30485 3.11577 +0.582462 0.763199 0 1.48802 +0.692218 0 0.459715 0.537221 +>MA1618.1 PTF1A(MA1618.1) lnR0: 1.932 +0 -0.0125265 -0.302149 0.144208 +0 -0.174432 -0.137294 0.703509 +0 1.16124 1.34578 3.52192 +7.10321 0 6.67445 6.73828 +0 6.3565 5.98817 6.96945 +6.10804 4.75996 0 4.73996 +0 2.32561 4.28385 6.28534 +6.71538 5.43726 6.34722 0 +6.24464 6.75032 0 6.44047 +3.11754 1.57527 1.10834 0 +2.43174 1.34553 1.37387 0 +0.0772389 -0.428173 -0.452943 0 +0 -0.436159 -0.309533 0.0511227 +>MA1619.1 PTF1A(MA1619.1) lnR0: 1.348 +0.539148 0.129374 0 0.754787 +0.754978 0 0.571032 1.44955 +0 1.54017 1.2535 3.00623 +7.55088 0 7.86796 8.3792 +0 6.87174 6.22605 7.86195 +7.96542 4.39753 0 5.31357 +5.30891 0 4.43683 8.00854 +7.96444 6.20497 6.90657 0 +8.37939 7.91829 0 7.55108 +2.98851 1.2475 1.54521 0 +1.44134 0.566053 0 0.755516 +0.761404 0 0.131543 0.539789 +>MA1620.1 PTF1A(MA1620.1) lnR0: 1.348 +0 -0.264214 -0.372765 0.283317 +0.95785 0 0.630718 1.6591 +0 2.04427 1.79972 3.02403 +6.14499 0 6.37554 6.91388 +0 6.8287 6.35473 6.384 +6.59484 0 2.82854 4.7454 +5.6351 0 4.97699 6.60873 +6.79642 6.19313 6.13421 0 +7.56615 6.43879 0 6.52509 +3.61552 1.5564 1.64671 0 +1.44449 0.398773 0 0.741711 +0.846791 0 0.455885 0.555936 +>MA1621.1 RBPJL lnR0: 2.516 +0.978024 0 0.216338 0.78958 +0.508377 0.0700364 0 0.664888 +0 -0.350075 0.432411 1.29108 +0 1.64608 1.52743 2.91055 +6.45157 0 6.41511 6.47213 +0 6.51661 5.87825 6.68739 +7.04562 0 3.62867 4.96776 +5.66976 0 4.77656 6.93387 +7.11484 5.48538 5.60879 0 +6.89341 6.07791 0 6.61686 +3.31055 1.2725 1.39115 0 +1.52719 0 0.270346 1.0307 +0.801083 0 0.552987 0.644174 +0.984156 0 0.392704 0.850682 +>MA1623.1 STAT2 lnR0: 1.932 +0 1.09859 0.0461453 1.20274 +1.68702 2.86941 0 2.95965 +0 5.01362 3.89063 4.41216 +0 5.10362 5.18086 5.52761 +0 5.16192 4.89495 5.83348 +3.7693 0 2.44546 4.00705 +0 3.86793 4.87706 2.39397 +5.01512 6.27087 0 6.45096 +0 5.68795 3.99103 6.20737 +0 5.82509 4.73012 5.6864 +0 4.06401 3.97061 4.58424 +1.47142 0 0.344431 1.92876 +0.0941053 0.360491 0.715484 0 +>MA1624.1 STAT5A lnR0: 1.348 +0.00322113 0.177253 -0.0586848 0 +3.48887 2.78633 3.62067 0 +4.71771 5.00527 4.32395 0 +6.43334 0 7.27061 7.10052 +6.21691 0 7.05491 3.87857 +0 1.95315 4.02625 2.3902 +0 4.85727 1.29424 4.96132 +8.17986 7.51909 0 7.46447 +0 6.16389 5.91482 5.56833 +0 5.47582 4.87542 5.79496 +0 0.0120133 0.0686539 0.421313 +0.31853 -0.211044 0.604923 0 +>MA1625.1 STAT5B lnR0: 3.1 +0.769156 0 0.158233 0.578106 +0 0.188185 0.0224014 0.52375 +0.383714 0.125942 0.300679 0 +5.59135 5.05012 5.13024 0 +4.75865 5.69361 5.69361 0 +6.73568 0 6.72951 6.46086 +5.27284 0 5.57359 2.65715 +2.35815 0 3.73375 2.47713 +0 4.82907 3.5342 4.95741 +8.33219 7.2492 0 7.62865 +0 5.62788 4.36732 4.84494 +0 6.15298 5.19051 6.85274 +0 0.0837059 -0.123195 0.748884 +0.309179 -0.139395 0.18411 0 +0.670832 0 0.0743521 0.813242 +>MA1627.1 WT1 lnR0: 2.516 +1.55194 0 1.23107 1.176 +1.73633 0 0.484358 0.85958 +2.25513 0 2.83619 2.99341 +6.93311 0 6.20669 7.22302 +5.06176 5.38251 3.21133 0 +8.09456 0 6.67609 7.802 +7.12612 0 5.78335 4.70669 +6.99138 0 5.08513 4.36305 +2.53611 0 5.10563 5.52532 +7.55026 0 6.53999 7.16178 +0 5.41201 1.25525 3.18292 +4.97626 0 3.07083 3.85316 +0 -0.153155 0.381833 1.16981 +2.39979 0 0.952596 1.31798 +>MA1628.1 ZIC1::ZIC2 lnR0: 0.764 +1.60627 0 1.05568 2.65485 +0 -0.223815 -0.321861 1.04254 +8.70082 0 6.4231 6.27415 +0 4.07882 4.60167 10.7454 +7.01436 5.54839 0 7.38182 +7.32738 0 6.51773 4.85492 +0 4.33392 3.33458 10.7001 +9.96212 4.1362 0 7.0679 +8.06496 6.64437 0 6.66758 +0.651276 0.139919 0 0.810965 +0.930419 0.695672 0 1.48804 +>MA1629.1 ZIC2 lnR0: 2.516 +0.616697 0 0.341559 0.941047 +0.661344 0.676607 -0.434443 0 +3.52656 0 4.04343 5.77385 +0 1.48348 2.56212 1.48393 +6.79746 0 5.86622 6.9644 +0 4.31201 5.36938 5.31105 +6.74687 5.59296 0 7.78866 +7.51213 0 5.33106 5.64642 +0 5.95595 3.35294 4.5425 +6.26059 6.3207 0 5.18073 +7.27886 5.74876 0 6.60927 +1.13673 1.71667 0 1.44146 +0.909278 1.56773 0 2.04613 +1.63675 1.28038 0 1.78427 +>MA1630.1 ZNF281 lnR0: 0.764 +2.00892 1.99014 0 2.33278 +2.35438 1.78301 0 2.7687 +9.35846 4.24293 7.17739 0 +8.71268 6.11886 0 9.32808 +8.31713 5.22492 0 8.37316 +7.81803 5.53995 0 8.43641 +8.50257 5.7299 0 8.123 +8.78773 7.19344 0 7.32222 +0 6.61273 8.94333 8.99346 +2.98705 3.33074 0 2.40781 +4.30386 3.91303 0 4.54841 +>MA0122.3 NKX3-2 lnR0: 1.932 +0 0.923519 0.689946 0.312544 +0.0153634 0.626959 0.530345 0 +0 2.0978 1.48157 1.43773 +0 1.85065 1.79388 1.23418 +1.41522 0 1.73788 2.73521 +7.34448 0 8.60334 5.90585 +0 6.37069 8.4037 5.48544 +6.4369 0 9.7272 7.10833 +7.55636 7.71714 7.8533 0 +6.62566 5.6358 6.63633 0 +0 5.51134 6.60149 4.84432 +0 2.01681 1.55665 1.31306 +0 0.237321 0.406697 0.230835 +>MA1724.1 RFX6 lnR0: 1.932 +0.67956 0.19875 0.901272 0 +0.350333 -0.188739 -0.150287 0 +5.7941 0 5.02643 5.2612 +2.98595 0 4.67418 3.41357 +4.29915 2.2251 5.05678 0 +0 6.26699 2.0946 6.6848 +5.91951 6.25587 0 7.61326 +4.7208 0 4.33316 4.87592 +0 5.57776 5.40681 5.16856 +0 4.39241 4.00367 5.12616 +4.04837 0 3.58726 3.84859 +0.540533 0 1.04386 1.39771 +0.834118 0.622059 0 1.49065 +>MA1684.1 FOXN1 lnR0: -2.156 +1.25791 11.2105 0 1.52638 +12.6944 12.2333 0 12.6944 +0 11.7722 11.7722 12.2333 +0.823659 0 11.4132 11.8743 +12.6944 12.2333 0 12.6944 +12.6944 0 12.2333 12.6944 +>MA1988.1 ATF3(MA1988.1) lnR0: 0.764 +0.614803 0.738593 0 0.499937 +0 0.549598 -0.013162 1.98437 +6.44743 5.78517 6.68052 0 +5.37718 6.71307 0 4.06454 +0 6.69077 6.29185 6.53968 +4.75364 0 3.31087 4.75364 +4.38853 6.11731 4.69577 0 +3.53449 0 6.27889 4.89772 +0 5.74843 5.06565 5.81562 +1.29431 0.173773 0.168088 0 +0 -0.302549 0.16322 0.157453 +>MA1989.1 BCL11B lnR0: 2.516 +0 0.0473678 -0.0237407 0.404918 +0 -0.0200908 -0.123759 0.565529 +0 1.79931 2.24853 1.96503 +0 3.24881 2.8726 3.3545 +0 4.18476 3.93679 5.84713 +5.13929 0 5.5371 5.85915 +5.55597 0 6.42628 5.88354 +0 4.77396 5.01122 4.74941 +4.80594 0 4.83703 5.77553 +0 4.18172 4.34501 4.9905 +0 2.25168 1.25604 2.10261 +1.10038 1.10949 0 1.99541 +0 -0.168387 -0.0866388 0.545569 +0 -0.197714 0.0911689 0.357891 +>MA1990.1 GLI1 lnR0: 2.516 +0.655529 0 0.307839 0.885562 +0.537348 0.0284431 0 1.04997 +0 2.33567 0.473076 2.1343 +5.36761 4.14699 0 4.85682 +0 2.74 2.1579 5.76939 +5.62261 0 5.3422 6.10612 +6.1307 0 5.61128 6.65162 +0 5.10963 4.8621 4.21615 +7.0133 0 5.59909 6.3057 +2.96528 0 4.42464 5.95646 +4.95043 0 4.95707 4.76781 +0 3.63013 3.21915 3.6746 +1.82948 0.0922599 0 2.23319 +0.818089 0.637999 0 1.63597 +>MA1991.1 HNF1A(MA1991.1) lnR0: 2.516 +0.680485 -0.202148 -0.215604 0 +1.57059 0.147647 0 0.650283 +3.27395 0 1.84339 2.34693 +6.29885 0 4.77425 4.58642 +5.8419 4.75472 6.68978 0 +5.98649 3.9282 3.70016 0 +6.09427 6.13075 6.0164 0 +5.47139 3.08867 0 4.32837 +0 4.45733 5.5292 3.88909 +3.3332 5.11838 4.5831 0 +3.43588 0 0.859711 3.23478 +2.2992 1.41579 2.48249 0 +1.002 -0.429445 -0.401156 0 +0.938536 0.200066 0 0.498106 +>MA1992.1 IKZF3 lnR0: 3.1 +0 0.0786808 -0.354357 0.848867 +0.819566 0.0805042 0 1.3714 +0 1.23218 0.367027 2.09057 +4.68326 0 3.23195 5.37685 +0 3.56484 3.92386 5.66509 +8.25075 7.11821 0 7.77008 +6.31267 6.01046 0 7.38012 +0 4.92855 5.1037 7.26421 +0 5.8248 5.13969 3.45969 +3.72533 4.41577 0 5.69194 +2.77811 1.96897 2.36714 0 +3.11756 2.48567 0 3.31156 +1.56983 1.04391 0 1.90833 +1.24908 0.546693 0 1.51871 +0.950855 0.560513 0 0.878375 +>MA1993.1 NEUROD2(MA1993.1) lnR0: 0.18 +0.530497 0.48051 0 1.64011 +0.55623 0 0.121541 2.67409 +12.157 0 9.73944 10.7558 +0 6.88681 6.40745 15.5476 +12.8886 11.6055 0 11.8984 +11.8984 0 11.6055 12.8886 +15.5476 6.40745 6.88681 0 +10.7558 9.73944 0 12.157 +2.67409 0.121541 0 0.55623 +1.64011 0 0.48051 0.530497 +>MA1994.1 NKX2-1 lnR0: 1.932 +0 0.285897 -0.141028 0.470097 +0.74763 0 0.293347 1.83159 +6.08734 0 6.29177 4.49025 +0 5.29152 6.19148 5.438 +6.92932 0 6.96932 6.03075 +5.29916 6.00913 4.13323 0 +5.84699 4.35944 5.06824 0 +4.40561 4.38556 0 5.18566 +0 5.4459 5.63332 4.76687 +0 1.19516 0.522217 2.7397 +0.557945 0 1.19478 1.31653 +0.243292 0.0912452 0.280852 0 +0.207592 -0.293108 0.0910674 0 +>MA1995.1 NPAS4 lnR0: 0.764 +0 -0.298018 -0.277135 0.419782 +0 -0.359514 -0.460499 0.203266 +3.70309 3.37471 2.86778 0 +4.94205 0 3.69434 4.94632 +4.37158 4.46093 0 6.37432 +6.0245 5.78552 4.5618 0 +7.62798 5.48501 0 6.57645 +0 3.08589 3.83798 3.82731 +4.5908 0 3.45826 3.98708 +0.420594 0.485331 0.605183 0 +0.816967 0 0.0200043 0.787422 +>MA1996.1 NR1H2 lnR0: 0.764 +0.990787 0 0.435924 0.684022 +0 -0.149448 0.0192404 0.10241 +0 1.11047 0.060282 2.2953 +0 4.96203 5.48652 6.35502 +6.97792 5.57559 0 5.87955 +6.96681 7.80695 0 6.77799 +7.08477 7.40026 7.18005 0 +6.245 0 6.79354 5.38613 +0 6.84355 4.64685 7.75274 +1.19587 0 0.306784 0.694067 +0 -0.202372 -0.325293 0.192652 +>MA1997.1 OLIG2(MA1997.1) lnR0: 0.18 +0 -0.126277 -0.268458 0.814664 +0.670443 0.10006 0 2.13779 +12.7757 0 8.9617 10.5844 +0 5.95586 5.80791 15.7109 +12.335 11.5362 0 10.8641 +10.8641 0 11.5362 12.335 +15.7109 5.80791 5.95586 0 +10.5844 8.9617 0 12.7757 +2.13779 0 0.10006 0.670443 +0.814664 -0.268458 -0.126277 0 +>MA1998.1 PRDM14 lnR0: 1.348 +0 -0.44803 -0.0714074 0.0617984 +0.479473 1.72872 0 1.27045 +4.3503 3.33872 0 4.18377 +5.81216 4.40025 0 4.96761 +4.37872 4.42528 2.74899 0 +5.95153 0 4.43001 5.04926 +4.79901 2.73564 5.50326 0 +6.89667 0 3.71682 4.35321 +5.9605 5.05212 6.15412 0 +0 4.12709 4.4845 4.97861 +0 1.04696 1.21851 0.971142 +1.90258 0 0.817579 1.48768 +>MA1999.1 PRDM5 lnR0: 3.1 +1.89547 0 1.90008 1.70471 +1.47185 0.396012 0.27025 0 +4.39515 3.21982 0 3.5902 +3.15468 2.16277 2.92574 0 +5.03101 3.37026 3.57969 0 +5.42485 0 5.54299 4.86848 +3.98519 3.84286 4.44459 0 +5.72672 0 4.40737 5.64507 +5.31165 0 5.12348 5.83009 +0 2.32374 3.31395 3.64206 +4.77099 2.66717 1.57364 0 +3.98641 0 2.55142 2.90197 +2.2863 1.11809 2.20966 0 +0.860732 0 0.0206544 0.747777 +1.12637 0 0.122616 1.02191 +>MA2001.1 SIX4 lnR0: 0.764 +2.3016 2.40757 0 2.58669 +0 0.774367 0.469261 0.106015 +0 4.8314 5.60958 5.74209 +0 4.62373 5.45838 4.69937 +4.48312 0 4.86989 3.35675 +3.23502 0 4.81811 3.70564 +4.11259 3.24933 3.59626 0 +5.37855 4.68585 0 5.4853 +0 5.51273 5.75965 6.19405 +1.0243 0.15436 0 0.624478 +0.521417 0 1.02005 1.1603 +>MA2002.1 ZFP335 lnR0: 0.764 +0.665535 0.579236 0 1.77009 +0 -0.0862988 -0.285959 0.448082 +2.00763 2.65108 1.2499 0 +5.20429 0 6.31263 6.77373 +0 3.80054 5.78096 4.26165 +6.75642 4.72587 0 5.76621 +6.77373 6.31263 0 5.20429 +5.18697 0 5.3051 6.75642 +0 4.67791 2.24256 5.13902 +1.31069 0 0.0501305 1.40288 +0.903604 -0.108448 0.719865 0 +>MA0037.4 GATA3 lnR0: 1.348 +0.251704 0.206039 -0.219342 0 +0.195062 0.114632 0.729859 0 +2.99756 1.60923 2.20036 0 +4.79714 0 3.15413 3.68969 +4.79873 4.1151 5.82332 0 +4.44817 4.35941 4.0223 0 +0 4.82718 4.92629 4.79472 +5.74459 5.87445 5.82973 0 +6.7356 0 6.47706 6.03718 +2.68118 3.981 4.5453 0 +0.825395 0.0368615 0 0.525972 +0.405639 -0.0914279 0.595636 0 +>MA0050.3 IRF1 lnR0: 3.1 +0 1.45109 1.39277 1.28419 +0 -0.264544 -0.231094 0.421567 +1.19362 2.24409 1.59548 0 +3.36431 4.27097 0 4.68148 +0 4.73721 3.25035 4.7834 +0 5.34572 5.31787 5.4114 +0 5.86969 5.42877 5.36912 +2.7783 0 1.55138 4.54061 +2.69438 3.2485 4.99522 0 +4.20713 5.42177 0 5.96693 +0 5.04853 3.68609 5.01402 +0 4.83521 4.34191 5.2526 +0 4.76241 4.03735 4.78643 +1.62262 0.245962 0 2.07997 +0.767446 0.105965 1.18335 0 +>MA0078.2 SOX17 lnR0: 2.516 +0 -0.0884698 -0.431979 0.24112 +0 -0.419343 -0.307431 0.568166 +0 2.54141 1.57072 2.26444 +1.73534 2.87714 0 2.14334 +0 2.47918 1.99374 3.22981 +0 6.03768 5.64975 5.95425 +5.77769 0 4.47281 5.70599 +0 5.87621 6.28381 6.37843 +0 4.97453 4.85299 6.59549 +3.41129 5.77771 5.33121 0 +3.38265 5.2926 0 4.85721 +3.33868 3.14904 0 3.8259 +0 -0.335533 -0.179551 0.731303 +0 -0.381525 -0.178962 0.162426 +>MA0080.6 SPI1 lnR0: 4.268 +0 0.948689 0.118269 1.00273 +0 0.858084 -0.426734 1.20447 +0 2.78374 1.06828 2.85812 +0 3.338 2.46443 3.6159 +0 4.61581 2.50417 2.83614 +3.64083 2.68609 0 4.61215 +0 4.60418 2.72986 4.85003 +5.02275 7.42111 0 6.75609 +6.04878 6.8612 0 7.12234 +0 6.01523 6.05756 6.56645 +0 6.17079 5.25315 5.056 +3.97516 3.62092 0 6.41973 +2.20125 3.91183 3.45184 0 +3.49482 3.74162 0 4.27729 +1.76225 2.29376 0 2.61611 +0 0.701022 0.0306337 0.926034 +0 0.658748 0.0455393 0.599874 +>MA0087.2 SOX5 lnR0: 1.932 +1.0698 0.961349 0 1.60507 +0 0.758166 0.158375 1.73771 +1.26056 0.564732 0 1.89175 +0 3.88821 2.5232 4.34932 +0 6.41344 5.42323 5.88434 +7.31223 0 5.28168 5.74279 +0 4.82058 4.82058 6.85113 +0 3.75771 4.01817 5.78826 +3.9986 4.33695 5.32716 0 +2.71889 6.6071 0 5.08779 +3.13511 2.57544 0 3.93456 +1.28693 0.146649 0 1.05787 +0 -0.343622 0.0271084 0.436259 +>MA0095.3 YY1 lnR0: 1.348 +0 0.2657 0.169125 0.187471 +0 -0.316012 0.108286 0.296267 +3.83412 0 3.13708 3.7048 +0 4.97063 6.64062 6.03663 +0 4.26795 4.39908 5.38323 +0 3.10398 1.35024 4.42874 +0 5.27826 5.3448 6.68625 +5.85976 6.89544 5.35984 0 +6.6328 7.91386 0 7.26909 +5.0474 5.29651 0 5.49397 +1.51642 0 2.14148 2.21952 +0.954358 0.90612 0 0.632356 +>MA0136.3 ELF5 lnR0: 1.348 +0 1.56665 0.363164 1.21661 +1.15853 0.672009 0 1.71935 +0 1.79496 2.01365 4.29956 +0 4.79476 3.73895 6.75832 +6.72066 7.73211 0 6.97944 +6.51176 6.25117 0 6.9789 +0 5.61613 6.1819 7.11494 +0 6.17349 5.87093 5.74885 +4.27977 4.88763 0 6.63762 +2.44378 2.60303 2.04812 0 +0.539291 0.776097 0 1.24574 +0 0.183873 -0.405589 0.695462 +>MA0152.2 NFATC2 lnR0: 3.684 +0 0.0272171 -0.068589 0.216553 +0 -0.0366456 -0.45788 0.126207 +1.42461 1.35309 0 1.88544 +0.757302 0 0.615404 0.937025 +0 1.7499 2.39736 2.72364 +0 3.14515 2.4789 4.36153 +4.01665 4.00319 4.29367 0 +5.71228 7.36414 0 7.24601 +6.92354 6.7398 0 6.46099 +0 5.7879 5.03634 6.14314 +0 6.76256 5.57269 6.38397 +0 4.30161 4.69009 4.65782 +0.66335 0 0.954494 1.31117 +0.576802 1.36958 1.42687 0 +0 0.123471 -0.145371 0.0122362 +0.505547 0.0644987 0.554754 0 +>MA0157.3 FOXO3 lnR0: 1.348 +0 -0.112446 -0.231832 0.138784 +0.102603 1.23907 0.13744 0 +2.90485 4.97287 0 5.29584 +3.70773 5.05581 3.60947 0 +0 4.01522 5.55837 5.82493 +0 4.28497 5.53991 5.45641 +0 5.02674 5.08395 5.70757 +6.12129 0 5.817 3.90059 +0 4.72247 5.41545 4.70152 +0 0.68586 0.528137 1.42833 +0 -0.155941 -0.357977 0.605927 +0 -0.311873 -0.260125 0.18253 +>MA0467.2 CRX lnR0: 0.18 +0.830979 0.551132 0 0.892193 +0 0.686205 -0.36445 0.954423 +8.07582 4.68025 0 7.44974 +7.67145 6.76023 0 6.27026 +0 7.33763 6.09359 6.39755 +8.3961 6.48985 8.19545 0 +6.31465 6.81602 7.12112 0 +0 6.81703 6.93138 6.49447 +0.465331 0.863098 0 1.05572 +0 -0.395663 -0.365586 0.498075 +>MA0474.3 ERG lnR0: 2.516 +0 0.182282 -0.256451 0.830237 +0 -0.0884106 -0.351981 0.917072 +0 2.35462 1.51504 2.84042 +4.17618 0 3.14833 5.4875 +0 2.89236 5.33218 6.58277 +7.82198 7.7092 0 7.61978 +7.01194 6.71312 0 7.10606 +0 5.837 6.20579 7.23321 +0 5.70966 6.12192 4.143 +2.70835 4.28696 0 6.30419 +3.18556 2.21572 2.41942 0 +2.33691 2.17214 0 2.90353 +0.728709 0.578313 0 1.47609 +0.753336 0.173577 0 0.926219 +>MA0480.2 FOXO1 lnR0: 0.764 +0 -0.0336613 -0.193992 0.489665 +0.170345 1.04153 0.0436808 0 +3.47839 4.55274 0 4.81238 +3.57975 3.8779 3.00268 0 +0 3.23265 4.18815 5.33206 +0 3.39787 4.52929 5.78337 +0 4.55264 4.16486 5.64166 +5.84202 0 5.10355 4.48902 +0 5.068 5.91182 5.17983 +0.621368 0.136792 0 1.00758 +0 -0.218678 -0.24633 0.370066 +>MA0489.2 JUN(MA0489.2) lnR0: 1.348 +0.0963485 0.159883 -0.43517 0 +0 -0.037528 -0.328993 1.73513 +6.23135 6.46613 6.46215 0 +6.91729 5.86179 0 5.43236 +0 5.38167 5.18209 5.70175 +4.62288 0 2.22742 4.50743 +4.82858 6.07106 5.93928 0 +4.99485 0 6.10513 6.90432 +0 5.09744 5.76201 5.71882 +3.5909 1.58837 1.75341 0 +0.600574 0 0.196908 0.520477 +0.0470165 -0.436847 -0.257638 0 +>MA0505.2 NR5A2 lnR0: 1.932 +0.656435 0 0.21715 1.11207 +2.36834 2.27012 2.70278 0 +4.16424 4.91567 0 6.2145 +0 3.56687 1.0854 2.83486 +6.90552 0 7.82256 7.36373 +7.02724 0 7.40298 6.83173 +6.25641 4.87529 5.81501 0 +6.72872 5.92654 6.16941 0 +6.80903 5.00827 0 6.8865 +0 4.83778 2.96111 4.50513 +0 0.146392 0.898212 2.38201 +1.90258 0 1.78966 1.66134 +1.49265 0.854001 1.30777 0 +>MA0506.2 NRF1 lnR0: 3.1 +1.61697 0.523424 0 1.62349 +1.22801 0 0.720336 0.810632 +2.91923 0 1.10294 3.42877 +3.60488 1.85838 2.93043 0 +5.14552 5.07209 0 7.21174 +5.26222 0 5.04837 6.31308 +5.79743 5.89579 0 6.14512 +6.72102 0 4.48969 6.06049 +0.795555 0 1.11157 4.16741 +6.42448 3.82086 4.18802 0 +7.86865 5.55708 0 7.5375 +6.9208 0 5.85189 5.98014 +5.75284 4.23306 0 4.39584 +4.72761 0 3.03804 2.02331 +0.663541 0.92807 0 2.34442 +>MA0514.2 SOX3 lnR0: 0.764 +0 0.558387 -0.355471 0.354886 +0 0.0925337 0.00622958 0.9131 +0 7.25652 6.72293 6.96117 +6.60362 0 5.89951 4.82073 +0 4.66036 6.3788 5.2305 +0 5.81177 5.81177 7.30333 +4.23821 5.68474 6.20377 0 +3.06908 6.1667 0 6.14409 +2.56303 2.25335 0 3.40826 +0 -0.446093 -0.223361 0.63119 +0 -0.204608 -0.21594 0.338442 +>MA0521.2 TCF12(MA0521.2) lnR0: 1.348 +0.673622 0.128448 0 0.641784 +0 -0.452734 -0.444384 0.682143 +0 0.890721 0.590467 2.00938 +8.01206 0 7.41409 7.43542 +0 6.08419 6.30731 7.64792 +6.78009 5.21325 0 5.88516 +5.88516 0 5.21325 6.78009 +7.64794 6.30733 6.08614 0 +7.43793 7.42109 0 7.98506 +2.00921 0.590048 0.890452 0 +0.683682 -0.444037 -0.452526 0 +0.642184 0 0.128061 0.673622 +>MA0606.2 NFAT5 lnR0: 1.348 +0 0.232478 0.382993 0.729751 +0.612954 0 0.820616 1.28172 +0 3.45949 2.05831 4.27962 +3.04316 4.27581 4.41196 0 +4.98837 8.29735 0 5.20858 +4.68065 5.1281 0 5.75747 +0 4.68009 3.85814 5.72043 +0 6.86309 4.42773 5.025 +0 5.5456 4.7059 4.88034 +0 4.62249 3.48177 4.35385 +0.837911 1.28893 0.847882 0 +0.473367 0.446095 -0.193301 0 +>MA0611.2 DUX lnR0: 3.684 +1.29026 0 0.347727 0.751866 +1.19636 4.24947 2.45693 0 +5.02154 7.34031 0 6.65231 +0 7.70702 8.21655 7.90766 +7.22273 7.5424 5.14291 0 +8.20937 3.1755 6.40788 0 +1.61725 0 0.152067 0.475133 +0 6.4906 5.41014 7.76677 +0 6.50961 8.42923 7.48915 +8.17187 8.2203 9.01976 0 +6.95104 0 8.425 5.02941 +0 5.33078 6.32099 3.54112 +1.14044 0 0.930605 1.69116 +0.461661 0.676511 1.10484 0 +0.25767 -0.0192949 -0.0793017 0 +0 0.0559299 0.342841 0.0736698 +>MA0624.2 NFATC1 lnR0: 1.348 +0.776061 0 0.0145691 0.97041 +0 0.331404 0.50328 1.0335 +0 1.0094 0.706051 1.7839 +5.42995 4.15522 5.92621 0 +7.16373 8.68305 0 8.78513 +6.9842 8.39441 0 7.15246 +0 7.08023 7.22564 6.72227 +0 8.22218 6.99725 7.18354 +0 5.73047 6.54835 5.51785 +0 1.12614 1.06082 2.31918 +0.185353 1.15699 1.12654 0 +0 0.328239 0.075013 0.276349 +>MA0633.2 TWIST2 lnR0: 0.18 +0.567483 0 0.123403 0.973777 +0.659894 0.11763 0 1.98175 +11.942 0 9.1464 10.0301 +0 6.61235 6.51655 15.4255 +12.6166 11.3974 0 11.4902 +11.4902 0 11.3974 12.6166 +15.4256 6.51664 6.62488 0 +10.0301 9.1464 0 11.942 +1.98175 0 0.11763 0.659894 +0.95767 0.116757 0 0.560838 +>MA0650.3 HOXA13 lnR0: 1.348 +0 0.284332 0.0635629 0.314563 +0.54335 0.122309 0 0.575582 +3.55689 0 2.71028 3.68633 +3.89551 0 7.4247 3.40255 +0 2.64914 6.05513 3.25629 +0 5.46128 4.02468 4.01093 +7.22501 5.53816 5.63876 0 +0 5.73919 4.76292 4.20435 +0 6.52987 6.87439 6.24096 +0 5.23512 6.29689 6.0011 +0 0.772012 0.997857 1.05645 +0 -0.145518 0.32745 0.143978 +>MA0659.3 MAFG lnR0: 3.1 +0.671316 0.470399 0 0.932807 +0.715192 1.2587 1.36326 0 +4.17704 2.68139 0 4.43602 +0.684534 0 3.24702 4.03537 +4.91946 3.79276 5.13913 0 +5.88289 5.4884 0 5.03484 +0 4.94945 3.42592 5.54151 +4.59563 0 2.08008 4.74006 +4.48935 5.07087 5.52167 0 +5.152 0 5.3139 5.90104 +0 6.21797 4.39584 4.77452 +6.49677 6.32989 0 4.81218 +5.54167 0 4.32237 5.30069 +0 2.19811 1.88214 1.88584 +0.819712 0.606006 0 0.9567 +>MA0668.2 NEUROD2(MA0668.2) lnR0: 3.1 +0.679447 0.48733 0 1.20081 +0.824839 0.885242 0 0.94136 +1.46746 1.38555 0 1.53524 +0 1.0522 -0.0256717 2.05234 +0 1.32911 1.34295 5.30427 +7.62256 0 6.96324 7.94134 +0 7.40396 6.72713 7.80156 +7.11313 5.78254 0 4.66175 +0 3.0205 4.86134 6.7777 +5.32678 5.31705 6.11521 0 +7.86975 7.65018 0 6.55443 +5.96457 3.8799 0 3.68597 +1.31236 -0.160742 0.625812 0 +0.637136 0 0.0923624 0.898014 +0 -0.419979 -0.398877 0.218985 +>MA0680.2 PAX7 lnR0: 3.1 +0 0.632367 0.224373 0.440333 +0.388952 0.607698 0.773953 0 +1.42552 2.36078 2.52065 0 +0 4.97565 4.90113 5.14993 +0 5.33445 5.24225 5.196 +5.41425 4.63208 5.02187 0 +5.16756 0 4.47373 2.43045 +0 3.85597 2.77185 5.64864 +0 5.64061 4.63731 5.36253 +5.12979 5.99021 5.79242 0 +5.04155 3.8838 5.21953 0 +0 3.86835 3.81328 2.36803 +0.194964 1.10235 0.878584 0 +0.434124 0.111499 0.491337 0 +0.242361 0.304 0.617663 0 +>MA0693.3 VDR lnR0: 0.764 +0.746747 0 0.393436 0.615762 +0.0586692 0.200745 0.216913 0 +2.43792 2.41441 0 3.98573 +0 5.28262 4.47151 5.41128 +5.88967 5.85021 0 5.4312 +5.12925 5.56926 4.00623 0 +4.35829 5.24569 5.43396 0 +4.8446 0 6.34181 4.48766 +0 5.25957 4.94166 5.54048 +0.371573 0.029043 -0.146763 0 +0 0.0914741 -0.154611 0.0540573 +>MA0697.2 ZIC3 lnR0: 1.932 +1.74104 0 1.33431 2.80095 +0 -0.0841094 0.0499462 0.691124 +6.57772 0 5.70667 6.62388 +0 4.2699 4.46793 5.27389 +6.6294 5.16311 0 6.94067 +6.49682 0 4.95394 5.34867 +0 4.82253 3.20211 4.69522 +6.35039 5.54606 0 5.06627 +6.52927 4.62451 0 5.92024 +0 1.20492 0.721903 2.00291 +1.88136 1.85363 0 2.54259 +1.16087 0.544032 0 1.34828 +1.42058 0 0.374999 1.034 +>MA0734.3 GLI2 lnR0: 1.932 +0.590306 0.016029 0 1.24224 +0 1.06664 -0.361397 1.85078 +5.61639 4.49266 0 5.12571 +0 2.58355 2.02112 7.66197 +6.14488 0 6.36157 7.45387 +8.47928 0 7.38699 8.64754 +0 5.23938 4.23185 3.80069 +8.32121 0 7.4853 7.2613 +3.20677 0 6.60977 7.55155 +5.66328 0 4.82737 5.46362 +0 4.10503 2.94288 4.16349 +2.22745 0.140867 0 2.62578 +0.763617 0.70453 0 2.17123 +>MA0768.2 LEF1 lnR0: 2.516 +0.190759 -0.0148553 0.0459442 0 +0.635878 0.261007 0.121966 0 +1.04173 0.194073 -0.215361 0 +3.84211 0 2.5651 3.54669 +5.60663 0 5.43809 4.84548 +6.25591 5.1794 5.59038 0 +5.55536 3.84359 4.10405 0 +5.70549 5.24439 5.48989 0 +4.0029 3.5037 0 4.50694 +0 4.57945 4.73545 4.51145 +2.70963 4.40267 3.56845 0 +2.20812 0.583882 0 1.80769 +1.05266 0.692284 1.33147 0 +0.792992 -0.320625 -0.138006 0 +>MA0869.2 SOX11 lnR0: 1.348 +0.544767 0.31831 0 1.17184 +0 1.61289 -0.0455488 1.04761 +3.42185 3.3647 0 4.72382 +0 2.87286 2.1202 4.8097 +0 6.08292 5.02368 6.84174 +6.70197 0 4.19642 6.30896 +0 5.9976 7.11092 7.0511 +0 4.67858 4.76754 7.23805 +0 6.69341 4.796 3.73525 +4.64563 5.9339 0 6.84158 +0.737253 0.754272 0 2.83364 +0 -0.125394 -0.0343181 1.45445 +>MA0885.2 DLX2 lnR0: 1.348 +0 -0.0685691 0.142815 0.370164 +0 1.69128 0.190102 0.161286 +4.37899 3.84195 0 4.55614 +4.81371 0 5.19726 3.17669 +0 4.91083 6.67475 5.61689 +0 5.17827 5.41787 5.55772 +5.46036 6.75298 6.32656 0 +6.5481 3.94954 5.5417 0 +0 7.69232 5.39313 4.15428 +2.92979 3.25365 0 3.29056 +0.508751 0 0.502667 0.751054 +0 0.110313 -0.00640609 0.201009 +>MA0909.3 HOXD13 lnR0: 0.18 +0 -0.0568901 -0.194616 0.282253 +0.831181 0 0.0506755 1.13238 +8.80951 0 7.31679 6.96105 +0 9.35276 4.76392 6.78492 +0 8.17848 8.3987 7.50397 +12.4214 10.3909 9.97991 0 +0 9.65706 8.98563 8.8675 +0 6.75201 10.3791 8.44883 +0 2.09788 2.98077 2.63599 +0 0.691326 0.688745 0.933693 +>MA1110.2 NR1H4 lnR0: 0.18 +0.521167 0 0.0262549 0.757994 +1.01413 0.465471 0 1.82226 +0 5.25684 5.99797 9.07705 +8.72151 4.86295 0 7.54054 +7.58054 9.77129 0 7.6259 +11.0997 11.6288 11.6288 0 +5.14471 0 8.54357 4.77125 +0 6.72524 4.75677 12.0452 +1.15431 0.0770722 0 0.860125 +0.537541 -0.0877913 -0.223361 0 +>MA1467.2 ATOH1(MA1467.2) lnR0: 0.764 +0.527472 1.06967 0 1.74496 +0 -0.217878 -0.221755 2.24737 +6.63643 0 6.56218 6.32812 +0 6.4097 5.82214 8.06738 +7.2262 5.41873 0 3.68713 +0 6.97102 6.26612 7.71743 +7.38241 4.71463 7.15775 0 +6.61279 6.95623 0 7.08434 +4.18811 2.835 0 3.13993 +1.45535 0 1.00977 0.846413 +0 -0.331011 -0.260962 0.393963 +>MA1472.2 BHLHA15(MA1472.2) lnR0: 1.348 +0.724463 0.183216 0 0.852455 +0 -0.358976 -0.0747261 1.3363 +0 1.71884 1.9109 4.7058 +6.69424 0 5.84617 8.12753 +0 6.8416 6.52282 5.72584 +7.90617 5.92664 0 5.60447 +5.60447 0 5.92664 7.90617 +5.72584 6.52282 6.8416 0 +8.12753 5.84617 0 6.69424 +4.7058 1.9109 1.71884 0 +1.3367 -0.0737965 -0.358574 0 +0.852455 0 0.18373 0.723919 +>MA1476.2 DLX5 lnR0: 1.348 +0 -0.163218 0.0914929 0.23451 +0 1.7979 0.283256 0.137201 +4.42974 4.2043 0 4.6271 +4.97259 0 5.3592 3.19872 +0 4.94159 7.07431 5.85163 +0 5.43224 5.50194 5.98705 +5.78592 6.6652 6.83346 0 +6.75638 4.2332 5.66109 0 +0 8.54823 6.13155 4.22734 +2.6993 3.09342 0 2.6814 +0.54786 0 0.563906 0.831177 +0 0.21812 0.0626138 0.221696 +>MA1518.2 LHX1 lnR0: 4.852 +0 0.0917241 -0.439622 0.403885 +0.78228 0.584038 0 1.16551 +0.988558 0.527453 0 0.988558 +1.33362 1.71532 1.05443 0 +2.9952 2.20926 0 2.32758 +3.17676 0 1.96409 1.95072 +4.83138 3.54196 5.36049 0 +0 3.2137 4.07195 6.60008 +0 6.65833 5.66812 5.26332 +5.26658 5.67138 7.24083 0 +6.6071 4.07897 3.316 0 +0 5.58416 3.54543 4.83484 +1.90488 1.9859 0 3.25197 +2.32758 0 2.18525 3.02593 +0 1.07217 1.66037 1.34923 +1.0692 0 0.482581 0.998114 +1.18456 0 0.632241 0.801328 +0.375873 -0.450404 0.139614 0 +>MA1524.2 MSGN1 lnR0: 3.684 +0.50068 0.906822 0 1.50703 +1.10399 1.21699 0 1.63274 +0 2.3268 0 1.25204 +1.1982 3.84683 0 6.42452 +0 1.02081 2.46319 5.86485 +9.44906 0 7.41851 8.45885 +0 6.54113 8.52155 7.41321 +0 5.162 2.62905 4.28272 +0 6.22235 8.52155 7.99244 +4.71667 5.68203 6.48148 0 +8.43753 7.39719 0 6.28885 +6.81613 5.77579 0 5.24668 +3.02594 0.691727 2.14449 0 +1.42384 0.845254 0 1.22123 +0.479902 0.371076 0 0.761328 +0.827847 0 0.332318 0.663463 +>MA1567.2 TBX6 lnR0: 1.348 +0.745873 0.762975 0 1.2706 +0 2.45786 0.49642 1.71012 +3.8865 5.42667 0 4.94415 +6.85418 4.66763 0 7.3795 +5.7838 4.79531 5.37765 0 +8.2596 6.22905 0 6.92232 +3.46466 4.61583 3.07356 0 +5.89193 3.3748 0 4.58917 +0 5.25329 4.25879 6.54209 +0 3.5001 2.64185 4.35585 +0.487075 0.721818 0 1.24554 +0.210716 0.117634 -0.196961 0 +>MA1573.2 THAP11 lnR0: 2.516 +0 3.41727 4.30161 5.24339 +5.25975 0 4.94162 5.32945 +6.60477 3.43349 5.92345 0 +0 4.61342 5.31696 6.42376 +7.39258 0 5.94126 6.55288 +0 4.9309 3.84213 5.87268 +0 2.65051 2.37493 1.50221 +1.59602 -0.414262 -0.0783769 0 +4.94162 4.33754 4.40724 0 +7.11415 0 7.64325 5.19453 +6.55956 0 6.67769 7.1388 +6.36391 0 5.76664 5.3737 +0 4.29919 1.20776 4.32846 +2.92899 2.587 0 2.54687 +>MA1647.2 PRDM4 lnR0: 4.268 +1.06565 1.50312 0 1.62031 +0 0.562201 -0.374953 0.765329 +1.43833 0.65974 0 1.26219 +2.19905 0 3.24417 2.84106 +5.42653 0 6.13444 5.30573 +5.59896 4.24852 5.78354 0 +1.84778 3.78042 1.37965 0 +5.61332 7.75871 0 7.73914 +0 5.95 6.64358 7.10469 +0 6.16999 4.83526 7.75746 +0 6.84173 6.3322 7.52305 +6.47905 0 6.9265 7.10094 +1.10652 -0.30273 3.10651 0 +2.50684 1.93332 0 3.09867 +1.74422 -0.292843 1.7677 0 +2.38073 0 2.48341 0.773818 +0 0.379293 -0.126445 0.815334 +>MA1540.2 NR5A1 lnR0: 4.268 +0 0.0944079 -0.199305 0.641326 +0.245434 -0.0889556 -0.290714 0 +0.986679 1.39588 0 1.66471 +0 2.39496 1.7334 2.00883 +2.43648 2.31495 0 2.65837 +2.88775 1.44785 1.48265 0 +4.53266 2.2781 4.36614 0 +6.28947 0 4.46185 5.56757 +0 3.96135 4.57789 5.47282 +0 5.12454 4.24526 5.2248 +5.79042 6.5353 0 6.10254 +6.06296 6.2995 0 5.64389 +2.99514 1.23978 3.70354 0 +6.37586 0 5.18921 4.5274 +0 4.3483 4.25302 4.35716 +1.29919 0.47924 0 1.01237 +1.29011 0 0.831915 1.30031 +>M01001 AHR lnR0: -0.404 +0.897364 1.56945 0 0.967065 +2.98543 2.40998 0.954884 0 +1.54859 0.128674 1.15099 0 +5.60987 6.13898 0 5.2911 +6.63844 0 6.17733 6.0592 +5.63873 6.16784 0 6.62895 +7.16754 4.72602 5.71623 0 +7.666 7.20489 0 7.666 +1.08299 0 1.98042 1.67855 +>M01002 AIRE lnR0: 4.852 +0 0.0364761 1.02669 0.75804 +1.14073 0.67962 1.03864 0 +1.6359 1.1748 0.815778 0 +4.05011 5.15845 0 3.63914 +5.49876 5.03766 0 2.35987 +0.884342 2.62387 3.20311 0 +0.30187 1.58902 2.898 0 +0 0.719865 0.719865 0.0921979 +0.337698 1.76482 0.965365 0 +0 1.65547 1.1748 0.99021 +0.30187 2.31877 1.90779 0 +1.25067 1.2991 2.09855 0 +5.61956 4.16824 0 3.32036 +5.76621 5.3051 0 4.776 +0.916934 1.44604 0.319672 0 +2.49886 0.87928 0.87928 0 +0 2.75503 0.774606 0.2455 +0 0.118131 1.3688 0.839695 +>M01008 ARID5B lnR0: 1.932 +0.579236 0.99021 0 0 +1.67153 0.480675 0 1.26056 +3.13889 0.37859 0.697367 0 +3.13889 1.10834 0.118131 0 +0 1.56945 0 0.260459 +1.90625 2.43535 0 2.89646 +3.96084 3.49974 3.49974 0 +0 3.30898 1.73953 3.77008 +3.77008 1.73953 3.30898 0 +3.77008 2.31877 2.31877 0 +2.03055 0.839695 0 2.60979 +1.56945 1.68758 0.37859 0 +0.941779 1.21043 0 1.26056 +>M01010 ASCL1 lnR0: 2.516 +3.25197 0 1.76255 2.20498 +0.821949 0.800596 1.89412 0 +2.83296 0.89875 0 3.26479 +9.18224 0 8.72113 9.18224 +0 8.26003 8.26003 8.72113 +8.33743 0.336163 0 5.77778 +9.16943 0 8.70832 6.87023 +8.71794 8.25684 7.26663 0 +9.17905 7.72773 0 9.17905 +5.4283 0 3.19621 3.38438 +2.48294 0 7.63873 0.61162 +2.93309 0 0.122659 0.85411 +2.68075 0 1.83116 1.45762 +1.68544 0 1.4123 0.734915 +>M01013 ATF2 lnR0: 0.764 +1.00701 2.34911 0 2.2416 +0 0.868146 -0.320245 3.88891 +5.37314 4.67339 5.55773 0 +6.11487 5.82202 0 5.29292 +0 5.49601 5.30525 3.61768 +3.7663 0 0.536704 0.484849 +8.25442 4.36775 0 5.69476 +2.57814 2.89984 4.28821 0 +2.72047 0 4.31306 5.01966 +0 4.94163 3.23603 4.27637 +2.94245 0.500928 0.957257 0 +>M01015 ATF4 lnR0: 1.348 +0.683611 2.4666 0 1.80837 +1.3875 0.94033 0 1.40143 +0 0.444609 1.39672 8.04459 +8.86941 6.10911 8.40831 0 +9.31898 6.55867 0 7.01978 +0 6.09467 6.82442 6.87455 +7.22926 3.68318 7.34739 0 +9.34197 8.88087 0 9.34197 +3.53228 0 8.60146 3.68942 +0 6.84173 7.42097 8.87229 +0 8.41691 7.4267 8.87801 +4.18106 0.365386 1.94396 0 +>M01017 BACH1 lnR0: 2.516 +1.56945 0.529105 2.09855 0 +2.44153 2.97063 0 3.43174 +3.6 0 3.13889 3.6 +2.97063 1.51932 2.50953 0 +3.6 3.13889 0 3.6 +0 2.50953 2.50953 1.98042 +3.24098 1.21043 0 3.24098 +3.13889 2.67779 2.67779 0 +3.6 0 3.13889 3.6 +0 2.67779 2.67779 3.13889 +1.30899 -0.142328 1.83809 0 +2.25077 2.77987 0 2.25077 +3.02076 0.99021 0 2.03055 +3.13889 2.67779 2.67779 0 +>M01018 BACH2 lnR0: 0.764 +1.4655 1.44066 1.36127 0 +4.19195 2.92437 0 4.19195 +4.54833 0 4.26984 4.86711 +3.13889 2.55349 4.12293 0 +4.09196 2.90111 0 3.57768 +0 4.0489 5.8788 2.83847 +5.29595 2.51538 0 6.50637 +5.54214 5.39981 7.38023 0 +5.52552 0 7.26505 8.30539 +0 8.39966 6.83021 6.30111 +4.81042 -0.137703 1.07788 0 +>M01019 BARX1 lnR0: 1.348 +1.32253 0.400318 -0.406153 0 +1.25607 -0.377864 0.400318 0 +1.6148 1.85305 3.08876 0 +0 2.71396 2.17183 5.84906 +0 4.68766 6.66808 6.13898 +1.94425 1.80192 0.492937 0 +2.46746 4.97698 0.497707 0 +5.95115 3.9206 0 6.53038 +2.76409 0.561209 3.18732 0 +2.14176 1.56154 4.59049 0 +2.02626 1.99699 1.83809 0 +1.43165 1.07263 1.57462 0 +>M01021 BATF lnR0: 4.852 +0 2.10575 -0.0186788 0.65289 +1.66678 0.593593 0 1.66678 +2.89735 2.67779 1.63227 0 +1.35767 -0.313859 1.21534 0 +1.77154 0.199428 1.66646 0 +1.62428 0 2.13931 1.3312 +0.747777 1.14327 0 1.67408 +0 1.31096 0.80142 1.38164 +0 2.83543 0.71885 0.0432934 +0 1.9056 3.26143 1.78747 +6.88612 7.41522 7.41522 0 +7.61279 4.67369 0 4.06293 +0 6.81276 5.82255 6.06344 +3.07908 0 0.961921 7.03992 +3.16185 4.68117 5.93184 0 +2.37895 0 0.84825 4.31913 +0 3.26391 2.09855 1.40118 +2.09405 0.997128 0 1.1478 +>M01020 BATF3 lnR0: 4.268 +1.48378 0 0.767704 0.856117 +0 2.5757 0.511577 1.14531 +4.39945 0.359021 0 3.09046 +4.83181 5.19266 5.36092 0 +4.16179 3.24576 5.94157 0 +4.06642 1.74331 3.60531 0 +5.83092 0 5.23366 3.42178 +0 1.00978 1.5654 1.30616 +0.878108 0.619361 0.364087 0 +1.5065 3.42047 2.84123 0 +0 0.80142 2.56981 0.855127 +6.55577 8.39386 5.83421 0 +6.26174 4.91629 0 2.81774 +0 6.23096 3.7956 3.23439 +2.62526 0 0.530805 2.36948 +0.921072 1.50756 1.23157 0 +1.12373 0 1.03509 1.4962 +>M01241 CBFB lnR0: 0.764 +2.674 0.423237 0.903912 0 +2.89646 0 1.44514 0.597262 +3.42556 3.95467 2.96446 0 +4.74072 2.2992 0 3.75051 +4.1291 0.888126 3.668 0 +3.30743 4.41577 0 4.87688 +3.95017 4.47928 0 4.94038 +4.20634 3.74524 1.18558 0 +2.55966 -0.336803 2.09855 0 +0 1.83809 0.529105 0 +2.60979 0.168261 0 0.629366 +>M01027 CDX1 lnR0: -0.988 +0 0.436908 1.83809 0.898012 +3.71813 4.24723 2.26681 0 +3.82021 4.34932 3.35911 0 +2.90983 2.44873 1.71898 0 +0 4.13729 1.57763 3.60818 +1.30899 1.83809 2.8283 0 +2.27963 4.59839 0 5.0595 +0.769995 1.10834 -0.336803 0 +>M01028 CDX2 lnR0: 1.348 +2.28002 1.37267 1.68276 0 +5.53623 6.06533 5.58466 0 +6.54995 5.60817 7.39784 0 +4.64524 5.02383 4.88767 0 +0 5.05723 5.20774 5.66885 +7.77797 3.35603 5.52721 0 +2.4602 5.79446 0 0.583721 +0.99546 5.28 0 4.17165 +4.65991 0 3.52737 2.79086 +2.22131 0 3.32965 0.54276 +2.02289 0.45344 1.08463 0 +2.55458 0.82769 1.69778 0 +>M01030 CEBPB lnR0: 0.764 +1.34439 1.76763 0 0.811691 +0.514516 1.64341 0 5.37337 +6.88612 7.41522 7.41522 0 +7.41851 6.9574 0.888126 0 +1.50483 5.44863 0 1.96386 +1.78125 0.484805 1.97988 0 +9.33626 7.88494 0 8.34605 +3.06623 0 7.62162 4.79331 +0 5.84578 8.40543 8.86654 +0 7.42384 8.41405 7.88494 +5.38966 0.320667 1.12486 0 +>M01031 CEBPD lnR0: 0.764 +0 0.894725 -0.209832 1.35583 +0 0.847882 -0.0364598 2.51941 +6.14866 5.68756 3.38836 0 +3.57932 4.10843 0.444215 0 +0.556378 2.92528 0 1.31935 +1.28277 -0.351161 0.118131 0 +4.16861 3.22683 0 5.4776 +1.6817 0 4.51 2.41145 +0 5.74433 4.75412 6.20544 +0 5.70674 3.72631 6.16784 +1.91962 2.22851 1.04754 0 +>M01032 CEBPE lnR0: 1.348 +2.33296 1.93535 1.03734 0 +9.42254 8.96144 2.66613 0 +1.47795 8.48219 0 1.0555 +3.96254 0 1.36872 2.23545 +3.81541 9.44385 0 9.90496 +0.932365 0 7.43037 1.38593 +0 1.98884 7.88474 9.33606 +0 9.11137 9.11137 9.57247 +9.32147 1.98582 5.57096 0 +1.3234 0 3.50361 1.65714 +1.31227 2.42061 1.08237 0 +1.67787 -0.218568 0.371961 0 +>M01033 CEBPG lnR0: 1.348 +0.666668 1.67645 0 1.81878 +1.5161 1.34823 0 1.23614 +0 -0.224156 1.38259 4.3369 +7.86185 6.82151 8.39096 0 +7.27637 7.22624 0 5.12769 +0 5.52102 4.63668 4.80116 +5.54999 3.14871 4.35914 0 +9.31317 7.86185 0 7.74372 +2.96092 0 8.46322 3.14854 +0 4.59148 8.36156 8.82267 +0 8.39966 8.39966 8.86077 +4.36061 0.24448 1.26261 0 +>M01034 CLOCK lnR0: 2.516 +2.33297 0 1.70748 3.59063 +0 1.3688 0.667911 0.640035 +1.77009 1.75707 0 2.29541 +0 -0.393065 0.529105 0.925264 +3.53505 0 4.12247 6.15302 +0 3.09575 3.59333 3.18853 +2.38692 0 2.20064 2.84633 +1.77448 3.40814 0 4.07368 +2.88224 2.11383 3.46966 0 +3.67396 4.91226 0 5.18261 +0 -0.114039 0.676511 1.84681 +0 0.13341 -0.0802068 1.73013 +1.24977 0 0.415793 2.37114 +0 0.249724 3.65661 1.3673 +>M01042 CTCF lnR0: 6.02 +2.35389 -0.259767 1.23447 0 +2.25891 1.5533 0 2.23998 +1.96431 2.62404 0 2.7603 +4.80393 0 4.09375 4.94691 +7.02844 0 8.86654 8.33743 +0 4.48548 0.675149 3.33029 +5.19329 0 0.700102 6.0592 +2.97047 0 3.76544 1.77943 +0 3.9676 3.53888 5.04411 +8.34318 8.87229 0 7.76394 +1.34984 8.267 0 7.73789 +4.57692 4.03857 0 1.58658 +8.32296 6.55287 0 6.75351 +5.64191 5.3051 0 4.33292 +4.16044 0 8.73699 5.23725 +1.9887 6.46744 0 7.33952 +3.77625 0 1.42404 5.3457 +2.20948 -0.216431 1.3688 0 +0.750425 0.23217 0 3.33954 +2.38732 0.563537 0 0.691883 +>M01041 CTCFL lnR0: 4.852 +1.73732 1.21849 0 2.33136 +4.28132 0 3.20736 4.62583 +6.14191 0 6.5205 6.9816 +0.670538 1.85612 0 1.82901 +2.8062 0 0.401594 5.80629 +3.87702 0 2.81915 1.56728 +0 4.48675 3.60241 5.16807 +7.74663 7.28552 0 9.31607 +2.70897 8.59451 0 7.48617 +4.50855 3.81839 0 3.1872 +7.00522 7.27386 0 7.73497 +8.25136 5.49106 0 4.96196 +4.71065 0 8.78962 7.2703 +3.08244 7.65899 0 7.54086 +5.43796 0 2.35888 4.63851 +1.82565 -0.410467 1.58476 0 +1.21267 0.340587 0 3.25548 +2.52226 0 0.480675 0.795667 +>M01043 CUX1 lnR0: 2.516 +0 1.13974 0.0573316 2.49886 +1.95535 0.809136 0 0.760706 +1.1723 1.74825 0 4.09758 +1.61958 0.839695 0 2.47363 +1.45132 0.140629 0 0.872079 +0.831835 2.10844 0 0.634477 +0 5.02383 4.03362 5.48493 +5.51533 4.47499 6.04443 0 +6.46781 0 3.70751 1.70752 +2.85886 3.86864 0 3.84907 +0 5.56676 0.858425 3.72867 +5.51533 4.47499 6.04443 0 +3.07908 0.934181 0 2.00226 +2.03055 1.02732 0 0.835911 +>M01044 CUX2 lnR0: 0.764 +0 0.817159 1.69069 0.953421 +0 3.46459 0.316902 3.1491 +0 2.57598 1.71007 3.96084 +3.33979 3.45792 3.57227 0 +6.65723 0 4.27651 6.91769 +0 3.13141 2.85659 5.03766 +0 1.72488 4.50475 5.37683 +3.415 6.13192 2.58206 0 +0.65289 1.13356 0 3.16412 +0 1.1701 0.918269 2.32694 +0 0.589619 0.734042 1.4617 +>M01045 DBP lnR0: 0.764 +0.747777 0.645693 0 2.89646 +2.90983 4.01817 3.02796 0 +2.71017 2.24907 2.24907 0 +0 2.0169 1.28715 2.06703 +3.28941 1.83809 2.24907 0 +3.30743 3.42556 0 3.88667 +3.86864 -0.142328 3.40754 0 +0 3.08876 4.07897 3.54987 +0 4.13729 4.13729 3.60818 +1.15847 0 0.359021 0 +0 0.184588 0.404803 1.12637 +>M01046 DDIT3 lnR0: 0.18 +0 -0.338581 1.0889 4.40927 +5.24884 5.0482 5.19871 0 +6.45864 4.90876 0 5.27767 +0 4.40092 4.22212 4.38135 +5.13902 3.36893 3.6877 0 +6.30121 6.51154 0 5.50176 +0.818246 0 6.11612 1.3682 +0 2.46821 6.67455 8.7051 +0 8.40255 6.10335 7.29421 +2.79632 0.630786 1.18104 0 +>M01050 DMRTB1 lnR0: 3.684 +1.70347 0.252158 0.275771 0 +1.03244 1.5904 0.0016521 0 +4.93054 5.01156 0 3.94033 +0.985698 0 3.27636 1.39983 +1.11762 1.75752 3.78478 0 +0 3.20975 4.15732 4.18659 +6.70919 0 5.03766 6.29821 +0 3.41617 4.06186 1.27497 +8.444 6.41344 1.01832 0 +2.62411 4.57655 3.92008 0 +4.82733 3.99142 0 4.11194 +4.16824 3.83144 4.47713 0 +0 2.09855 1.46239 0.678419 +1.01127 2.3829 -0.19366 0 +4.04214 0 4.20292 4.1741 +0.512746 0 2.29077 0.750598 +>M01051 E2F1 lnR0: 1.348 +1.9489 1.62078 0 2.17176 +0 1.21127 -0.316519 1.04471 +2.35154 4.58958 0 2.41958 +4.21063 2.93653 0 6.28961 +6.33378 6.54411 0 7.73497 +6.09039 0 7.19874 4.41886 +5.58042 6.48433 0 5.11553 +3.89638 5.41569 0 5.74064 +5.73687 5.68674 0 9.28674 +0 3.21306 0.163486 5.11931 +0 0.36962 1.13674 3.31208 +0 0.342342 -0.227526 1.32101 +>M01052 E2F2 lnR0: 0.18 +2.03055 1.56945 0 2.03055 +3.6 3.13889 0 3.6 +3.24098 0 1.21043 3.24098 +3.6 3.13889 0 3.6 +3.24098 0 1.78966 2.25077 +3.6 3.13889 0 3.6 +0 0.529105 1.10834 2.55966 +0 1.51932 2.50953 2.97063 +0 2.09855 1.10834 0.99021 +2.25077 0 2.77987 2.25077 +>M01054 E2F4 lnR0: 2.516 +0 0.529105 0.010669 1.28684 +1.80832 2.54558 0 3.67253 +1.87437 2.95524 0 2.08308 +1.53994 2.93877 0 2.19546 +5.52756 3.53412 0 8.20156 +6.51867 6.53824 0 6.73889 +5.41852 0 6.74708 4.06929 +6.9816 7.82948 0 5.23335 +8.21731 4.14802 0 4.85821 +4.11902 6.17733 0 5.90869 +0 3.04033 0.353202 3.50144 +0 -0.453908 1.40221 1.89002 +0 -0.35379 0.30353 0.314085 +0.224551 0.268646 0.268646 0 +>M01055 E2F5 lnR0: 0.18 +1.19086 0 0 1.19086 +4.01097 2.55966 0 4.01097 +4.12532 0 3.66421 4.12532 +4.12532 3.66421 0 4.12532 +3.88667 0 1.85612 3.88667 +3.24098 0 0 3.24098 +0 3.20311 3.20311 3.66421 +0 3.20311 3.20311 3.66421 +0 3.20311 3.20311 3.66421 +1.04034 0 0.99021 1.45132 +>M01056 E2F6 lnR0: 1.348 +0.499817 0.425677 -0.380883 0 +1.63757 2.79997 0 1.2031 +2.72041 2.57679 0 5.93913 +5.60094 4.97157 0 7.46701 +3.31519 0 8.24046 5.53127 +4.3497 4.86576 0 5.58214 +7.0508 3.77426 0 7.13741 +6.89574 6.43463 0 6.89574 +0 7.21313 1.62862 8.15491 +0 2.97634 0.23018 6.32318 +1.44984 1.58725 0 3.7788 +1.82169 1.10561 0 2.59874 +>M01057 E2F7 lnR0: 1.932 +1.87307 1.80858 0 2.49627 +0.756156 3.58446 0 1.40425 +2.86362 3.17251 0 7.40369 +4.77751 7.22624 0 6.69713 +3.74385 0 7.08644 4.25814 +2.95909 5.44863 0 5.08779 +5.73093 6.03982 0 6.9816 +2.35946 6.53898 0 6.00987 +0 6.37021 0.890408 6.42034 +0 1.63209 0.850241 4.87307 +0 0.675934 0.457824 1.43027 +0.509811 2.00457 0 1.1829 +1.34963 1.64766 0 2.66957 +>M01060 EHF lnR0: 3.1 +1.07026 0.869614 0 1.7192 +0 1.02775 0.94008 0.927817 +0 6.19758 5.8788 2.52958 +2.0952 0 1.20832 1.5028 +1.8384 0 0.788377 8.38836 +0 1.23884 4.72791 8.47842 +9.34197 8.88087 0 9.34197 +8.34891 8.87801 0 9.33912 +0 8.41691 7.4267 8.87801 +0 8.41691 8.41691 7.8878 +2.19602 6.20172 0 8.96202 +4.40812 1.51932 3.57868 0 +1.04034 1.95268 0 1.31771 +1.15643 0.718183 0 2.50566 +1.54088 0 0.0238764 2.03847 +>M01061 ELF1 lnR0: 2.516 +1.51656 0.65117 0 3.28633 +0 1.16226 0.443537 2.14868 +0 2.24128 1.4869 2.00403 +1.83683 0 1.08201 2.4959 +5.3668 0 1.18277 7.22292 +2.63629 0 7.59731 6.74943 +9.33912 8.87801 0 8.34891 +8.34605 7.88494 0 9.33626 +0 6.83886 8.40831 7.29997 +0 7.4267 8.41691 8.87801 +3.60968 5.56943 0 8.17922 +3.04391 0.881763 3.43004 0 +2.54207 1.86075 0 3.41793 +2.03055 0.955785 0 2.73726 +>M01062 ELF2 lnR0: 3.1 +1.56945 0.529105 1.10834 0 +0 1.83809 -0.142328 0.729751 +0.872079 0.410974 0 0.872079 +3.43174 0 1.40118 3.43174 +0 1.51932 1.51932 2.97063 +3.75051 3.28941 0 3.75051 +3.75051 3.28941 0 3.75051 +0 2.8283 2.8283 3.28941 +0 2.8283 2.8283 3.28941 +2.60979 3.13889 0 3.6 +2.55966 0.529105 0.529105 0 +0.721564 2.55966 0 3.02076 +0 0.847882 -0.142328 1.30899 +0.872079 0 0 1.45132 +1.56945 1.10834 0.529105 0 +>M01063 ELF3 lnR0: 2.516 +0.843218 1.17681 0 1.89175 +0 1.07075 0.770643 1.06182 +0 6.24082 4.3526 3.1226 +1.93061 0 0.802906 1.43076 +0.958072 0 0.171948 7.98662 +0 3.29967 5.15579 7.18634 +8.32876 8.85787 0 6.34834 +9.33052 6.88899 0 8.34031 +0 8.40543 5.84578 8.86654 +0 8.38805 5.82839 6.06928 +1.6385 5.04604 0 7.80634 +4.1404 1.86077 3.32027 0 +0.63563 2.57401 0 1.53971 +1.17316 1.04464 0 2.351 +>M01065 ELK1 lnR0: 0.764 +0 1.17046 0.289055 2.07465 +3.10447 0 2.29533 7.33565 +2.93209 0 6.60008 4.62583 +8.34031 8.86941 0 7.3501 +8.34891 8.87801 0 9.33912 +0 6.42789 8.40831 7.8792 +0 7.40075 7.40075 5.71317 +3.68942 4.25214 0 4.30227 +4.33793 1.64258 3.40754 0 +2.32868 2.23697 0 2.46123 +0.936019 0.739403 0 2.54628 +>M01066 ELK4 lnR0: 1.932 +1.50809 0.735949 0 2.4602 +0.812298 1.36502 0 3.39557 +0 2.07633 0 3.42556 +2.07451 0 1.29463 4.05493 +1.80149 0 3.63958 3.95017 +5.83425 7.35356 0 6.82446 +5.00118 6.32974 0 6.79084 +0 4.06186 4.54254 7.30284 +0 6.88413 4.90371 5.77579 +2.05359 4.59839 0 4.38807 +2.54288 0 1.84961 0.541609 +1.2644 2.12582 0 3.38638 +1.74388 1.11933 0 1.9786 +>M01067 EPAS1 lnR0: -0.404 +1.40118 0.788334 0 3.11296 +1.61958 2.3689 0.613661 0 +0 4.78911 2.48991 6.69536 +5.78509 0 4.97947 4.79488 +6.15965 6.27778 0 7.7291 +8.87801 8.41691 7.4267 0 +9.33912 8.87801 0 8.34891 +0.785947 0 2.89978 2.70684 +2.04808 0 1.83689 1.62394 +>M01073 ESR2 lnR0: 3.1 +0 1.84971 -0.0169744 3.33048 +3.19812 5.75777 0 3.65922 +4.57692 4.88581 0 4.03793 +2.47972 1.7533 0.799879 0 +5.87429 0 3.84374 3.00648 +0 3.6049 0.847882 2.63536 +2.87698 0 0.929878 2.39197 +8.75845 0 8.29735 1.45561 +2.21071 0 0.648598 1.6162 +3.99446 1.0434 3.92183 0 +3.8299 4.93824 0 9.16943 +0 0.454182 2.07674 2.09477 +5.42922 0 5.08247 3.36868 +3.7573 0 5.85585 4.23797 +2.82333 0.118131 3.31434 0 +>M01075 ETS2 lnR0: 1.932 +1.36894 1.60913 0 1.60983 +0.580936 1.22141 0 1.31069 +0 -0.262767 -0.351161 1.6511 +0 2.12277 -0.0934835 2.44439 +2.40044 6.17544 0 4.33735 +7.72616 6.27484 0 6.0062 +0 5.25497 8.39386 7.86476 +0 5.06322 4.68841 7.24428 +0.899712 2.57617 0 5.43979 +0 0.110898 0.507515 1.37959 +0.583721 3.17649 0 3.11667 +1.04034 2.47609 0 2.90509 +0 1.80408 0.161822 2.50893 +>M01076 ETV2 lnR0: 3.684 +0.588578 0.99021 0 1.67735 +0.984855 1.28793 0 2.70482 +0 1.58476 1.00552 2.79057 +0 2.53314 -0.0105553 4.08302 +0 3.20311 0.0642163 5.38417 +5.25738 0 3.16037 6.46781 +0 2.5448 7.1432 6.61409 +8.22979 7.76868 0 8.22979 +8.22356 6.77225 0 8.22356 +0 7.28882 5.3084 7.74993 +0 7.20458 7.20458 3.61823 +0.549239 4.50391 0 7.26421 +3.18354 0.324676 2.72243 0 +0.673741 1.53937 0 2.2971 +2.77125 1.09189 0 3.55703 +1.74903 0.586326 0 2.51406 +>M01077 ETV4 lnR0: -0.988 +1.73799 0 0.547132 2.57768 +0 0.94008 2.9205 2.97063 +4.2648 4.38293 0 4.2648 +3.91877 5.43809 0 5.89919 +0 4.87842 2.09855 5.33953 +0 3.81851 4.80872 2.2992 +1.87596 4.08886 0 5.54017 +3.08498 0.529105 1.05443 0 +>M01078 ETV6 lnR0: -0.404 +0 0.741742 -0.166813 1.18532 +2.60979 0 1.07187 4.59021 +0 5.73502 6.72524 3.63647 +7.3501 8.86941 0 8.34031 +7.74081 6.28949 0 7.01106 +0 3.20956 3.64882 8.70832 +0 6.31737 4.74792 3.9986 +0.825783 4.61543 0 2.92786 +1.74282 1.1924 -0.125219 0 +>M01080 FEV lnR0: 0.18 +1.65152 1.32279 0 3.75051 +1.50068 0 1.94317 3.12704 +0.793996 0.143399 0 3.44788 +1.4999 5.50021 0 5.96132 +5.21236 6.81829 0 6.28918 +0 4.81762 6.79804 6.84817 +0 2.9902 0.94008 5.02075 +2.1237 2.14631 0 3.34429 +1.76275 0 2.08742 0.528965 +3.4123 1.31881 0 2.79497 +>M01081 FLI1 lnR0: 2.516 +2.6515 1.06403 0 3.46291 +1.70123 1.05639 0 2.93519 +1.16271 0.611582 0 2.47751 +0.950208 2.41154 0 2.60679 +3.98955 0 1.28121 5.46044 +1.6427 0 3.73129 5.44307 +6.7506 6.54995 0 7.74081 +6.7506 8.84915 0 6.53038 +0 6.41924 8.39966 6.56157 +0 7.38318 5.59352 5.54509 +2.70897 6.29531 0 7.07519 +1.93152 -0.380704 1.24237 0 +2.62732 2.16621 0 3.78579 +1.80466 0.939884 0 3.75622 +>M01085 FOS lnR0: 1.348 +1.55878 0.956114 0 1.57374 +1.15469 1.46358 0 1.16664 +0 1.21971 -0.112252 6.83927 +8.87801 7.4267 8.41691 0 +9.31898 8.85787 0 6.18008 +0 7.41522 8.40543 6.56734 +9.31026 8.84915 0 5.76039 +8.87801 7.4267 8.41691 0 +7.35297 0 8.87229 9.33339 +0 8.41976 8.41976 8.88087 +5.91876 -0.0195716 1.51932 0 +1.47753 0 1.37544 1.70659 +>M01082 FOSB lnR0: -0.404 +0 0.143352 0.028167 2.66333 +5.65982 5.55773 4.46896 0 +5.87357 5.03766 0 3.92932 +0 4.6909 5.68111 3.29589 +9.01676 8.55566 0 2.39572 +5.39294 3.41082 3.41082 0 +4.3518 0 6.45035 5.66079 +0 5.59352 6.80395 5.69561 +2.99278 -0.196243 0.197203 0 +>M01083 FOSL1 lnR0: 1.348 +1.4796 1.10689 0 1.39636 +0.589122 1.06564 0 1.47602 +0 0.199786 0.138111 4.38956 +8.87229 8.41118 6.43076 0 +9.25679 7.22624 0 4.4965 +0 7.41234 7.41234 6.56446 +3.95637 8.76509 0 9.2262 +8.88087 8.41976 8.41976 0 +6.02376 0 7.86185 9.31317 +0 6.8446 8.41405 8.87515 +4.52941 0 1.32286 0.48898 +1.38229 0 1.35937 1.22908 +>M01084 FOSL2 lnR0: 0.764 +1.51482 1.25482 0 1.33856 +0 0.50855 -0.237435 3.74953 +6.05757 6.80689 5.40571 0 +8.27863 7.23829 0 4.78957 +0 8.37045 4.94488 5.86092 +3.48369 8.72113 0 9.18224 +7.28552 5.61399 7.40365 0 +8.32586 0 5.88434 8.32586 +0 6.82732 6.09757 7.28842 +5.27153 0 0.762975 0.673133 +1.47177 0 1.36773 1.41786 +>M01086 FOXA1 lnR0: 0.18 +5.29637 7.39492 8.38513 0 +1.96305 8.45556 0 8.91667 +8.88087 8.41976 8.41976 0 +7.22017 8.32851 3.46966 0 +8.37662 7.91551 0.757461 0 +0 7.32302 3.27558 7.20489 +6.4339 0 8.75267 4.01722 +0 1.23087 7.23757 0.0131063 +3.09865 -0.0520728 1.89762 0 +0 4.60036 2.90096 0.0602862 +>M01088 FOXA3 lnR0: 1.932 +1.99438 0 1.09139 1.97664 +0.946057 0.354452 1.9936 0 +6.0751 8.39386 6.41344 0 +2.02285 6.14866 0 6.60977 +6.51752 4.80574 5.38498 0 +6.83927 8.35859 4.15225 0 +6.11349 7.95158 0.923034 0 +0 6.2177 2.39749 4.99501 +7.58054 0 5.13902 3.5331 +0.353863 1.14497 5.05121 0 +2.5447 0.810774 1.91533 0 +0.244798 4.47874 2.68908 0 +2.33706 2.27478 0 2.3555 +>M01089 FOXC1 lnR0: 3.1 +1.82612 0 1.36502 1.34545 +0 1.71996 0 0.509536 +0.799451 1.00978 1.73953 0 +4.70834 4.24723 4.24723 0 +5.16944 4.70834 0 5.16944 +3.66421 4.19332 4.19332 0 +3.66421 4.19332 4.19332 0 +4.65442 4.19332 3.20311 0 +0 4.19332 4.19332 3.66421 +4.74072 0 4.27962 1.77009 +1.34923 1.68758 3.668 0 +4.41577 1.39501 3.95467 0 +0 3.668 3.668 0.839695 +0 0.643452 0.232478 2.09477 +3.43174 0.99021 0 2.44153 +>M01090 FOXD3 lnR0: 3.1 +1.2049 0.579829 -0.16703 0 +1.71485 0.397144 0.106656 0 +2.52196 6.0217 3.29378 0 +4.83878 3.58901 0 5.75572 +3.08747 3.43396 3.90325 0 +4.33412 2.33027 3.46204 0 +3.89406 8.08738 2.64929 0 +0 0.289766 0.118131 0.52632 +3.75051 0 3.19085 1.54624 +0.640035 0.712326 2.93825 0 +2.39482 0.929839 2.5407 0 +0 2.54783 0.978382 0.00757865 +1.34137 1.56232 0 1.53971 +2.26767 0 0.0600689 1.40176 +0 -0.178229 1.17847 0.570707 +>M01091 FOXI1 lnR0: 1.348 +1.99194 0 2.26058 1.09012 +2.43535 4.09083 2.84016 0 +3.95017 0 0.815064 1.04034 +7.18634 4.42604 6.72524 0 +7.53076 3.02221 0 7.53076 +0 6.7621 6.7621 7.22321 +7.22321 6.7621 6.7621 0 +7.22321 6.7621 6.7621 0 +7.67518 7.21408 0 6.68497 +7.68431 7.22321 0 7.68431 +3.21613 -0.442183 5.72566 0 +6.68497 0 4.24345 0.479538 +>M01096 FOXM1 lnR0: 1.348 +3.8979 4.583 4.11811 0 +1.94558 4.85488 0 6.30619 +4.94145 4.28959 3.44001 0 +8.68235 3.14217 3.27019 0 +7.77797 7.31687 3.14862 0 +1.32621 3.36396 0 4.30574 +3.72778 0 5.17382 2.62901 +1.15847 1.3057 3.30387 0 +3.35092 0.368772 1.37869 0 +0.663519 3.34922 3.7602 0 +2.46727 1.45314 0 1.09229 +1.48493 0 0.399943 0.999405 +>M01099 FOXO4 lnR0: -0.404 +3.42556 1.97425 1.97425 0 +4.81042 4.34932 4.34932 0 +5.27153 4.81042 0 5.27153 +4.81042 4.34932 4.34932 0 +4.81042 4.34932 4.34932 0 +4.59839 4.13729 1.83809 0 +0 3.88821 2.898 1.37869 +2.674 -0.222456 0.643452 0 +3.96084 1.51932 0.0741715 0 +>M01100 FOXP2 lnR0: -0.404 +1.12508 -0.432944 0.344257 0 +5.68006 5.85899 5.85899 0 +3.25332 8.10311 0 9.14345 +8.25084 4.59889 8.05019 0 +10.7571 8.72651 3.29904 0 +7.83965 5.12076 2.17129 0 +0 1.78597 3.41722 3.63744 +2.55837 0 5.57478 2.46414 +0.150278 0.393142 0.440371 0 +>M01101 FOXQ1 lnR0: 1.348 +0 0 1.30899 0 +0 1.83809 0.847882 3.28941 +2.43535 1.39501 2.96446 0 +3.77008 3.30898 3.30898 0 +4.23119 3.77008 0 4.23119 +3.77008 3.30898 3.30898 0 +3.77008 3.30898 3.30898 0 +3.77008 3.30898 3.30898 0 +0 3.30898 3.30898 3.77008 +3.66421 3.20311 2.2129 0 +1.56945 2.67779 0.697367 0 +3.28941 0.529105 2.8283 0 +>M01104 GATA2 lnR0: 0.764 +0 1.10025 -0.386119 0.779302 +1.84715 0 0.320408 3.45144 +0 5.45387 6.03311 1.67153 +9.33339 7.88208 0 7.76394 +0 5.41741 6.40763 7.85894 +5.58543 3.9139 3.66482 0 +0 3.55365 4.24723 3.81033 +0 4.49737 1.55681 4.95847 +2.36825 1.22386 0 4.05681 +0 0.781425 -0.287732 3.35911 +0 1.04839 0.138686 1.3261 +>M01107 GATA6 lnR0: 0.18 +0.859537 1.17558 0 1.53698 +2.03744 0.305106 0 2.26111 +0 2.8058 4.46745 1.08877 +6.75932 7.86766 0 7.74953 +0 6.41634 6.41634 7.28842 +5.19027 4.50895 3.73896 0 +0 6.34505 6.02627 4.13215 +0 4.26694 2.85464 5.90901 +2.98397 2.16116 0 4.26895 +1.17865 1.12514 0 3.70823 +>M01110 GFI1 lnR0: 0.18 +1.43535 2.98677 0 3.73455 +3.41793 0 2.20527 3.12131 +0.0453553 1.51932 1.93029 0 +3.66886 0.940659 0 2.84691 +1.42036 4.13729 2.4535 0 +7.62865 7.16754 0 7.62865 +0 6.70644 6.70644 7.16754 +7.16754 6.70644 6.70644 0 +7.16754 6.70644 6.70644 0 +2.4515 1.74489 1.09238 0 +>M01112 GRHL2 lnR0: 1.348 +0 4.60567 1.35977 2.76757 +0 6.24082 1.38197 1.94163 +9.32187 0 5.89013 9.32187 +2.86864 0 6.82331 2.61179 +0.983931 3.99942 0.102484 0 +9.33626 7.30571 0 9.33626 +4.44601 1.39751 8.03235 0 +4.28437 0.29741 4.26635 0 +3.28072 1.04863 3.00421 0 +1.96214 2.7277 -0.146919 0 +0.535276 2.19075 -0.108448 0 +9.22 0 6.4597 4.02345 +>M01113 HAND1 lnR0: 4.268 +1.30988 1.91103 0 1.55172 +2.11931 1.87537 0 1.62821 +2.16231 0.753015 0 2.06237 +3.63647 -0.128254 2.74665 0 +5.60163 0 6.82431 5.71597 +5.71898 8.39677 8.39677 0 +8.33455 7.87344 0 7.02556 +7.65675 1.43245 0 2.36918 +1.07316 -0.114588 1.13049 0 +1.24575 0.399681 1.78966 0 +0.658698 1.88139 3.65738 0 +0.776593 0.0030755 -0.385401 0 +3.59049 0.956492 2.58726 0 +1.66678 0.345817 0 2.15745 +5.09157 4.5246 4.16558 0 +5.71461 0 4.02464 4.18912 +0 1.99534 3.51376 1.30666 +>M01116 HIF1A lnR0: -0.988 +1.75668 1.65841 0 2.8724 +1.28457 2.9843 0 0.941779 +0 5.3674 1.90521 6.62796 +2.9996 0 6.0067 4.26717 +5.4299 7.84723 0 9.29855 +6.55867 6.09757 8.39677 0 +9.33339 7.30284 0 8.34318 +1.31615 0 2.54879 2.71733 +>M01117 HINFP lnR0: 3.684 +0.639909 2.06703 0 1.21915 +0.639909 0 1.26758 1.72868 +3.24098 0.220215 0 2.83 +1.28305 0 0.99021 0.757733 +0.854053 0.392948 1.83809 0 +0 0.118131 0.917582 2.77987 +2.08887 2.03874 0 2.27963 +3.75051 0 5.26983 5.73093 +5.83425 5.37314 0 5.83425 +4.16149 4.27962 0 5.73093 +0 3.88821 4.87842 5.33953 +5.76621 0 3.73566 5.76621 +5.61956 3.17803 0 3.63914 +4.34932 4.87842 4.87842 0 +1.67153 3.35911 1.78966 0 +0 0.0364761 0.0364761 1.74825 +>M01118 HLF lnR0: 0.764 +0.621883 1.56678 0.0903909 0 +1.8713 1.33964 0 3.90703 +6.88227 4.12197 6.01019 0 +8.47084 6.44029 4.34552 0 +0.882993 4.9188 0 6.17936 +5.77921 0 6.30832 3.16124 +0 4.38979 4.65025 4.73655 +5.41891 0.108511 3.20956 0 +0 2.33603 4.41068 7.30714 +0 7.04588 5.25622 8.49719 +3.58549 0 0.947134 1.8526 +>M01122 HNF4G lnR0: 2.516 +0.7839 0.471076 0 2.11315 +0 3.25391 -0.26767 1.96183 +3.94849 5.35643 0 4.1559 +1.19257 2.07185 -0.0943622 0 +1.47924 0 0.145404 0.679785 +6.93317 0 6.21161 4.42195 +0 4.79677 5.20774 6.02787 +0 5.88217 2.05214 7.65227 +0 8.30399 3.22492 6.20544 +6.99641 6.85408 0 6.0062 +4.99981 5.3784 0.166892 0 +3.92741 0 1.91867 1.02323 +5.79723 0 5.48664 3.10141 +0 2.9205 1.93029 2.70477 +>M01129 HOXA1 lnR0: 0.18 +0.729751 0.847882 0.847882 0 +2.55966 2.09855 0.118131 0 +2.44153 2.97063 0 3.43174 +0 2.67779 2.67779 3.13889 +3.13889 2.67779 2.67779 0 +3.24098 2.77987 0 1.67153 +3.6 3.13889 0 3.6 +0 1.51932 2.50953 2.97063 +3.13889 2.67779 2.67779 0 +2.03055 1.56945 0 2.03055 +>M01127 HOXA10 lnR0: 1.348 +1.19086 1.30899 0 0.779881 +0 0.529105 0.529105 1.56945 +2.77987 0.338346 1.32856 0 +0 1.30899 0 1.30899 +0 1.10834 0.118131 1.56945 +2.2992 2.8283 2.8283 0 +3.42556 2.96446 2.96446 0 +2.2992 2.8283 2.8283 0 +0 2.96446 2.96446 3.42556 +3.42556 2.96446 2.96446 0 +2.60979 3.13889 0 2.60979 +0 0.268646 0.847882 0.318777 +>M01131 HOXB4 lnR0: -0.988 +2.26709 -0.274051 1.77459 0 +1.71363 7.01572 4.23585 0 +0 4.76152 1.44383 6.21284 +0 8.40831 6.42789 7.8792 +8.84331 4.61212 8.3822 0 +4.889 4.03942 0 2.10913 +0.51285 7.90484 0 5.80629 +5.55641 0 1.43109 5.55641 +>M01132 HOXB7 lnR0: 0.18 +1.06745 2.75503 2.75503 0 +4.81042 4.34932 4.34932 0 +3.6 4.70834 0 5.16944 +0 4.34932 4.34932 4.81042 +4.81042 4.34932 4.34932 0 +4.81042 4.34932 4.34932 0 +0 3.30898 0.0195698 0.99021 +0 3.30898 4.29919 4.76029 +4.70834 2.67779 4.24723 0 +2.34933 2.2992 0 1.04034 +>M01133 HOXB8 lnR0: 0.764 +1.85612 3.95467 3.95467 0 +4.65442 3.20311 4.19332 0 +3.49005 4.59839 0 5.0595 +0 4.24723 4.24723 4.70834 +4.70834 4.24723 4.24723 0 +4.70834 4.24723 4.24723 0 +0 3.40754 0.436908 1.30899 +0 4.24723 4.24723 4.70834 +3.66421 4.19332 4.19332 0 +2.25077 2.20064 0 1.09229 +0.61162 0 0.509536 1.77009 +>M01124 HSF1 lnR0: 3.1 +1.27766 0.132275 0.799451 0 +0 4.03243 0.343084 4.11031 +7.02844 8.86654 0 8.33743 +0 4.2841 5.19266 6.01278 +0 4.99904 3.93913 4.78871 +0 -0.305106 -0.260459 0.488578 +1.21993 0.63119 0 1.34545 +3.16746 2.95389 3.906 0 +3.8488 5.05923 3.03967 0 +7.7582 0 6.88612 9.32764 +5.66283 0.511136 3.34561 0 +0 5.53275 0.56395 5.99385 +9.33339 8.87229 0 7.35297 +0 5.00838 4.09145 4.89025 +0 3.58634 2.48179 4.30791 +>M01125 HSF2 lnR0: 2.516 +0 -0.0818778 -0.317706 1.91762 +3.91743 3.14967 0 3.62711 +0 2.94448 2.17945 3.48724 +0 2.9764 2.14897 2.32116 +1.58065 0.204389 -0.0698352 0 +0.902085 1.11062 0 2.64317 +2.99343 3.8917 2.81273 0 +3.569 3.49113 2.60046 0 +4.55948 0 2.68962 4.68655 +3.16294 1.71162 1.48293 0 +0 1.22623 1.24946 3.10396 +5.879 2.72665 0 4.30956 +0 3.04222 2.16636 2.8319 +0 1.27723 1.50446 1.87029 +>M01135 IKZF1 lnR0: -0.988 +2.72792 0.118131 0.37859 0 +3.69143 2.65108 5.21074 0 +4.28132 5.80063 0 6.26174 +5.27153 4.23119 0 6.26174 +6.31017 4.85885 0 6.31017 +0 5.18353 1.89412 5.64463 +1.1765 3.42556 0 2.48548 +0 2.62387 -0.285959 1.10456 +>M01136 INSM1 lnR0: 1.348 +2.55966 3.668 1.10834 0 +4.66745 4.20634 0 1.88757 +4.1291 1.3688 1.68758 0 +1.28305 0 3.96084 3.43174 +0 4.07897 4.07897 3.54987 +5.0595 4.59839 0 5.0595 +5.0595 4.59839 0 5.0595 +5.0595 4.59839 0 5.0595 +5.0595 4.59839 0 5.0595 +4.94038 3.48907 0 3.95017 +3.95017 0 3.48907 4.94038 +0 3.49974 0.210329 3.96084 +>M01138 IRF2 lnR0: 6.02 +0.821235 1.02161 0 1.56437 +0 2.16036 1.03135 2.98466 +0 2.7732 2.20689 2.69421 +0 3.20311 2.7437 2.72413 +0.899481 0.939314 0 1.97253 +0.586543 0.338346 1.1378 0 +2.67012 4.89145 0 6.71757 +0 8.3822 4.95664 7.8531 +0 7.41522 6.83599 8.86654 +0 8.37339 5.2345 6.05463 +2.60013 1.14882 0 5.44646 +2.89735 1.15937 5.57514 0 +4.45971 6.19924 0 6.24937 +0 5.77189 3.79147 8.79265 +0 8.39677 5.61689 8.85787 +0 8.3822 5.60233 6.28365 +6.58543 0.616538 0 4.43675 +2.49637 0.648438 2.62886 0 +0 1.15872 -0.388573 2.2101 +0 0.332503 -0.223875 1.61707 +>M01139 IRF3 lnR0: 6.02 +1.22636 2.66297 0 2.66914 +0 3.22209 0.533828 3.45414 +0 2.8283 1.1772 3.91129 +0 2.75503 2.20108 2.85294 +1.02792 2.0377 0 2.23834 +1.75739 3.28941 0 2.19817 +2.29023 3.67594 0 6.11746 +0 4.84748 1.96905 5.62736 +0 3.92358 2.18866 5.04116 +0 5.13067 4.30872 3.97038 +1.43862 0.755492 0 3.11296 +0.915155 2.14515 0 1.32937 +2.40209 6.55359 0 6.43546 +0 4.19332 0.738094 5.53877 +0 4.03119 3.07908 5.91876 +0 6.76513 3.98526 5.82505 +2.92532 0.79168 0 4.06929 +0.253334 0.67962 -0.24979 0 +1.80203 2.22349 0 3.58549 +0 2.75503 1.44604 3.21613 +>M01140 IRF4 lnR0: 4.852 +0 0.963184 -0.316519 1.23094 +0 2.13851 1.5095 1.60941 +0 2.68219 1.69198 2.17306 +0 3.50443 1.72555 1.40588 +1.35424 1.71625 0 3.34513 +0 1.11407 0.307258 3.28941 +1.69839 5.54719 0 5.01809 +2.91043 5.04812 0 6.27922 +0 7.38906 5.24038 6.28072 +0 4.51836 5.14955 4.20947 +1.93333 0 0.0757492 4.45588 +3.01978 3.24158 5.00838 0 +5.14274 7.82053 0 6.49197 +0 5.61834 2.50615 4.22333 +0 2.93039 0.327305 3.82021 +0 3.33685 3.6072 3.44993 +1.53481 0 0.672682 3.68349 +0.575421 -0.037341 1.34006 0 +>M01141 IRF7 lnR0: 0.18 +1.88004 2.72792 0 3.6 +0 2.39815 4.69735 5.15845 +0 4.844 4.844 5.3051 +0 3.70714 4.69735 3.17803 +2.29101 0.260459 0 2.03055 +3.13889 -0.37945 0.888126 0 +1.79583 3.19085 0 4.23119 +0 4.73545 3.74524 3.62711 +0 1.39501 4.53391 4.99501 +0 4.29919 2.31877 1.33473 +>M01142 IRF8 lnR0: 6.02 +0 0.569124 -0.248761 1.18436 +0 1.86755 0.749321 1.19688 +0 1.96925 1.5446 1.53968 +0 2.742 1.32856 1.12741 +1.04034 1.78076 0 3.21152 +0 1.3374 0.00786011 3.79978 +2.36753 7.55106 0 7.43292 +3.05438 7.67234 0 8.13344 +0 6.42789 7.4181 8.86941 +0 5.22564 6.38411 5.68674 +2.3466 0.70453 0 4.86602 +3.51073 3.17042 8.20807 0 +6.00325 6.85113 0 6.733 +0 5.91876 2.51941 5.38966 +0 5.04584 2.28883 5.67521 +0 5.20474 5.373 5.25487 +2.55587 0.168261 0 5.28379 +2.05822 0.717703 2.74497 0 +0 0.703538 -0.367812 0.941779 +0 0.67879 -0.1254 1.31649 +>M01143 IRF9 lnR0: 1.348 +1.77009 2.2992 0 2.7603 +0 2.09855 2.09855 2.55966 +0 2.09855 2.09855 2.55966 +0 2.09855 2.09855 2.55966 +2.44153 0.99021 0 1.45132 +1.45132 0 1.98042 1.45132 +2.7603 2.2992 0 1.77009 +0 2.09855 2.09855 2.55966 +0 2.09855 2.09855 2.55966 +0 2.09855 2.09855 2.55966 +2.44153 0 1.98042 0.872079 +2.2992 1.83809 0.847882 0 +>M01146 JUNB lnR0: -0.404 +0 0.183573 0.183573 2.07594 +6.04872 6.38707 5.07808 0 +5.25169 6.36003 0 3.39557 +0 6.39297 6.80395 5.28463 +2.39572 8.55566 0 9.01676 +5.80678 4.10996 4.89074 0 +4.63397 0 5.48186 6.93317 +0 5.24915 7.39784 7.2797 +3.92932 0 1.09178 0.585407 +>M01147 JUND lnR0: 0.764 +1.63792 1.03463 0 1.79583 +1.16326 1.47393 0 1.612 +0.5009 1.28563 0 3.54608 +4.78391 7.20123 4.90204 0 +8.14996 7.10962 0 5.37009 +0 5.23081 5.42157 5.52366 +4.11152 5.46257 0 9.06257 +5.89919 5.6583 5.6583 0 +5.68474 0 4.68836 9.1103 +0 6.69058 7.26982 8.72113 +3.70751 -0.2468 1.15163 0 +>M01150 KLF15 lnR0: 5.436 +1.25237 3.82021 0 2.71187 +1.86514 5.52176 0 4.71529 +9.27782 7.8265 0 9.27782 +6.10574 6.80311 0 8.25442 +0 0.126461 7.47169 2.26095 +4.12208 6.71822 0 7.17932 +6.32707 5.67521 0 3.7338 +0 3.38957 -0.246905 3.15709 +3.30401 6.63827 0 6.7806 +0.596402 0 0.203106 3.34817 +0 0.617865 -0.197199 0.70981 +1.75739 3.63392 0 2.48294 +2.82907 5.07163 0 4.99746 +2.48067 4.48702 0 6.12909 +1.6093 2.0709 0 4.44797 +2.33821 2.62356 0 4.04714 +1.13653 1.75358 0 2.0439 +3.48473 2.92728 0 3.69942 +2.42132 5.23366 0 3.796 +>M01152 KLF3 lnR0: 5.436 +1.59111 1.29994 0 2.32532 +1.46999 1.03417 0 2.7979 +1.15975 1.03122 0 2.33758 +1.46288 1.38591 0 3.17898 +0 -0.0616979 -0.40786 1.53502 +0.517769 2.93923 0 0.97064 +5.15764 8.82563 0 9.28674 +7.34434 8.86365 0 8.33455 +7.74663 6.55577 0 8.32586 +3.30004 0 8.24492 1.68794 +7.01106 6.86873 0 7.74081 +7.30829 4.64655 0 2.00319 +2.4606 5.18523 0 4.51997 +3.85978 6.07268 0 3.97412 +3.27845 0 2.02265 2.48375 +1.50465 0 1.20793 0.935808 +2.35221 1.25529 0 1.99079 +2.93194 1.10816 0 2.40428 +2.01874 1.12045 0 2.22725 +>M01154 KLF5 lnR0: 3.1 +1.42174 2.07302 0 1.92127 +2.80858 2.81925 0 2.85394 +1.91143 1.8613 0 2.84562 +2.17408 1.57999 0 2.64434 +1.98212 0 0.661615 2.80407 +0 3.77008 0.956595 0.419208 +4.78355 8.80172 0 6.96363 +7.7582 7.87633 0 8.33743 +6.74768 6.54704 0 7.73789 +0.690249 -0.000317849 6.21436 0 +5.12769 6.23603 0 6.47692 +3.22699 4.21103 0 1.59404 +4.84101 6.81526 0 6.95759 +4.2548 4.37293 0 4.45923 +1.99271 0 2.86888 2.68105 +>M01155 KLF6 lnR0: 5.436 +2.14771 1.43534 0 2.20374 +1.55672 0.937403 0 3.6302 +0 0.751467 0.197517 2.34497 +0 4.01195 -0.148553 1.55702 +4.43969 6.59656 0 3.05287 +5.60163 8.80474 0 5.84028 +4.68693 3.99676 0 6.38633 +1.26369 0 7.75621 1.14766 +3.28189 6.66542 0 5.55708 +4.93208 4.78975 0 1.8471 +2.13966 3.33205 0 4.3724 +3.67038 4.65442 0 4.53629 +1.42625 0 1.10878 2.47996 +0.573207 0 1.19257 0.804806 +3.45388 1.70176 0 1.46235 +2.47492 2.22121 0 2.79853 +2.33158 1.78491 0 3.61435 +0.769995 1.92847 0 2.44153 +1.26844 0.946823 0 3.5027 +>M01156 KLF8 lnR0: -0.404 +2.7603 0 2.2992 1.77009 +0 -0.0501305 1.51932 1.98042 +2.7603 2.2992 0 1.77009 +2.44153 1.98042 0 0.872079 +3.02076 2.55966 0 3.02076 +2.44153 1.98042 0 0.872079 +3.02076 2.55966 0 3.02076 +2.2992 0.847882 1.83809 0 +2.7603 1.30899 0 2.7603 +>M01158 LHX2 lnR0: 0.18 +1.25841 0.956195 0 0.531666 +1.44667 0.504892 1.34699 0 +4.02018 6.33895 6.02017 0 +0 4.70377 2.91411 6.73432 +0 5.22564 6.38411 5.68674 +6.26598 6.38411 4.81466 0 +4.80054 4.65821 0.0741715 0 +0 6.82442 0.461065 7.28552 +5.04514 2.49615 0 4.5267 +1.18819 -0.23387 0.0972756 0 +>M01160 LHX6 lnR0: -0.404 +1.28123 0.352001 0 1.53587 +3.36438 0 3.06217 1.62946 +6.25407 6.3722 7.36241 0 +3.6 4.0683 0 6.50983 +0 7.36838 6.37817 6.83927 +5.01954 6.34809 7.3383 0 +7.79941 7.3383 4.36767 0 +0 6.55697 -0.00748337 3.87919 +1.43751 0 0.308412 4.30227 +>M01161 LYL1 lnR0: 2.516 +1.54683 0 1.10101 1.98853 +2.67689 0 4.55828 2.81092 +0 3.10357 3.22787 1.26547 +3.4773 1.9239 0 1.03714 +2.90509 0 3.94373 3.34817 +3.01017 8.1088 6.12838 0 +7.91101 2.16233 0 6.34157 +5.8129 0.314133 1.01958 0 +2.97063 0.81441 0.726919 0 +1.07061 0.522016 1.26598 0 +3.89898 0 2.06244 1.10943 +3.02076 0 2.34875 1.87679 +1.76112 0.900073 0.950797 0 +2.09819 0.464254 0 1.18811 +>M01166 MAF lnR0: 4.268 +0 1.03367 0.377197 1.01127 +0 1.94916 2.04339 0.781288 +0.546733 2.02289 1.83213 0 +1.48637 -0.278875 0.0229956 0 +3.07324 3.16129 4.97345 0 +7.24887 4.63908 0 6.44941 +3.40503 0 8.64248 5.43937 +5.50021 5.35788 6.34809 0 +6.03053 5.92845 0 4.21837 +0 3.14708 3.9784 4.87576 +3.0267 0 0.849211 2.07266 +0.972682 1.53706 1.4009 0 +1.63012 0 2.14568 1.75814 +0 1.34371 1.4545 0.90254 +2.06633 3.52485 0 2.05089 +2.96918 0 1.30636 2.52813 +0 0.297654 1.76123 0.56495 +>M01163 MAFF lnR0: 7.188 +0 1.26505 0.427661 1.51484 +0 3.5437 0.752531 2.238 +0 3.23481 1.36254 2.12646 +0 2.39907 1.91355 1.74001 +0 0.205494 0.0705076 0.904079 +2.60129 2.91678 3.55681 0 +5.28073 4.57413 0 8.25136 +3.11029 0 6.67547 6.8178 +4.64524 4.26579 6.33281 0 +6.64787 4.69897 0 4.60913 +0 5.03911 5.03911 5.01954 +4.19094 0 0.1866 3.66562 +3.35911 2.24153 3.0223 0 +2.67319 0 3.0318 2.93768 +0 4.05496 1.68154 2.63421 +3.76783 5.18626 0 3.91448 +5.81417 0 3.20439 4.50519 +0 3.13783 2.63754 3.09865 +0 0.946931 0.152723 1.35412 +0 1.86638 1.36544 0.984619 +0 2.06238 1.74361 0.374806 +0 1.0429 1.02173 0.116208 +>M01165 MAFK lnR0: 6.02 +0 1.40426 -0.231643 0.41405 +0 2.27435 0.739331 0.386129 +0 3.12404 2.69532 0.687787 +0 1.298 1.49634 0.216359 +1.81274 0 1.02423 0.888986 +4.1291 3.48538 7.09356 0 +8.16953 8.69864 0 9.15974 +8.16629 0 7.70518 9.1565 +5.21691 5.04248 8.18137 0 +9.117 6.09623 0 5.82759 +0 4.88182 8.17123 4.96812 +5.99139 1.08241 0 4.59021 +4.59839 3.61885 5.53847 0 +3.67144 0 5.47336 4.09468 +0 6.48517 2.9353 4.38662 +4.03582 2.6226 0 1.01895 +4.55211 0 2.40144 3.85276 +0 1.29413 1.17978 0.825826 +0.726919 -0.0501305 1.27024 0 +0.700142 1.3703 0.712405 0 +>M01167 MAX lnR0: 0.764 +1.80611 0.881804 0 3.06287 +0 -0.429706 0.137674 3.24357 +1.7789 0.685555 0 4.76434 +5.87592 0 6.54118 9.30148 +0 6.08593 6.40471 6.28658 +6.29306 0 4.19605 3.22387 +4.99522 8.81373 0 6.97564 +3.44971 1.21176 6.37021 0 +8.31713 7.27679 0 6.01793 +2.69639 1.48779 0 3.98323 +1.66046 0 1.81773 2.44709 +>M01168 MAZ lnR0: 7.188 +1.66402 1.77561 0 2.31722 +1.6427 4.60716 0 4.38316 +1.60277 5.53877 0 5.99987 +3.79735 5.38637 0 5.00778 +4.36115 2.83259 0 6.50983 +0 2.36341 4.03142 1.42333 +4.44095 6.18048 0 5.2404 +3.31302 5.22698 0 6.14302 +1.76582 4.17253 0 4.63363 +1.76382 6.03206 0 4.44305 +2.94055 1.67298 0 4.87254 +0.522276 1.28355 0 1.0706 +2.43339 4.01916 0 3.39149 +1.18062 3.27917 0 3.64171 +2.20321 2.38993 0 4.30794 +0.938448 2.65742 0 3.90908 +1.37355 2.92153 0 3.68224 +0.920725 1.73459 0 2.91846 +1.54113 3.09354 0 2.60979 +1.15309 1.10988 0 2.95837 +0.729523 1.98042 0 2.41531 +1.48204 2.47126 0 3.48331 +>M01169 MBD2 lnR0: 0.764 +1.77009 0 0 3.11932 +3.13511 0.238649 0 2.68017 +6.79084 1.51932 0 6.79084 +5.27153 5.80063 0 0.563189 +7.20182 0 6.74071 7.20182 +7.20182 0 6.74071 7.20182 +7.20182 6.74071 0 7.20182 +7.20182 6.74071 0 7.20182 +0 0.118131 1.72375 4.85885 +2.78211 2.32101 0 1.96705 +1.0012 1.82991 0 3.02076 +>M01170 MECP2 lnR0: -1.572 +4.25145 0 0.7164 4.57023 +7.30038 0 6.83927 7.30038 +7.30038 0 6.83927 7.30038 +7.30038 6.83927 0 7.30038 +7.30038 6.83927 0 7.30038 +0 4.59741 -0.029275 6.04872 +0.795963 5.01649 0 6.46781 +>M01171 MEF2A lnR0: 2.516 +0.47362 1.81703 0.368724 0 +1.71535 1.81062 -0.353101 0 +4.13375 0 3.56677 2.1127 +5.57905 2.98701 5.95764 0 +0 5.3021 4.14362 4.25455 +3.47466 4.82165 5.46734 0 +3.93286 5.14328 5.31155 0 +3.85876 3.39765 4.78251 0 +1.91396 1.93029 4.07897 0 +2.27228 4.11037 2.60587 0 +0 4.93557 0.320946 4.75099 +2.71828 3.65148 0 2.67746 +0.787006 0 1.80036 1.72463 +0 0.322561 1.31277 0.124302 +>M01172 MEF2C lnR0: 3.1 +1.42059 1.26315 0 0.476718 +0.904348 1.48188 0.307085 0 +1.96847 2.0169 -0.183739 0 +5.27855 0 3.63647 2.75332 +7.87633 3.54658 5.4348 0 +0 6.39002 5.08104 3.635 +2.60522 4.70377 5.69398 0 +2.9332 3.73265 7.28252 0 +4.71421 3.72778 6.40178 0 +2.14145 2.87999 4.1157 0 +2.71017 3.23928 2.62864 0 +0 6.73454 0.0457828 4.89645 +2.48342 4.58197 0 2.35346 +1.01064 0 1.83231 2.20936 +0.0789467 0.00733354 1.73442 0 +>M01173 MEF2D lnR0: 2.516 +0.22297 1.99504 -0.276232 0 +3.16159 2.66239 0 0.870137 +5.16944 0 3.57272 2.66174 +7.84429 4.70918 6.39297 0 +0 8.36453 6.79508 4.69653 +3.92467 6.75298 6.75298 0 +3.40964 4.70377 5.95444 0 +3.21613 4.17707 6.24409 0 +1.00452 2.22242 4.72128 0 +3.43882 5.65172 3.55695 0 +0 8.03609 1.28268 5.71732 +3.59639 4.41216 0 3.50216 +1.10166 0 2.82252 2.00085 +0.0361683 -0.31059 1.38316 0 +>M01175 MEIS2 lnR0: 1.932 +1.4297 1.52497 1.69323 0 +8.76509 8.30399 8.30399 0 +9.2262 8.76509 0 9.2262 +0 7.11859 8.1088 2.74486 +9.2262 0 8.76509 9.2262 +0 8.30399 8.30399 8.76509 +5.46787 2.6317 0 4.03458 +2.65925 0 0.617131 1.26243 +7.74993 5.3084 8.27903 0 +6.11487 5.65376 0 1.62527 +5.03383 4.70889 1.90875 0 +3.79551 0 1.67276 1.7868 +0 -0.0455881 1.56073 2.13851 +>M01178 MTF1 lnR0: 4.268 +0 -0.164477 1.20054 1.66164 +2.71187 3.24098 0 5.27153 +2.22592 2.75503 -0.0248453 0 +1.67153 1.56945 0 3.82021 +1.52855 0 2.6369 1.69682 +3.33954 0 3.86864 3.75051 +5.58042 5.11931 0 5.58042 +2.72792 3.25702 1.68758 0 +5.54017 4.08886 0 5.54017 +4.59839 0.587423 4.13729 0 +5.58042 5.11931 0 5.58042 +5.54017 0 5.07907 4.54996 +0 4.65821 4.65821 5.11931 +0 1.51932 1.03864 1.49975 +0 0.529105 2.38522 2.84633 +0 1.10834 -0.0180264 0.898012 +2.12275 0 0.410974 1.86229 +>M01179 MXI1 lnR0: 3.1 +1.22493 0.377695 0 2.81922 +7.72616 0 5.06442 8.30539 +0 7.37728 4.40665 7.25915 +5.62598 0 3.67708 5.62598 +2.55587 3.43698 0 6.37608 +3.518 2.56427 3.61528 0 +7.02267 8.86077 0 7.34145 +3.64876 1.75884 0 2.21994 +2.12859 0 0.0671515 2.1522 +0.957854 0.238649 0 0.501634 +4.40197 1.26686 0 2.18442 +2.15948 0 0.288285 1.64519 +1.80586 0.238649 0 1.3601 +1.8921 1.02865 0 1.85808 +1.65786 0.420161 0 2.46927 +>M01180 MYBL1 lnR0: 3.1 +0 0.35458 -0.378025 1.54544 +3.02076 1.61386 0 2.59528 +1.5249 0.330289 0.990518 0 +2.98172 4.41938 0 4.66027 +2.66671 5.36203 0 4.1516 +6.51867 0 5.86681 7.7291 +0 0.185529 0.134685 5.12591 +9.32764 7.29709 0 7.34722 +8.85787 5.61689 6.82732 0 +7.8792 7.4181 6.83886 0 +1.13042 3.9503 0 2.92856 +1.75465 0.518436 0 3.88047 +0 0.258496 0.0804357 1.28625 +1.76737 1.49508 0 2.97779 +0 0.186991 -0.42709 1.48779 +>M01184 MYF6 lnR0: -1.572 +3.43174 0 2.97063 3.43174 +0 2.50953 2.50953 2.97063 +2.7603 0.318777 0 2.7603 +3.43174 0 2.97063 3.43174 +2.97063 2.50953 2.50953 0 +3.43174 2.97063 0 3.43174 +2.03055 0 2.55966 2.03055 +>M01187 NANOG lnR0: 4.268 +1.97354 0.329746 0.248091 0 +4.03245 0 1.57479 1.55064 +3.39987 0 4.01558 0.956897 +0.525321 4.32948 4.32948 0 +6.01278 4.90598 4.46291 0 +4.47617 5.99548 4.01506 0 +3.91524 1.17626 0 3.31848 +1.56945 3.34674 3.6072 0 +1.07877 0.0164506 0.346174 0 +0 3.08876 2.40366 1.31817 +4.37182 4.71016 3.78075 0 +5.17823 4.49691 0 1.55113 +3.92932 0 2.11238 1.34996 +0 2.60138 3.42332 0.587107 +0 3.18182 1.3611 2.65271 +0 4.4587 3.41458 2.80823 +1.50047 2.19783 1.37995 0 +>M01188 NEUROD1 lnR0: 0.18 +0.574443 2.64702 0 4.60237 +0 0.8506 0.502201 6.97001 +5.75747 0 7.85602 9.30734 +0 8.41691 8.41691 7.8878 +8.3142 8.84331 0 5.6402 +0 1.24333 3.3168 8.43233 +6.57022 8.40831 8.40831 0 +8.34031 8.86941 0 7.3501 +6.66654 3.90624 0 2.5534 +2.34958 -0.439729 1.18087 0 +>M01206 NEUROG2 lnR0: 1.348 +1.1703 1.30124 0 2.32241 +2.17534 0.614081 0 1.24345 +0 2.17183 0.529105 3.41371 +0.47689 1.68379 0 6.90519 +7.06119 0 6.60008 6.48195 +0 7.15706 7.15706 7.61817 +8.03725 7.57615 0 5.25738 +0 1.28893 5.79893 7.25025 +6.02787 7.13621 6.146 0 +7.02556 6.56446 0 5.04514 +4.48976 2.75177 0 2.86836 +2.84691 0 0.877157 0.888986 +>M01194 NFATC3 lnR0: -0.404 +2.20064 1.73953 2.31877 0 +4.66745 4.20634 0 4.66745 +4.66745 4.20634 0 4.66745 +0 3.668 2.67779 4.1291 +0 3.58634 2.0169 4.04745 +0 3.74524 3.74524 4.20634 +0 1.42712 2.41733 3.86864 +0.651864 0 1.98042 1.13254 +1.71996 0.0484308 1.83809 0 +>M01195 NFATC4 lnR0: 0.18 +0 0.697367 0.37859 0.839695 +4.66745 4.20634 0 3.67724 +4.74072 4.27962 0 4.74072 +0 3.81851 3.81851 4.27962 +0 3.81851 3.81851 4.27962 +0 3.81851 3.81851 4.27962 +0 1.22269 1.22269 2.674 +0.839695 0.118131 1.10834 0 +1.30899 0.847882 0.529105 0 +0.509536 2.8283 0.529105 0 +>M01196 NFE2 lnR0: 2.516 +0 4.10007 0.740966 7.34105 +7.87344 8.40255 5.84289 0 +8.33743 8.86654 0 7.02844 +0 6.82151 5.8313 6.87164 +4.7594 0 2.192 4.91829 +3.89069 5.72879 4.86288 0 +4.20125 0 3.83542 4.90061 +0 5.92204 3.06279 4.02792 +6.15671 8.8345 0 6.15671 +5.70692 0 5.24582 6.28616 +0 4.5603 3.41409 4.08722 +0.99893 1.48779 0 1.66222 +0.253226 1.26128 0.7737 0 +0.413002 1.56252 2.21899 0 +>M01190 NFE2L1 lnR0: -1.572 +0 0.288216 1.80923 0.799451 +2.1405 3.71813 0 4.75847 +6.74071 6.27961 5.2894 0 +5.07371 0 6.59303 3.76473 +0 4.64492 5.22415 4.69505 +5.38966 1.71242 2.94813 0 +0.839695 0.0037843 -0.37945 0 +>M01197 NFIA lnR0: 3.1 +1.81852 0.819592 1.78206 0 +4.4514 4.15856 3.08174 0 +4.51554 6.03485 0 4.01796 +4.06929 4.59839 0 4.36592 +3.08119 0 2.56813 4.12532 +0 0.263795 1.23 0.961349 +1.04965 0 0.616832 0.841488 +1.22011 7.13887 0 7.59998 +1.01413 0.633151 0 1.17915 +0.612383 1.33512 1.5864 0 +3.60833 3.30612 0 3.00425 +4.08821 0 3.53491 3.99601 +4.23119 0 3.77008 4.33706 +0 3.02018 2.93357 3.09281 +0 1.74416 -0.169802 1.86075 +>M01198 NFIB lnR0: -0.404 +4.71498 0 1.3619 1.78314 +6.91041 0 8.01875 0.736238 +8.86077 8.39966 5.42903 0 +9.34197 8.88087 0 9.34197 +8.34031 8.86941 0 7.3501 +5.63433 0 7.26799 8.30834 +0 4.02702 6.22765 0.981419 +3.65559 0.936699 0 2.19201 +1.29277 0 0.672776 2.88643 +>M01199 NFIC lnR0: -0.404 +1.51685 0.833078 1.03864 0 +4.32413 0 1.65044 1.18524 +8.20886 0.267125 6.75755 0 +8.8345 8.37339 4.32595 0 +9.33339 8.87229 0 7.35297 +8.33743 7.87633 0 7.34722 +5.23632 0 6.52347 9.28377 +0 2.21767 6.11771 0.943368 +1.7774 0.480675 0 1.57297 +>M01200 NFIL3 lnR0: 0.764 +0 1.35863 -0.336803 0.312413 +0.571581 1.66564 0 3.65417 +8.86365 5.84289 7.41234 0 +6.83927 5.38796 0.94008 0 +0 5.36049 2.9067 3.13197 +4.05094 3.0106 3.05085 0 +5.60463 5.25787 0 7.6994 +2.80455 0.345704 5.34935 0 +0 2.42715 5.92858 7.11944 +0 7.42097 7.42097 7.88208 +3.26782 -0.386683 0.507515 0 +>M01202 NFKB2 lnR0: 0.764 +2.91367 3.59329 0 2.45011 +4.22499 7.76868 0 6.08111 +4.81659 7.78105 0 5.27153 +0 5.98298 -0.0930853 3.96608 +0 2.85309 2.39815 7.59381 +0 6.08008 5.5994 6.54118 +1.73937 1.87278 0 1.41453 +2.83453 0 3.94287 0.65445 +3.13347 0 8.67907 9.14017 +8.31713 0 7.85602 5.88177 +3.49803 0 5.19997 4.54656 +>M01204 NFYB lnR0: 1.932 +2.3083 0 1.50898 1.33284 +0 3.31548 0.210761 4.3711 +1.39143 3.53682 0 3.11558 +8.94832 0 7.497 9.52755 +8.94581 0 7.08352 9.52505 +0 6.62492 9.59555 9.06645 +0 6.29987 7.60886 9.06017 +7.48569 7.02458 6.61361 0 +3.85655 0 0.763487 4.16948 +0 3.2842 0.651486 5.67377 +2.86008 1.93577 0 4.08067 +0 0.136276 0.665818 2.97898 +0.965458 2.03455 0 2.12891 +>M01205 NFYC lnR0: 2.516 +1.32172 -0.452627 0.288507 0 +2.40202 0 1.70227 0.78993 +0 2.14633 0.687999 4.29854 +1.21915 3.72867 0 2.82476 +9.33052 0 7.8792 7.3501 +8.34605 0 8.87515 8.34605 +0 8.39386 8.39386 5.56556 +0 7.41522 6.42501 7.87633 +8.87515 6.8446 8.41405 0 +3.09646 0 1.36778 4.00178 +0 3.93544 1.21689 6.46357 +2.10383 2.05872 0 3.41281 +0 1.2493 1.2814 3.37841 +0 3.00489 -0.447754 1.89655 +>M01114 NHLH1 lnR0: 6.02 +1.30899 0.0484308 -0.228935 0 +2.80055 2.55966 0 2.29101 +4.2648 3.8037 0 2.54484 +3.43174 5.53029 0 4.01097 +2.1449 1.68379 0 1.06808 +0 -0.355236 2.31877 4.76029 +2.08887 1.4595 0 1.01205 +4.09758 0 4.04745 6.078 +0 4.24723 4.24723 5.69855 +6.02085 3.26055 0 4.04043 +6.21161 0 5.7505 6.21161 +3.69143 5.21074 5.21074 0 +6.18587 5.72476 0 5.19566 +5.0595 0 3.60818 4.48026 +3.95017 4.47928 0 3.15072 +4.76029 0.634974 0.25174 0 +5.0595 0 3.60818 4.48026 +3.17128 0 2.97063 2.7603 +2.22131 0 1.76021 0.651864 +1.50865 0 2.18008 0 +>M01208 NKX2-2 lnR0: 0.764 +2.05829 0 0.606976 1.62646 +4.80337 2.95389 2.5526 0 +2.47098 0.864694 0 0.814929 +0.679447 3.25605 0 5.81193 +0 7.42384 8.41405 7.88494 +7.75242 6.88034 0 7.75242 +0.651997 7.64854 2.99412 0 +7.34145 7.29132 0 7.75242 +3.57714 0.967353 0 1.73033 +2.41949 0 0.360078 1.23852 +1.28468 0.421237 0.46074 0 +>M01210 NKX2-8 lnR0: -0.404 +0.99021 0.529105 0.529105 0 +2.77987 2.31877 2.31877 0 +3.02076 0 1.56945 3.02076 +0 2.31877 2.31877 2.77987 +0 2.31877 2.31877 2.77987 +3.24098 2.77987 0 3.24098 +2.7603 2.2992 0 1.19086 +0 1.83809 0.268646 2.2992 +1.45132 0 0.99021 1.45132 +>M01213 NKX6-1 lnR0: 5.436 +0 1.7134 1.80134 2.2178 +1.17221 0.331527 0.893017 0 +1.10536 2.7671 2.51434 0 +0 2.35901 0.966783 2.06208 +0 5.53643 4.44766 5.00733 +3.79894 4.43392 2.22545 0 +3.49576 2.65984 0 0.920314 +1.39326 2.73452 0 1.08718 +1.75947 0.418099 0 1.96798 +0 -0.0854728 1.02806 0.35431 +0.169028 2.61775 2.24702 0 +0.965873 2.9353 2.52433 0 +1.56526 3.21573 3.52084 0 +2.86 2.67039 3.62775 0 +0 1.68521 0.925912 3.8734 +0 5.06023 5.78998 5.67185 +2.69067 4.76521 2.61653 0 +1.14148 3.30216 -0.279107 0 +0 1.77978 -0.247488 1.95421 +>M01215 NR1D1 lnR0: 5.436 +0 1.88606 -0.0768335 1.23993 +1.24866 3.18202 0 2.83666 +1.42269 1.2085 0 3.73327 +0.711021 0.579236 0 1.17915 +0 -0.387197 2.81635 3.85669 +0 6.00634 3.17633 1.85483 +2.82834 0.222432 0 2.19218 +2.84272 4.41595 2.74063 0 +2.40868 7.52183 0 5.0123 +3.85578 5.65246 0 2.35814 +5.75028 4.06032 0 4.82653 +1.78966 1.3677 0.912764 0 +2.8525 0 2.48511 3.30178 +0 3.88497 4.68442 3.7897 +1.59236 1.24336 0 2.2692 +0 1.11626 -0.257889 0.764368 +0 1.01133 -0.397953 1.27089 +1.09229 2.23274 0 1.32136 +1.33141 1.27323 0 1.88663 +>M01216 NR1D2 lnR0: 5.436 +0.608173 1.40118 0 1.56437 +0.51333 1.36502 0 2.52447 +0.953073 2.75202 0 3.37657 +0.695823 2.90024 0 1.27506 +0 1.05119 1.39826 3.35911 +0 3.34608 1.4429 0.954042 +2.3466 1.09189 0 2.82728 +3.12751 4.58037 1.81917 0 +1.03292 4.54008 0 5.12548 +0.944822 7.06966 0 4.31463 +5.42801 3.87814 0 6.41822 +5.19655 3.02984 1.74707 0 +5.12519 0 3.67388 6.20201 +0 6.36921 6.36921 4.6044 +2.07024 0.579236 0 2.13191 +0 1.19173 0.375648 0.455855 +1.27251 1.76021 0 2.48996 +1.19502 2.06391 0 1.89383 +0.8795 1.25809 0 1.59936 +>M01217 NR1H3 lnR0: 3.1 +1.50904 0.360031 0 2.51406 +0 2.95312 1.0041 0.834015 +2.68597 3.50398 0 2.76881 +1.66791 3.05452 0 1.88602 +1.27282 -0.326778 -0.326778 0 +3.38822 0 3.80738 3.74317 +0 2.04504 4.7835 3.539 +0 1.83248 0.071107 3.3704 +0 6.14249 1.77627 5.61339 +6.49496 6.51453 0 5.50475 +3.54608 4.41577 0 1.18753 +4.0369 0.529105 1.22401 0 +5.24166 0 4.29988 3.77078 +0 4.90871 4.90871 2.93446 +1.91143 0.79085 0 1.45823 +>M01219 NR1I2 lnR0: 5.436 +0.136157 0.665263 0.184588 0 +0.721564 1.98042 0 1.04034 +0 1.36502 0 2.674 +1.60183 4.27962 0 3.17128 +2.93911 1.26758 0 1.9489 +4.70834 3.25702 2.67779 0 +4.59021 0 2.55966 1.16464 +0 0.598806 3.88821 4.34932 +0 1.68758 1.10834 1.82991 +0 0.0484308 -0.31059 0.509536 +0 -0.142328 -0.142328 0.509536 +0 2.09855 0.242433 4.1291 +0 4.29919 2.72974 4.76029 +5.31996 4.85885 0 5.31996 +4.20634 2.17579 0.455829 0 +2.55966 2.50953 3.08876 0 +4.94038 0 2.18008 2.95996 +0 3.25702 2.67779 4.70834 +1.58747 0.454934 0 0.747777 +>M01220 NR1I3 lnR0: 4.852 +1.04034 3.86864 0 1.77009 +0 2.20064 0 3.77008 +2.31722 4.41577 0 3.30743 +4.81042 2.05012 0 2.51123 +4.76029 4.29919 3.30898 0 +5.00118 0 2.97063 3.02076 +0 2.67779 4.24723 4.70834 +0.597262 0.865908 0 1.58747 +1.04034 0.99021 0 1.45132 +0 0.30889 0.118131 1.25067 +0 2.0169 0.296936 3.05724 +0 4.19332 2.2129 4.65442 +4.23119 4.76029 0 5.2214 +4.34932 2.31877 1.10834 0 +1.78966 1.90779 3.88821 0 +4.81042 0 2.77987 2.03055 +0 2.31877 1.58902 2.77987 +1.32701 1.12637 0 0.597262 +>M01221 NR2C1 lnR0: 1.932 +1.71177 1.98042 0 3.02076 +2.60979 0.359021 0 1.61958 +2.31722 0 2.43535 1.32701 +1.04034 0 0.839695 2.60979 +0 3.20311 0.423237 3.66421 +1.58747 1.44514 0 2.89646 +0 3.668 2.67779 4.1291 +4.66745 4.20634 0 4.66745 +4.32975 3.86864 0 2.03055 +4.20634 3.74524 3.74524 0 +4.66745 0 4.20634 4.66745 +0 3.668 3.668 3.13889 +1.67153 0.220215 0 0.68132 +>M01222 NR2C2 lnR0: 1.932 +0 2.01016 -0.159235 3.2565 +2.2342 3.93582 0 3.68635 +3.27707 2.52156 0 3.50798 +2.45988 1.96516 0.872407 0 +2.81525 0 1.96008 3.61191 +0 3.47767 2.1633 6.32121 +0 2.75564 0.184414 5.43687 +0 7.07987 2.51358 4.652 +4.61382 5.97124 0 4.55779 +5.14914 4.27706 0 3.25038 +3.26483 2.03466 1.038 0 +2.78657 0 2.80516 4.61353 +0 4.07897 2.202 3.86602 +>M01036 NR2F1 lnR0: -0.404 +3.02076 0 2.72792 2.19881 +0 2.05012 2.20064 2.51123 +0 2.96446 1.05732 2.75413 +0 5.56676 1.51932 6.02787 +5.78352 6.31263 0 6.77373 +6.40237 5.94126 0 2.05305 +5.15845 2.71693 4.11811 0 +5.65766 0 5.19655 3.868 +0 2.65781 3.32924 4.5201 +>M01037 NR2F2 lnR0: 1.932 +1.4595 0 0.457998 1.0609 +1.09155 0 1.52976 1.84231 +0 1.04236 1.81235 1.81852 +0 2.03479 -0.113891 2.88437 +0 6.46664 1.29538 5.93754 +5.14872 8.81672 0 6.71816 +6.13594 6.83331 0 5.61062 +5.32929 3.20654 2.7195 0 +7.63494 0 4.39396 4.60599 +0 7.38906 5.81962 5.70149 +0.655107 1.24614 0 1.85977 +0 1.01529 -0.23055 2.18697 +0.968641 1.87255 0 1.45132 +>M01224 NR4A1 lnR0: -0.404 +0 0.989225 0.149529 1.25482 +0 3.26391 0.613996 3.85497 +0 4.36064 1.39001 5.9263 +0 2.10647 1.8263 5.446 +0.581901 3.90778 0 0.900678 +3.95017 5.71499 0 4.86711 +2.964 1.14196 -0.292013 0 +2.42996 0 3.40634 6.12523 +0 6.77719 6.04744 4.6014 +>M01123 ONECUT1 lnR0: 0.764 +0.879141 1.15154 1.35308 0 +2.08071 0.765555 0.590958 0 +3.85954 1.33542 1.46997 0 +0 6.42789 8.40831 7.8792 +7.29132 8.39966 5.84 0 +6.05561 1.91209 6.58471 0 +7.76681 8.87515 0 9.33626 +0 7.42097 8.41118 7.30284 +6.85996 5.08987 6.80983 0 +7.30714 0.568247 5.05637 0 +1.54274 1.14244 0.0236186 0 +>M01229 OTX2 lnR0: 1.348 +0.801083 1.06973 0.890924 0 +0 1.19072 0.355381 1.75319 +0 1.89304 0.54537 2.19526 +0.788619 1.61908 0 1.99613 +0 2.54368 -0.000535547 2.83141 +2.96081 7.63873 0 5.95115 +6.01207 6.28072 0 9.30148 +0 2.1769 8.20476 6.68545 +6.56157 8.39966 6.41924 0 +4.84389 5.373 6.04443 0 +0 7.21124 4.65158 2.81349 +0 2.16951 0.324256 1.03496 +>M01230 OVOL1 lnR0: -0.404 +2.2992 0.847882 0.268646 0 +2.25077 2.77987 0 3.24098 +2.77987 2.31877 1.32856 0 +0 2.50953 2.50953 2.97063 +0 1.32856 2.31877 2.77987 +2.25077 0 2.77987 3.24098 +1.30899 1.83809 0.268646 0 +2.25077 2.77987 0 3.24098 +0.99021 2.09855 2.09855 0 +>M01231 OVOL2 lnR0: -0.988 +0 0.772456 0.445539 1.07897 +7.55467 7.09356 7.09356 0 +0 7.09356 7.09356 7.55467 +0 7.03464 3.89575 7.49575 +8.01577 0 7.55467 8.01577 +8.01577 7.55467 0 8.01577 +8.01577 7.55467 0 8.01577 +0 1.70728 0.328595 0.0599489 +>M01236 PAX6 lnR0: 1.348 +2.58958 3.99979 2.85068 0 +4.59839 0.333592 3.40754 0 +0.628607 0 3.14498 3.22285 +4.05179 0 3.72065 1.14466 +1.52855 3.04787 0 4.34867 +6.47136 0 2.24017 5.60545 +1.17063 1.61442 4.37374 0 +4.82675 3.00063 4.94488 0 +5.56546 0.470685 0 5.97643 +0 4.79276 1.10433 4.11314 +1.73095 0 0.30889 1.2311 +3.53932 2.58559 4.06843 0 +>M01237 PBX1 lnR0: 0.764 +2.82085 3.57902 2.86174 0 +6.50093 5.15548 0 7.30038 +0 6.80395 5.59352 5.69561 +4.47928 0.87928 0.37408 0 +4.20975 4.61456 2.54753 0 +5.96738 7.80547 0 4.97717 +0 5.56676 0.670314 6.02787 +7.6064 0 6.15508 3.6161 +0 4.65379 1.05197 2.40473 +3.73578 3.47068 0 3.53135 +2.01111 0.35344 0 2.88995 +>M01238 PBX2 lnR0: 3.1 +2.14868 0.697367 -0.292843 0 +0 1.10834 -0.292843 1.56945 +0 0.665263 0.665263 2.43535 +0 0.984039 1.97425 0.865908 +2.55966 2.09855 0.30889 0 +3.13889 2.67779 3.668 0 +3.43174 3.96084 0 2.44153 +0 3.49974 1.51932 2.97063 +4.04745 1.60592 3.58634 0 +2.55966 3.668 3.668 0 +4.42195 3.96084 0 2.12275 +0 2.31877 1.73953 1.78966 +1.10456 1.63366 3.20311 0 +1.15847 3.13889 0 0 +1.61958 0.839695 0 1.3008 +>M01239 PBX3 lnR0: 2.516 +2.23357 0 1.14027 0.617965 +2.50654 0.489964 0.156521 0 +3.08552 0 1.10984 0.544623 +3.51769 1.55869 4.5079 0 +7.19756 1.74144 0 4.14032 +0 10.2492 6.95978 5.59098 +10.5706 4.28441 2.90457 0 +9.7421 9.281 6.40256 0 +11.1903 9.15974 0 6.98395 +1.19622 9.08511 0 10.5364 +2.42071 0 4.30074 1.10701 +1.33836 1.07226 0.786909 0 +1.9664 2.42866 0 1.77084 +1.34699 1.24204 0 1.84793 +>M01257 PGR lnR0: 3.1 +0 4.76644 -0.442592 2.70813 +3.2723 5.83195 0 4.53285 +0 1.02879 0.65398 1.27479 +0 5.02075 4.03054 5.48186 +8.29059 0 4.77225 6.9816 +0 5.12034 2.71783 2.82731 +1.14944 1.18498 0 1.71177 +0 7.77935 0.345058 8.24046 +0 0.153758 0.175569 2.35663 +1.88186 1.95315 3.88821 0 +5.13071 5.24884 0 9.25981 +4.07941 4.50264 4.72286 0 +1.07345 0.450449 0.931123 0 +4.89049 0 5.49683 3.39828 +2.27616 -0.107053 3.44281 0 +>M01244 PKNOX1 lnR0: 0.764 +2.11748 2.35991 2.149 0 +4.77766 4.01145 0 6.56732 +0 5.50857 4.51836 6.18989 +3.88443 0.0195698 -0.277058 0 +2.77168 3.04033 2.14868 0 +5.67942 7.19874 0 6.66963 +0 5.70674 0.30889 5.84906 +5.41852 0 7.15805 5.14115 +0 3.04695 1.05286 2.57387 +4.13748 2.60892 0 3.37633 +1.89175 0.203309 0 2.53178 +>M01242 POU1F1 lnR0: 1.932 +2.60979 0 1.56945 0.820125 +1.18987 1.45852 2.44873 0 +0.629366 0 1.56945 3.6 +0 1.89412 4.19332 1.36502 +3.13889 4.65821 4.65821 0 +4.66745 5.19655 0 5.65766 +0 1.2383 1.45852 1.91962 +0 4.65821 4.65821 3.13889 +1.28277 4.24723 2.67779 0 +0 3.58634 3.58634 3.05724 +1.38486 4.34932 4.34932 0 +0 3.88821 1.10834 0.685104 +1.18097 -0.164477 0.94008 0 +>M01245 POU2F1 lnR0: 3.684 +0 1.94141 1.48647 2.59327 +0 0.823872 0.823872 0.919357 +2.8165 3.00109 0.475861 0 +2.49984 0 0.119117 1.19086 +1.09726 1.73492 0 2.63228 +0 1.06632 2.98594 0.667176 +0 3.91071 5.48016 5.94126 +4.36061 4.88972 5.46895 0 +4.24248 6.92027 0 7.38137 +4.81042 0 0.118131 2.60979 +0 4.44459 4.12581 4.58692 +0 3.70714 2.13769 5.15845 +0 2.37872 2.69749 0.629017 +1.75319 -0.359021 2.20064 0 +0 1.55459 1.29413 2.74545 +0 1.90779 2.03209 0.27413 +>M01246 POU2F2 lnR0: 0.764 +0 1.0058 0.535765 1.02383 +1.71535 -0.418878 2.03083 0 +0 3.27772 4.50264 6.43463 +5.62929 5.01767 3.8913 0 +6.9905 7.25915 0 5.62549 +3.83237 0 4.47582 4.02837 +0 5.79595 6.37519 4.94807 +0 2.47143 2.26199 1.22011 +0 4.52148 3.63714 6.19301 +2.99125 2.31468 2.00738 0 +1.46567 1.36359 0 1.09866 +>M01247 POU3F1 lnR0: 3.684 +2.48548 0 1.02147 1.60114 +1.94379 2.05291 1.78349 0 +2.54288 0 2.38489 2.15842 +0 3.62612 3.74524 4.47928 +6.52347 6.38114 4.59148 0 +4.6015 4.2101 0 2.65551 +0 -0.203005 2.22178 3.36206 +0 3.42108 3.42108 4.1024 +1.02008 2.20064 2.93039 0 +0 4.77865 5.54864 4.92097 +1.30687 4.42773 3.50398 0 +2.63347 3.80827 0.258405 0 +2.51001 0 1.67018 1.20102 +0 0.959619 2.86919 3.11667 +0 2.95826 1.2383 0.326562 +0.95994 1.77099 0 1.05926 +>M01248 POU3F2 lnR0: 3.684 +1.99295 0 2.54073 0.939242 +0.146828 1.62263 1.87171 0 +3.43174 0 4.70076 2.99068 +0 4.19941 5.76886 6.00975 +4.93006 5.55773 5.77795 0 +2.67263 4.9914 0 5.71296 +0.786636 0 5.67185 4.15253 +0 4.68841 7.36241 5.8431 +3.96084 4.48995 4.83446 0 +0 4.81197 7.24732 3.19842 +2.086 3.81475 4.15245 0 +2.08472 4.70171 0 0.501539 +3.75511 0 2.66942 1.93291 +0 2.14893 4.44813 4.36711 +1.10456 2.77669 2.68738 0 +0 1.82638 0.910984 1.05639 +>M01249 POU5F1 lnR0: 3.684 +3.57137 0 1.07971 1.59095 +3.49924 0 3.40375 0.924304 +0 4.21513 4.36564 0.260459 +6.03087 4.92407 5.379 0 +4.10993 6.2668 3.38836 0 +3.03025 1.37928 0 3.49954 +0.963836 4.64936 4.81762 0 +0.845254 0.422247 1.04062 0 +0 5.64842 4.33943 3.08058 +7.87633 6.83599 7.41522 0 +7.24268 8.762 0 4.06465 +5.45612 0 3.30126 2.40654 +0 4.55965 4.55965 1.18097 +0 3.55397 1.60797 2.74749 +0 4.98648 3.86011 4.60789 +1.61821 2.44394 1.60832 0 +>M01250 PPARA lnR0: 4.268 +0 0.821669 1.73601 2.01252 +0 2.96945 2.00698 1.02549 +2.2295 0 0.0960125 2.20508 +2.30783 2.10718 2.21505 0 +0 4.21152 -0.418275 3.05122 +3.31963 5.97072 0 3.31963 +3.61344 5.22698 0 4.90731 +2.32749 0.858425 -0.274342 0 +2.59528 0 0.681968 2.67541 +0 4.86288 3.52815 5.77892 +0 3.31782 0.832533 3.60378 +0 7.18102 2.16452 4.86225 +3.92827 6.75657 0 6.41822 +4.07996 6.01025 0 3.11225 +3.97417 2.41954 0.97742 0 +2.97779 0 1.1763 2.12057 +0 2.70919 2.28046 3.10059 +>M01251 PPARG lnR0: 4.268 +0 1.211 1.66174 1.70612 +0 4.25251 1.81716 0.683078 +2.08505 0.0785127 0 1.67408 +2.41354 1.95244 1.97645 0 +0.863123 4.1024 0 3.89207 +3.31885 7.48443 0 2.78708 +2.66174 4.98051 0 5.03064 +2.39446 1.14148 0 0.963822 +2.83124 0 1.20878 3.43669 +0 4.06322 3.79029 5.3051 +0 3.864 0.99118 5.23366 +0 6.51793 1.50856 6.56806 +3.59675 8.69539 0 5.38642 +3.79857 6.55359 0 2.94639 +3.75297 1.52506 0.042705 0 +2.1449 0 1.71996 2.04158 +0 2.8036 1.6406 2.87429 +>M01254 PRDM1 lnR0: 2.516 +1.30381 3.26456 0 3.58504 +0 2.37124 0.735338 3.57348 +0 2.74951 2.46601 3.91733 +0 8.29157 3.02174 6.45347 +3.5078 3.34332 0 5.48822 +1.01991 2.43507 0.671154 0 +4.72576 6.82431 0 9.26584 +0 7.4181 6.42789 8.86941 +0 5.97669 2.83779 8.73699 +0 8.39966 5.61979 7.87055 +4.64852 4.31172 0 6.21797 +3.89863 1.88989 1.59326 0 +1.65717 1.62622 0 1.67153 +0 0.688422 0.103845 1.26655 +>M01253 PRDM16 lnR0: 0.18 +3.26984 0 1.92439 1.15326 +5.28901 0 5.4591 2.98982 +4.23483 0 6.23482 2.77125 +4.41886 0 7.77797 5.93988 +0 5.84289 7.41234 8.86365 +3.73419 6.37987 0 4.86055 +1.73992 5.3051 0 3.69918 +2.81703 5.30858 0 7.07867 +1.01922 1.35532 0 4.05417 +0 0.582131 0.802346 2.75124 +>M01256 PRDM9 lnR0: 5.436 +0 0.830976 1.66229 1.58655 +0 2.14633 1.14162 2.82765 +0.775735 1.22434 0 1.08677 +0 2.41733 0.592099 1.60346 +0.444468 2.06086 -0.0270264 0 +3.35562 6.58594 0 3.9484 +2.25659 5.47336 0 5.35523 +4.50329 0 6.43358 0.866817 +0 8.18474 2.31206 5.86597 +3.90922 7.72773 0 6.87985 +4.76434 0 4.71421 0.551742 +0 5.47696 3.21918 6.15828 +1.83683 1.02016 0 2.92339 +7.32106 0 8.84038 8.31127 +0 2.83306 6.12246 0.902766 +2.616 -0.29383 0.0907704 0 +4.77766 0 4.70503 4.47255 +1.10117 1.74462 3.11441 0 +2.46414 0.628699 0 0.97814 +>M01258 PROP1 lnR0: 0.764 +2.06608 3.53804 4.24723 0 +0 6.30489 3.74524 4.4668 +0 8.41976 8.41976 8.88087 +4.69838 3.11905 3.65804 0 +3.0157 2.03775 1.40839 0 +0.586399 7.95478 0 8.41588 +0 1.35493 0.245604 2.6311 +0 4.72412 1.84569 3.13511 +6.06928 6.8186 6.40763 0 +4.25009 2.67448 6.63532 0 +0 3.19918 3.5437 1.97649 +>M01261 RARA lnR0: 6.02 +1.61528 3.4028 0 2.35796 +2.83 2.60107 0 4.19979 +1.1781 2.64546 0 2.43513 +3.21142 1.78261 2.08448 0 +3.76943 0 2.46863 2.75561 +0 1.75843 1.57678 2.6386 +0.910692 2.33537 0 2.08887 +0 3.30259 -0.333888 5.16487 +0 7.02711 2.05391 6.498 +5.53335 4.9579 0 6.52356 +4.54008 5.76276 0.903912 0 +7.65227 4.75581 4.6315 0 +6.32371 0 5.21691 6.32371 +0 6.24082 5.44137 7.69214 +0 4.23965 2.42113 5.33195 +4.03678 5.55609 0 4.85873 +4.37105 4.15902 0 4.922 +2.71321 2.34633 2.34633 0 +4.5581 0 3.07151 3.71841 +0 3.86806 2.61041 3.14296 +>M01313 RBPJ lnR0: 0.764 +2.21902 0.0997082 0 1.17489 +3.12566 0 1.08157 1.17618 +2.55587 0.0631904 0 2.52642 +3.80905 4.82807 4.2928 0 +7.70837 6.25706 0 5.31698 +2.9192 6.91651 0 3.27522 +6.72412 5.05259 0 7.71433 +0 5.42489 2.30886 6.68545 +0 6.70644 3.28087 4.86835 +0 0.86224 0.847882 2.16304 +0 0.501894 0.360844 1.49583 +>M01264 REL lnR0: 3.1 +0.168261 1.49682 -0.0425518 0 +1.25237 1.47417 0 3.07089 +0 1.07123 1.30988 0.386129 +0 2.94813 0.194002 1.42882 +2.92612 6.12923 0 4.60991 +6.27806 7.38641 0 6.8573 +3.76826 7.26799 0 6.15965 +0 4.28637 0.348032 4.74748 +0 5.83421 3.27455 5.3051 +0 3.88821 2.31877 1.95792 +2.76706 1.6684 1.40794 0 +4.69059 0.565274 -0.0501305 0 +2.21634 0 3.73566 3.56557 +3.27284 0 2.66876 4.91953 +0 2.0169 2.15987 2.34804 +>M01325 RELA lnR0: 0.764 +3.43669 3.4965 0 1.36035 +5.58651 6.8092 0 5.20328 +6.927 7.77488 0 4.14713 +0 3.02796 0.0874079 4.0683 +0 -0.0104778 0.651526 2.00128 +8.79265 3.57126 6.35113 0 +6.50253 4.47198 5.05121 0 +5.46949 1.15169 4.84012 0 +6.95759 0 6.81526 4.77751 +6.68192 0 7.79026 4.43115 +1.73636 0 3.11952 2.775 +>M01263 RELB lnR0: 1.348 +1.09229 1.47088 0 2.25077 +2.57768 2.84633 0 3.88667 +3.54608 3.66421 0 5.11553 +2.44153 4.54008 0 5.00118 +1.24188 4.20634 0 4.66745 +0 -0.355236 3.30898 1.78966 +3.60818 4.13729 2.15687 0 +3.54987 4.07897 1.77978 0 +3.54987 1.77978 4.07897 0 +2.36825 0 1.64669 3.67724 +2.03055 0 2.77987 4.81042 +0.721564 0 1.56945 1.45132 +>M01265 REST lnR0: 7.188 +1.67592 1.69549 0.316805 0 +4.39945 1.32037 2.45055 0 +4.33428 0 4.79692 3.64594 +0 4.86131 2.67349 5.99385 +5.80911 3.6103 0 5.64085 +3.83865 0 1.62548 2.63753 +0 7.00808 5.6991 7.46919 +8.93195 0 7.48063 7.3625 +7.86766 0 5.83711 4.81042 +0 2.08562 1.44344 1.69848 +1.71511 0.364087 3.03161 0 +7.36629 8.47464 0 8.93574 +7.94931 8.47842 0 8.93953 +0 3.97882 6.37021 6.10156 +7.7768 0 3.10935 5.98713 +0 7.01572 6.43649 7.47683 +6.36467 8.46322 0 8.92433 +3.00035 0 3.33112 3.64171 +1.61162 4.43992 0 1.09318 +2.3524 0 1.82379 3.83253 +3.28025 0 4.46004 3.59034 +1.03181 0 2.15297 1.7873 +>M01267 RFX2 lnR0: 7.188 +2.27326 0.503172 0 3.26347 +2.88643 1.01047 0 2.5032 +3.88667 0 0.832293 3.52765 +1.32701 0.807591 0 0.493947 +3.86286 5.83711 0 5.308 +5.90738 3.46586 6.43649 0 +3.38161 1.35105 4.07897 0 +3.18549 4.03337 0 3.28405 +4.52249 0 4.32184 2.66637 +5.03064 0 3.9903 2.25077 +0 4.07897 1.93029 2.39139 +2.55966 3.08876 0.962937 0 +3.27874 5.20903 0 6.24937 +3.21524 3.74434 0 6.18587 +0.820125 0 1.34923 1.95331 +0 3.6877 0.230034 2.35915 +0 1.79458 2.30411 4.2361 +3.79735 0 3.04958 2.45697 +1.96409 0.480675 0 3.82021 +0.623003 1.98042 0 2.25077 +2.03055 1.63025 0 2.52318 +0 0.659065 -0.0706858 0.43183 +>M01268 RFX3 lnR0: 3.684 +4.76901 0 1.37344 2.16251 +3.75889 0.79528 0 1.77847 +8.83366 8.37255 0 8.83366 +8.3144 4.08322 6.86309 0 +5.46059 3.18096 6.78914 0 +4.61336 5.64005 0 4.38119 +8.71489 0 7.26358 3.9546 +8.5805 0 8.1194 2.77987 +0 4.26824 3.01757 2.54927 +2.44399 4.45034 1.77634 0 +4.40053 8.28874 0 8.74985 +3.64594 6.65304 0 8.68359 +1.33994 0 1.19761 1.70407 +0 3.27723 -0.2261 3.85268 +0 2.90285 3.06475 5.56459 +5.1838 0 5.5886 3.45091 +>M01270 RORA lnR0: 1.932 +0 0.747545 1.37735 2.48691 +0 1.29096 1.68758 0.4605 +1.73799 0 0.515733 1.6359 +1.01253 2.35238 1.15907 0 +0 4.42915 -0.0909496 5.46949 +4.00452 7.13243 0 4.7472 +5.84028 6.82431 0 5.49576 +2.7307 1.08628 0.603259 0 +8.27863 0 4.32846 7.6994 +0 6.06533 5.80487 5.40007 +0.86172 1.86655 0 2.95374 +0.968734 2.39585 0 1.54797 +2.01661 2.55966 0 3.23167 +>M01271 RORC lnR0: 1.348 +1.27719 1.17343 0 2.05053 +0 1.71778 0.476298 1.41118 +0 2.35982 2.1948 2.88046 +0 4.51648 3.15147 1.18724 +2.85042 0.18631 0 3.31787 +4.18659 3.92515 3.34591 0 +0.495669 5.59431 0 6.78516 +1.46481 5.67633 0 4.34777 +5.58347 5.23671 0 5.95827 +5.07907 2.57404 2.14762 0 +6.70919 0 5.51833 5.71898 +0 7.39784 5.41741 6.86873 +>M01273 RUNX2 lnR0: 1.348 +2.22021 0.398162 0 1.02116 +2.00871 -0.0686836 0.630671 0 +4.50855 0 2.83702 1.59872 +4.74521 4.90598 6.03235 0 +7.71729 5.53623 0 6.14785 +4.58488 2.52659 4.40115 0 +9.33912 8.87801 0 8.34891 +5.86709 7.2621 0 6.733 +6.183 1.62489 3.07004 0 +4.78558 1.04702 2.96864 0 +0.932535 2.92228 1.39145 0 +2.548 0.356767 0 0.82804 +>M01274 RUNX3 lnR0: 1.348 +2.08322 1.20612 0 1.36966 +3.21064 1.00872 0 1.38542 +2.31547 0 3.09733 1.53266 +5.53029 5.38796 5.79893 0 +8.34031 7.29997 0 8.34031 +4.18915 2.13712 7.15361 0 +7.7582 7.87633 0 7.7582 +9.33052 6.88899 0 8.34031 +8.59451 2.5448 2.76026 0 +4.08432 0.832046 2.31422 0 +0.406612 2.47074 0.74061 0 +2.12275 0.682465 0 1.47906 +>M01276 RXRB lnR0: 0.18 +1.74825 2.0169 1.28715 0 +2.25077 0.344517 0 4.23119 +0 2.44873 2.44873 4.47928 +4.01097 4.54008 0 3.43174 +4.94038 2.90983 0 3.37094 +3.60818 4.13729 3.14708 0 +5.00118 0 2.97063 4.01097 +0 3.20311 4.19332 4.65442 +2.66174 0 0.63119 2.25077 +0 0.665263 -0.174432 1.12637 +>M01277 RXRG lnR0: 7.188 +1.63393 1.88822 0 2.80873 +0 2.18649 0.139614 1.65739 +1.50606 1.9912 0 1.72256 +1.9582 1.8225 0 2.61909 +0.528186 1.66427 0 1.96648 +1.95268 1.38571 1.10834 0 +2.98365 0 1.1491 2.40442 +0 1.1378 0.917582 2.09153 +1.10012 1.62923 0 1.8545 +0.737752 2.87341 0 4.76099 +0 7.35642 2.0866 5.25787 +5.93059 8.02914 0 7.50004 +4.74318 4.54254 0.152976 0 +5.95791 3.60858 4.69735 0 +5.90448 0 5.70383 6.89469 +0 7.55765 4.77778 6.44931 +0 5.00216 2.0677 4.21259 +4.11429 5.6336 0 7.40369 +4.61271 4.95105 0 5.60292 +2.64842 0.969058 1.89068 0 +5.00118 0 3.19969 2.98162 +0 3.71356 2.72335 3.07011 +>M01278 SALL4 lnR0: 0.18 +1.94982 1.86352 0 2.04726 +2.26272 0.875864 0 2.30537 +0 4.9849 -0.396526 0.306986 +6.52161 7.85017 0 6.33085 +8.32586 7.28552 0 6.5362 +5.60545 2.2746 0 6.06038 +0.638768 3.69745 5.09864 0 +7.34434 7.87344 0 7.75531 +3.16124 5.14985 0 1.98385 +3.19957 4.92331 0 4.56935 +>M01279 SIX2 lnR0: 2.516 +1.63726 5.13699 1.11783 0 +7.01688 7.86476 0 7.01688 +0 2.49457 3.26456 0.80699 +0 2.9843 5.07907 4.32975 +0 6.84173 7.42097 8.87229 +3.53624 0 2.88437 0.706235 +1.15823 0 2.2101 1.03681 +2.26185 1.30045 2.05201 0 +2.09759 4.23529 0 4.17107 +0 6.84173 7.42097 8.87229 +2.11953 0.822338 -0.408606 0 +0 -0.359925 3.28476 2.71425 +2.50065 0 3.22339 1.92813 +2.13017 0 0.911025 0.830739 +>M01281 SMAD2 lnR0: -0.404 +1.48284 1.14451 0.77535 0 +2.79497 0 1.43418 3.04047 +5.54803 5.59646 8.37634 0 +6.65412 5.08846 0 4.50544 +4.95662 -0.0812872 2.12662 0 +5.304 0 5.42213 4.13498 +3.68602 7.31378 6.00479 0 +5.22458 3.86547 0 6.04653 +2.38957 0.229061 0 1.3008 +>M01282 SMAD3 lnR0: 1.348 +1.5906 0 0.209844 1.64319 +1.99312 0.253972 0.935872 0 +3.83048 0 3.45869 2.38141 +1.79899 6.47037 5.06918 0 +3.38125 0.900584 0 3.16104 +0.789883 -0.218961 1.3057 0 +4.86383 0 6.38315 3.77031 +0 1.48315 3.78234 0.238649 +6.23187 0 0.758543 3.00078 +5.1632 0 5.77892 4.79488 +0.729751 2.85272 6.0937 0 +3.17898 0.847783 0 2.04212 +>M01285 SNAI1 lnR0: -0.988 +1.04034 0 0.579236 1.04034 +3.02076 0 2.55966 3.02076 +0 2.09855 2.09855 2.55966 +3.02076 2.55966 0 3.02076 +3.02076 2.55966 0 3.02076 +2.55966 2.09855 2.09855 0 +3.02076 2.55966 0 3.02076 +1.04034 0.579236 0 1.04034 +>M01286 SNAI2 lnR0: 0.764 +0.49553 2.60107 0 2.54009 +0.571272 7.92168 0 6.40237 +9.32187 0 8.86077 8.33166 +0 8.40255 8.40255 8.86365 +8.33166 8.86077 0 9.32187 +8.33166 8.86077 0 9.32187 +7.87055 8.39966 8.39966 0 +9.31898 8.85787 0 7.74953 +4.83928 0 1.94282 1.9339 +0 0.106075 0.298551 0.844546 +1.65064 0.276561 -0.211653 0 +>M01290 SOX4 lnR0: 1.348 +3.19085 -0.24089 0.25174 0 +5.15348 0 2.08588 1.14868 +7.05059 0 6.27071 2.57132 +2.95734 4.23394 5.63513 0 +7.22926 5.19871 4.13126 0 +7.83246 5.58169 4.59148 0 +5.55708 3.14563 0 4.82733 +6.03386 4.92706 5.38199 0 +5.01115 0.20073 1.648 0 +4.68241 0 2.65185 1.33697 +2.83509 -0.249888 0.889094 0 +2.09168 0 0.868404 0.825478 +>M01292 SOX9 lnR0: 3.684 +0 2.03953 3.62953 5.59928 +0 6.66808 3.42711 3.79294 +0 5.17664 0.0474452 0.479295 +1.94422 3.51745 0 2.66957 +1.60062 1.40482 0 3.76146 +0.982696 0.383234 0 1.43461 +1.09866 0.0782975 0 0.828312 +3.09579 0 0.729751 1.22447 +4.81042 0 3.60461 3.31822 +0.327238 2.17954 4.47874 0 +8.50834 1.99851 2.51695 0 +8.88087 8.41976 8.41976 0 +7.7582 7.29709 0 8.33743 +6.08089 7.40945 8.39966 0 +3.95637 1.76818 1.22493 0 +3.72065 0 2.95065 1.32618 +>M01294 SP2 lnR0: 7.188 +2.57268 1.16601 0 3.82775 +1.9718 1.06866 0 3.76146 +2.17919 0.825089 0 3.4149 +1.88275 0.395263 0 2.40807 +0.862193 0.769995 0 2.27326 +2.34499 2.66319 0 3.66212 +2.75223 3.57025 0 3.25317 +1.5351 3.4622 0 5.39419 +4.93727 7.18634 0 4.86757 +6.49795 5.39115 0 6.71816 +4.69336 0 5.93166 4.41235 +5.14115 5.43809 0 4.53418 +6.46476 5.35796 0 5.19718 +3.37822 3.12803 0 5.12648 +1.83795 1.67645 0 5.14029 +2.95173 0 1.4475 3.46513 +3.71716 0 1.09521 1.72307 +1.41551 1.02694 0 1.30661 +2.44153 1.13832 0 2.7282 +1.7886 0.833577 0 2.71802 +2.39859 1.63383 0 3.3888 +2.44153 0.590803 0 3.52701 +>M01295 SP3 lnR0: 6.02 +1.4595 0.872727 0 1.94346 +1.86711 1.09497 0 2.29101 +1.38273 0.982425 0 2.37294 +0.938256 0.808297 0 2.16936 +2.12646 1.44514 0 3.28494 +2.82063 3.02537 0 2.36825 +3.02479 7.39853 0 7.2804 +8.05491 6.28482 0 6.74593 +6.72827 5.42747 0 7.45802 +1.86593 0 3.539 3.25743 +4.70648 4.58307 0 5.14274 +6.90126 5.6407 0 3.44359 +2.34456 4.18265 0 4.06452 +3.33255 2.42605 0 4.67681 +2.7057 0 1.19607 2.96616 +2.11716 0 0.210909 1.28409 +1.25298 1.73013 0 1.93503 +1.80371 1.5828 0 2.5737 +1.90813 0.767848 0 2.39711 +1.7363 0.887602 0 2.26989 +>M01296 SP4 lnR0: 6.02 +1.4766 0.858617 0 3.02076 +1.24524 1.61321 0 2.34625 +2.53404 1.71839 0 3.42703 +0 0.220215 0.231598 2.03055 +0 1.72875 0.751126 1.91692 +1.11498 4.25388 0 3.21524 +1.90625 4.94658 0 2.89646 +1.2934 4.76029 0 5.0971 +4.1127 5.9508 0 5.90237 +5.03829 7.21408 0 5.58042 +3.04697 0 5.94498 3.40599 +4.30657 5.517 0 3.95854 +4.36668 5.37646 0 4.08932 +1.13657 4.10912 0 3.87664 +2.23557 5.90357 0 5.05568 +2.02578 0 2.03397 3.65354 +1.18857 0 1.70629 1.41069 +0.617704 2.1723 0 1.11238 +1.17193 2.11201 0 2.94292 +0.828654 1.56945 0 2.60979 +>M01297 SP5 lnR0: 8.356 +1.18683 1.7362 0 2.54182 +0.730249 1.85612 0 1.6359 +2.04054 2.33447 0 2.58267 +1.63012 2.88898 0 2.30155 +1.05905 3.18202 0 3.69326 +2.03959 3.10769 0 3.25002 +1.9513 2.02918 0 3.83952 +0 0.575948 -0.281276 1.54659 +1.92609 3.24098 0 2.31887 +2.14844 2.33742 0 3.09329 +1.30626 2.36617 0 2.94639 +2.52509 3.38161 0 3.75865 +0.745456 1.24095 0 2.65942 +0 1.9575 0.0141891 1.07345 +1.84214 3.22082 0 3.04437 +1.64887 3.95558 0 1.92883 +1.88244 6.41634 0 5.56846 +5.28988 5.23975 0 6.95153 +5.44057 4.7021 0 5.34201 +0 0.738539 5.42555 2.41007 +3.20306 5.45213 0 4.45373 +6.94848 5.12236 0 5.28684 +0 7.4324 -0.426541 5.33385 +4.3363 5.02141 0 4.60665 +>M01298 SP7 lnR0: 2.516 +0.604504 0 0.516431 2.55855 +0 1.05639 1.79752 0.926963 +0 4.78713 1.79875 4.3313 +0 -0.236411 0.662583 4.10912 +4.00327 0 2.35832 3.95791 +2.39015 0 4.1824 3.65329 +3.19449 2.45602 3.94381 0 +0.570801 2.39554 0 4.10069 +5.72105 1.69317 3.27952 0 +0 1.54843 3.29668 2.85597 +0 3.28087 5.71623 5.18712 +6.87745 7.40656 6.09757 0 +7.10304 2.24797 6.64193 0 +0 3.81374 4.54349 0.717066 +>M01300 SPIB lnR0: 4.268 +0 2.63482 0.41392 3.19449 +0 4.30702 2.35433 3.48128 +0 4.56889 2.12178 4.32646 +0 4.52957 2.58532 1.95034 +3.09281 3.57348 0 5.92281 +0 2.63754 1.08139 6.23754 +4.36999 8.66918 0 9.13028 +9.21689 8.75579 0 9.21689 +0 8.29468 8.29468 8.75579 +0 8.28531 8.28531 6.766 +5.1045 2.68698 0 8.97314 +5.27307 5.45766 6.66808 0 +9.19177 5.76004 0 8.20156 +0 2.15288 0.518484 4.02628 +0 1.35179 0.227549 2.09696 +0 2.24256 1.82349 2.10294 +0.936151 0 0.180058 1.63137 +>M01302 SREBF2 lnR0: 1.932 +0.980659 0.596403 0 2.11077 +1.69589 0.443885 0 2.30887 +1.87629 1.76312 0 3.78632 +2.28282 3.4158 3.08465 0 +5.79261 4.70633 0 5.04615 +4.58309 7.22645 0 8.89798 +1.92752 1.13935 0 2.55256 +2.97441 1.47731 0 6.06487 +0.914607 1.39206 5.06034 0 +5.50086 3.43117 0 5.54929 +0 4.58267 1.15981 3.59863 +1.67594 0.964057 0 0.82982 +1.9516 1.09109 0 1.75797 +>M01303 SRF lnR0: 4.268 +2.21608 1.00059 2.06601 0 +2.95204 2.1429 0.988726 0 +2.45085 -0.22712 0.0676462 0 +6.56267 0 6.10156 5.57246 +6.87344 0 8.39276 4.80642 +0.936521 3.2092 5.76886 0 +3.66421 4.13729 3.93286 0 +0 3.15607 3.40157 1.18868 +4.90988 3.668 5.31468 0 +0.100292 2.27897 3.64399 0 +2.02124 4.31945 3.74022 0 +3.20581 6.2645 0 6.14636 +5.17756 7.39046 0 5.55237 +2.57215 0 1.54197 2.34759 +1.18243 0 3.04881 1.40966 +0 1.87426 1.66983 1.0786 +1.33728 0.189934 0.697367 0 +>M01304 SRY lnR0: -0.404 +2.09477 0.232478 1.22269 0 +0.543961 3.08876 2.8283 0 +3.38161 5.06918 3.7602 0 +3.07997 5.05422 4.06401 0 +7.02556 3.42556 0 5.45612 +3.78459 6.10335 3.80416 0 +1.84426 3.49974 3.49974 0 +1.10834 2.03209 2.31877 0 +0.176591 0.2037 2.93162 0 +>M01307 STAT1 lnR0: 7.188 +0 1.83213 0.0595748 2.20663 +0.919544 2.71954 0 3.72277 +1.15713 3.69876 0 5.43674 +0 4.67006 1.08492 5.44994 +0 4.10996 4.1872 8.77741 +0 4.0489 2.80486 4.35949 +0 -0.410381 0.782936 0.863142 +0.250444 1.32497 0.822975 0 +2.94138 5.84906 0 7.52059 +0 5.14642 3.57698 5.19655 +0 4.8938 3.84009 7.21102 +0 5.33645 3.767 5.62929 +1.76726 0 0.967713 3.88101 +1.58011 0.740497 2.67249 0 +1.22279 0.712845 0 1.8526 +0 2.45647 2.71693 2.97837 +0 1.42969 1.28304 1.97018 +0 1.9247 0.268646 2.3858 +1.23219 0.363393 0 2.01535 +0 0.784889 1.49609 1.3326 +0 0.878532 0.351887 1.23993 +0 1.59853 0.345775 1.7867 +>M01026 TBXT lnR0: 8.94 +1.40118 1.13608 0.817305 0 +3.0068 2.87366 2.21961 0 +3.77574 3.39629 0.276195 0 +0.487296 0.640702 0.981976 0 +1.18161 0 0.0375962 2.31722 +5.24475 0 4.31876 3.71241 +0 3.10629 3.60829 2.31232 +1.78113 -0.326657 0.740792 0 +0 0.227235 1.43766 0.509536 +0.752609 1.77164 1.30494 0 +1.44492 2.10764 0 2.51379 +1.08341 0.866804 0.687999 0 +3.81697 0 0.351619 3.51186 +5.6583 5.02894 7.17762 0 +6.24047 4.14346 0 5.73093 +3.3897 2.6185 4.49804 0 +4.50855 0 0.0866066 1.97071 +0 3.67217 3.74941 2.51456 +0 2.47711 1.81486 3.17686 +1.5366 2.00221 1.97148 0 +4.15369 1.87764 1.5242 0 +2.03903 0 1.76868 0.495324 +0 0.167166 0.371596 1.01675 +2.76909 1.47667 1.45581 0 +2.50566 1.45564 0 1.3375 +>M01314 TAF1 lnR0: 2.516 +0.679912 0 0.105218 2.79452 +0 4.66612 1.11626 4.86677 +0 3.80719 1.68379 3.93456 +1.40353 2.58911 0 5.2911 +0 3.52595 3.28324 6.3962 +0.77601 3.06791 1.93029 0 +2.92987 5.4591 0 5.63353 +4.63089 5.98831 0 6.09039 +1.64757 0 4.64169 5.4776 +2.07358 4.10806 0 3.54185 +2.65137 3.05919 0 4.9326 +1.37149 0 2.30468 2.73857 +2.19043 1.47201 0 2.08188 +2.41541 1.27513 0 2.79229 +>M01315 TAL1 lnR0: 6.02 +2.6635 0 1.39592 2.3349 +3.0337 1.12745 1.66404 0 +5.44307 3.79209 0 1.63274 +2.67059 0.650425 0 1.49156 +1.17168 0.152662 0 0.613766 +0.525081 0.313572 0 0.580675 +0.782061 0.570552 0 1.18217 +0 0.0554855 -0.359021 0.235071 +0.66233 0.165657 0 0.580675 +0 1.0606 0.22988 1.03244 +1.54253 0 0.180278 2.45633 +0 4.5891 7.87851 1.18156 +8.34891 8.87801 0 9.33912 +0 7.41522 7.41522 6.88612 +6.86289 5.60233 6.08301 0 +0 7.40365 8.39386 5.71608 +0 6.32666 3.49665 5.79755 +2.39499 1.74542 0 3.53979 +0 0.648222 -0.372711 3.02895 +0 0.369826 0.14028 1.42333 +>M01316 TBP lnR0: 0.18 +2.05332 0 0.865908 3.50709 +2.3528 2.11893 3.32117 0 +0 4.90464 4.37932 1.96933 +4.38817 3.65413 2.48877 0 +0 4.33072 4.08522 5.32711 +0 4.90204 5.63179 2.77987 +0 8.34062 3.6862 7.23228 +0 6.05193 2.8739 2.21567 +0.854551 4.70834 0 4.25251 +2.33944 0.213617 0 2.73409 +>M01317 TBX20 lnR0: 2.516 +0 1.05528 -0.122892 0.768892 +1.25909 2.28749 0 2.19881 +4.68612 1.19964 0 3.17747 +3.58197 2.44403 4.56601 0 +5.40619 6.03386 0 7.70539 +1.06808 0 1.38557 0.909187 +4.22259 5.46089 3.33507 0 +5.41513 6.84225 0 7.71433 +0 3.89746 4.54315 7.78413 +3.05022 0 3.41106 5.56591 +0 7.33221 5.03301 4.30425 +2.83096 5.03383 0 3.39022 +2.51123 0.446456 0 2.7057 +0.172545 0.011041 0.822447 0 +>M01318 TBX21 lnR0: 1.348 +1.38486 2.66552 0 2.0825 +1.38486 1.19464 0 1.62469 +0 2.67779 0.78323 1.55366 +1.89118 5.09429 0 1.8241 +5.77007 1.57331 0 7.91876 +5.55682 6.40471 8.38513 0 +9.25679 7.22624 0 4.4965 +0.953511 2.93295 1.42182 0 +4.75847 1.46736 0 3.18902 +0 4.28051 1.26199 1.61723 +0.65819 1.45623 0 1.89707 +0 0.971416 0.126609 0.0692776 +>M01319 TBX3 lnR0: -0.404 +0 1.08164 -0.162402 3.69143 +0 5.76276 0.857069 3.25324 +2.93415 4.95105 0 5.99139 +7.20182 5.17127 0 6.21161 +6.75341 6.29231 4.72286 0 +7.2271 5.77579 0 7.2271 +4.48026 0 0.99021 0.779881 +1.46358 -0.037868 -0.346758 0 +0 3.6072 0.827327 2.00128 +>M01145 TCF4 lnR0: -0.404 +0.498213 0 0.0752053 6.68497 +9.20439 0 8.74328 9.20439 +0 8.28218 8.28218 8.74328 +9.20439 8.74328 0 9.20439 +9.20439 8.74328 0 9.20439 +8.74014 8.27903 7.28882 0 +9.20439 8.74328 0 9.20439 +5.0595 0 7.15805 1.50963 +0 1.6792 -0.356529 0.877157 +>M01326 TCF7L1 lnR0: 0.764 +1.87815 0.0190479 0 0.489773 +2.21071 0 0.983456 1.20903 +6.0815 0 3.83073 3.22707 +6.26894 4.59741 8.36749 0 +8.76818 3.26942 5.74742 0 +5.87268 8.3822 5.60233 0 +4.63119 2.39017 0 4.63119 +0 5.29893 4.98016 3.6516 +0.502516 6.06928 4.85885 0 +2.72488 0.320272 0 3.68623 +2.15923 2.06533 2.96026 0 +>M01327 TCF7L2 lnR0: 1.932 +2.25891 0 0.181513 0.972961 +3.06865 0 1.61734 1.91018 +5.68809 0 5.51366 3.33787 +5.67185 4.30219 8.34963 0 +7.75934 3.52815 4.241 0 +5.71317 8.39096 6.82151 0 +4.94038 2.23141 0 5.21775 +0 5.47696 5.11794 3.41284 +1.50031 5.66027 4.82058 0 +4.78934 0.333456 0 5.31466 +2.73425 1.44941 3.20733 0 +2.41752 0.45191 0 0.669265 +1.96877 0.635581 0 0.787796 +>M01321 TEAD1 lnR0: 0.764 +0 7.70608 0.287568 3.96084 +2.20704 0 4.48702 5.77007 +0 6.42213 6.42213 8.86365 +8.87229 6.84173 7.42097 0 +3.38161 7.26982 4.71016 0 +9.32187 0 5.89013 9.32187 +7.28542 0 7.81453 4.78656 +0 3.03044 2.63383 0.857665 +2.47322 2.53744 0 3.02525 +4.22188 0.971657 0 4.28834 +1.04034 0.0168069 0 2.21773 +>M01322 TEAD2 lnR0: 1.348 +1.38381 0 1.35583 1.17938 +1.99845 0 1.10275 1.28787 +0 6.146 0.557395 5.03766 +2.53744 0 5.21523 3.88667 +0 6.11771 6.69695 5.36839 +6.5548 4.88327 4.88327 0 +3.51472 6.60348 5.29449 0 +8.61412 0 5.85382 6.31492 +8.56585 0 6.5353 4.5184 +0 2.76823 4.03581 0.379195 +2.74783 3.88756 0 3.73804 +2.75234 1.44714 0 2.9206 +>M01323 TEAD4 lnR0: 3.1 +0 4.52304 -0.158593 3.539 +1.91242 0 3.65195 7.25195 +0 5.59646 5.81668 6.53824 +8.86365 6.10335 6.8331 0 +4.31172 5.96719 3.55805 0 +9.24768 0 5.49717 4.7076 +7.99762 0 8.52673 2.27286 +0.90958 3.52766 4.30843 0 +2.24818 1.80527 0 2.40071 +1.09711 2.07633 0 2.14644 +1.79748 0 0.615868 3.993 +0 1.96943 1.53875 1.8513 +3.29831 1.56438 1.67873 0 +0.531916 1.05032 0.329124 0 +2.23662 0 1.17995 0.814046 +>M01005 TFAP2A lnR0: 1.348 +0 0.501365 0.320946 1.37344 +1.28634 0.673112 0.702268 0 +1.40716 1.57587 0 1.72594 +6.82446 0.139484 0 5.25501 +8.34605 0 7.88494 9.33626 +9.30441 0 8.84331 5.53433 +4.58197 1.21548 2.7325 0 +3.95017 8.75889 0 7.65055 +0 1.98744 0.128674 6.43884 +4.29663 8.78658 0 8.25747 +9.34197 8.88087 0 9.34197 +5.90316 0 1.44812 6.89337 +>M01006 TFAP2B lnR0: 0.18 +3.95017 4.47928 0 2.38073 +4.66745 0 1.23571 2.68703 +5.2214 0 4.76029 4.23119 +2.52813 0 4.04745 1.21915 +3.54608 3.66421 0 5.11553 +0.597262 0.136157 0 3.88667 +3.49005 3.60818 0 4.06929 +5.27153 4.81042 0 5.27153 +2.18107 2.2992 0 3.75051 +1.34545 0 0.693583 2.1449 +>M01007 TFAP2C lnR0: 1.932 +1.27188 -0.161003 0.739331 0 +1.16703 1.68543 0 1.78989 +6.2568 0.584188 0 4.4269 +9.33339 0 7.88208 7.76394 +8.07236 0 7.61125 2.66637 +7.73729 -0.389499 1.33492 0 +8.17599 0 8.7051 3.36557 +0 5.28514 0.775139 3.89013 +6.76799 8.86654 0 9.32764 +9.33052 8.86941 0 7.03132 +5.20601 0 0.375322 6.515 +1.73951 0 1.32974 1.14357 +0 0.255479 0.0828559 0.958812 +>M01329 TFE3 lnR0: 0.18 +1.05298 3.40061 0 2.08181 +3.09082 5.98882 0 6.71039 +5.22028 4.41465 3.83542 0 +6.03053 0 4.93824 7.18901 +0 5.70674 4.97698 6.4283 +6.17609 0 5.71499 5.01762 +2.8413 5.20031 0 5.98019 +5.52033 4.32948 4.06902 0 +6.42452 7.75307 0 6.42452 +0 3.59396 2.2091 4.6022 +>M01330 TFEB lnR0: -0.404 +0.743713 3.5137 0 1.99438 +1.78545 7.47301 0 7.93412 +7.94383 7.48273 7.48273 0 +8.40494 0 7.94383 8.40494 +0 7.48273 7.48273 7.94383 +8.40494 0 7.94383 8.40494 +8.40494 7.94383 0 8.40494 +7.94383 7.48273 7.48273 0 +6.38553 6.3354 0 6.7965 +>M01331 TGIF1 lnR0: -0.404 +5.40599 4.94488 5.52412 0 +7.45802 5.01649 0 7.45802 +0 3.71264 6.49252 5.96341 +5.87787 0 5.996 6.45711 +0 5.55622 5.55622 7.00754 +3.40773 4.51607 0 6.28616 +3.56428 0 1.33637 2.35386 +1.25886 1.32856 1.25886 0 +1.95225 1.27912 0 2.682 +>M01333 THRA lnR0: 4.268 +0.55042 1.406 0 2.54628 +0 4.42915 0.0874079 3.12345 +3.2928 5.6617 0 5.04599 +4.19427 4.82924 0 2.67678 +3.50232 2.00087 1.32636 0 +5.34177 0 3.23977 3.30743 +0 3.22018 4.04213 3.63732 +1.00617 0.118131 0.17893 0 +1.42882 0 1.02851 1.02905 +3.43037 0.587822 2.55829 0 +1.07948 1.21257 0 2.80607 +0 5.97511 1.01294 5.27774 +5.87004 7.26505 0 6.99641 +6.26481 5.48493 0 4.88613 +0 0.947205 1.80994 0.103138 +4.32975 0 3.86864 3.6 +0 4.25054 3.40096 4.01806 +>M01232 TP53 lnR0: 6.02 +1.19086 3.16929 0 4.66745 +1.97291 4.55698 0 3.92932 +0 5.86863 0.681511 4.88459 +4.52711 0 6.21468 7.25502 +0 6.74379 4.76337 4.35856 +1.49393 4.24316 3.94653 0 +5.97944 5.66885 0 6.48897 +5.19566 0 5.50455 1.55918 +3.28928 0 4.97686 3.54974 +3.45702 0 3.29779 2.46681 +0 4.10843 -0.345786 3.50962 +3.82544 3.29289 0 5.63353 +1.79663 5.29637 0 3.45827 +6.24937 0 3.9986 6.66034 +0 3.01327 4.62537 2.44276 +0.316908 2.91304 -0.0173463 0 +3.54369 3.31841 0 4.80684 +2.41335 0 2.06845 1.42314 +2.23925 0 2.85096 2.75569 +2.17433 0 2.41523 2.20834 +>M01233 TP63 lnR0: 5.436 +0.97064 2.44217 0 1.3979 +0.697084 4.70834 0 2.83885 +9.31898 0 7.28842 6.5391 +0 2.55537 2.46511 3.67554 +0.30187 4.34315 1.08991 0 +8.34318 7.88208 0 8.34318 +2.42916 -0.436042 4.74792 0 +2.40428 0 2.24628 1.6413 +5.57681 0 2.43174 4.34795 +0 1.11345 3.30898 1.3218 +2.10779 3.83801 0 2.93911 +0.664623 5.855 0 2.70792 +8.34318 0 7.30284 9.33339 +0 1.12467 4.53391 0.856022 +2.8394 2.31877 1.9151 0 +5.73687 6.26598 0 7.30632 +3.50472 0 4.39945 0.841395 +1.48462 0 2.21608 1.13914 +2.00939 0 0.983121 1.04034 +>M01234 TP73 lnR0: 5.436 +0 0.671662 -0.309703 1.09792 +0.76926 2.07594 0 1.54683 +0 1.8454 -0.424189 1.31629 +5.02089 0 4.33957 4.44165 +0 1.54761 2.63638 1.78035 +0.925052 4.90728 2.41733 0 +7.00814 6.28658 0 7.32692 +3.21746 0 4.86479 0.591347 +2.53178 0 2.92285 1.95946 +3.01692 0 3.07857 4.15253 +0 1.05853 5.17434 1.91732 +1.30413 2.52681 0 2.56885 +0 3.30387 0.351205 2.54438 +6.71518 0 5.14952 6.49496 +0 1.1603 3.668 0.675976 +2.58911 2.31877 2.12801 0 +5.12466 6.01278 0 6.28313 +2.91652 0 3.47773 0.889257 +1.87725 0 2.58215 1.65489 +>M01334 TWIST1 lnR0: 4.268 +0 0.196429 0.816483 2.2992 +4.42513 0 4.67687 5.89602 +0 4.84716 3.73265 4.68638 +4.99933 2.83262 0.874015 0 +2.10361 0 2.74266 6.49317 +6.56734 7.41522 8.40543 0 +9.31898 7.86766 0 6.34834 +5.47997 2.23899 0 1.66524 +1.01062 2.44031 2.12927 0 +0.93337 1.92503 2.23682 0 +2.2026 0.266688 1.46736 0 +2.94153 0.0408921 1.56107 0 +0 -0.0977122 0.323149 1.53175 +0 3.27106 3.13491 3.63997 +4.69505 3.84547 2.96113 0 +2.69663 1.59474 3.77827 0 +0 3.21678 2.5984 1.28649 +>M01336 USF1 lnR0: 1.932 +2.28596 0.952778 0 2.37967 +1.41069 1.24519 0 2.19025 +3.34658 7.59381 0 9.04512 +7.73729 5.29576 6.28597 0 +9.2231 0 8.762 9.2231 +0 8.30089 8.30089 8.762 +9.20124 0 7.17069 6.64159 +3.3027 6.0067 0 9.02746 +7.76558 7.30447 8.29468 0 +9.2231 8.762 0 9.2231 +0 1.1362 0 2.2992 +3.70208 0 1.05315 1.70686 +3.43174 0 0.935469 3.00964 +>M01337 USF2 lnR0: 5.436 +1.49647 1.08877 0 2.23498 +1.85882 1.92921 0 2.72936 +3.30853 5.53359 0 7.56414 +5.59178 3.67117 4.06322 0 +8.34891 0 8.87801 9.33912 +0 8.40831 6.83886 7.29997 +9.23237 0 5.2214 4.52403 +3.54397 8.7275 0 9.1886 +7.28842 6.09757 6.82732 0 +8.34605 8.87515 0 8.34605 +0.686114 1.21522 0 2.43436 +3.2927 0 0.740372 1.43239 +2.37563 0 0.467249 2.90877 +0.843677 0.144789 0 1.89127 +1.96305 0 0.0154442 1.87773 +2.03797 0.215289 0 1.70145 +1.69865 0.247333 0 2.0752 +1.99344 0 0.26347 1.51277 +2.09071 0.486578 0 1.27164 +>M01339 VSX2 lnR0: 1.348 +1.73857 -0.38271 1.81062 0 +5.87852 6.8186 6.8186 0 +0 5.82839 6.08885 7.2797 +0 6.8446 8.41405 8.87515 +8.87515 8.41405 6.8446 0 +8.87801 7.4267 8.41691 0 +0 8.40831 6.10911 8.86941 +6.33962 6.54995 0 9.31026 +9.33339 0 7.88208 7.76394 +4.11503 0.267075 6.71116 0 +1.12159 1.19457 1.08463 0 +0.55609 0 0.824736 1.6009 +>M01341 XBP1 lnR0: 1.348 +9.95502 10.4841 0 5.71157 +0 10.0588 10.0588 10.5199 +10.981 0 10.5199 10.981 +10.981 10.5199 0 10.981 +10.5199 10.0588 10.0588 0 +9.98805 10.5172 0 9.40882 +8.71314 9.24224 -0.0896618 0 +2.65537 0 5.04245 4.07709 +0 0.0962292 1.45651 1.80682 +1.00574 0.620789 2.0455 0 +0.847728 3.76465 4.23394 0 +0 1.30882 0.867895 0.14507 +>M01342 ZBTB17 lnR0: 5.436 +2.87852 1.0374 0 3.15589 +2.18975 1.30899 0 3.32661 +1.79527 0.521168 0 3.56914 +2.1522 1.97074 0 3.11102 +3.4066 2.1132 0 3.31025 +0.100452 0.0789896 0.546852 0 +4.71566 4.77299 0 5.53072 +3.78579 3.88617 0 4.34728 +2.68519 4.65076 0 4.8514 +3.79306 5.73447 0 5.8768 +6.34254 7.28262 0 8.32296 +0 0.645693 4.99501 3.33029 +3.2043 6.65868 0 5.23156 +4.89226 5.64158 0 6.4617 +2.97302 7.03202 0 4.93346 +3.87362 4.20307 0 6.84425 +0.760706 0 1.7547 3.02076 +1.62762 1.85256 0 2.9734 +2.56405 1.44759 0 3.33709 +>M01149 ZBTB33 lnR0: 3.1 +2.07946 0 0.144423 2.8525 +0 1.56328 0.869693 1.89636 +0 1.80474 -0.0159797 4.62107 +0 1.1289 -0.0903746 1.76605 +2.54255 0.46735 1.14319 0 +1.48057 0 2.5988 4.92598 +2.63219 1.35473 1.71615 0 +6.2922 0 5.25186 6.2922 +4.69229 6.47207 0 6.09348 +5.80063 0 6.20544 4.74692 +5.99139 6.83927 0 6.31017 +0 4.33872 1.88493 5.79004 +4.92394 4.62173 0 4.09263 +0 3.41849 1.96339 5.10845 +0 0.237802 -0.443996 1.35654 +>M01343 ZBTB7A lnR0: -0.404 +1.28232 0.906342 0 2.4349 +1.11758 6.18676 0 6.64787 +5.82212 8.78658 0 4.7684 +8.34891 8.87801 0 9.33912 +7.34722 7.87633 0 8.33743 +5.33466 7.65343 0.0631332 0 +8.33455 0 7.87344 7.02556 +4.38595 0.954214 0.0304611 0 +5.78925 0 1.0847 1.38434 +>M01344 ZEB1 lnR0: 0.18 +3.50536 0.65974 0 1.30865 +0 -0.372043 0.194716 2.31498 +2.64893 0 7.01457 6.48547 +0 7.39199 7.39199 5.29344 +5.72198 7.24129 0 5.72198 +6.73595 7.26505 0 6.0062 +2.47345 5.19038 6.18059 0 +1.54323 6.33398 0 6.47631 +0 1.94545 1.12133 0.383234 +1.97034 2.08847 0 3.91052 +>M01345 ZFP42 lnR0: 1.348 +1.88161 1.94425 0 2.62557 +3.04739 3.7219 0 3.86423 +2.48067 0 1.56463 3.43174 +0 0.126763 2.01499 2.41259 +5.4525 4.67262 0 2.70706 +3.8611 0 5.27953 6.02731 +9.31607 0 6.55577 6.75642 +0 6.10624 7.41522 8.86654 +7.8531 6.08301 5.24331 0 +3.7561 0.779297 2.15103 0 +3.53932 3.03681 3.25702 0 +4.6022 1.40263 4.58417 0 +>M01346 ZFP57 lnR0: 0.18 +2.42916 0 1.54481 1.73937 +3.08841 1.215 1.63709 0 +6.60332 6.72145 0 6.19235 +4.52249 0 6.04181 4.93346 +7.15646 7.68557 0 4.85727 +8.19839 6.74708 0 7.20818 +7.20818 0 6.74708 8.19839 +0 3.10962 6.16685 5.63775 +0 1.35384 0.455829 2.22592 +0 0.613661 -0.0224977 1.18332 +>M01348 ZIC1 lnR0: -0.404 +3.02076 1.82991 0 1.16464 +3.29111 3.24098 0 5.27153 +5.41216 3.96084 0 4.42195 +5.41216 3.38161 0 5.41216 +0.621883 2.59613 0.806471 0 +2.81633 4.65442 0 2.81633 +3.43174 1.40118 0 5.00118 +3.35911 1.90779 0.598806 0 +1.45132 0 0.671434 2.8525 +>M01351 ZKSCAN1 lnR0: 5.436 +0.698352 1.35742 1.05231 0 +1.57762 1.85429 0 2.70639 +0 0.496856 1.59294 0.847545 +1.0249 2.15179 0 2.20192 +2.36959 0.569211 0 1.6604 +0 0.374515 0.797751 1.21043 +5.37599 0 5.23366 6.10574 +4.39945 0 7.12919 4.20869 +6.94259 1.63859 3.45254 0 +0 4.01817 4.74792 5.20903 +5.94296 0 4.35549 6.26174 +4.50391 4.77255 6.342 0 +1.04529 3.96579 0 6.2568 +2.37688 3.28922 2.32675 0 +9.26283 4.52211 0 6.12394 +4.96953 1.94877 3.1526 0 +4.06408 4.11871 0 3.90064 +3.24098 0 3.14306 2.65206 +1.06021 0 1.95694 0.655251 +>M01352 ZNF143 lnR0: 7.188 +2.00623 3.02691 0 1.32804 +5.22818 4.97151 0 5.04938 +3.22186 0 1.58395 3.78459 +0 -0.249888 2.52998 2.11522 +4.48371 1.27219 2.75503 0 +3.71609 1.069 0 0.965672 +3.02076 0 3.1517 3.57471 +5.89206 1.76674 4.44075 0 +6.42452 6.76286 0 9.20439 +7.63494 7.17384 0 6.64473 +5.39934 7.71811 0 6.38955 +0 4.25778 3.36613 4.62668 +0 1.80033 0.0741715 2.35778 +0.198946 1.76839 1.49103 0 +4.62855 2.6301 3.43769 0 +5.75667 6.16148 0 8.19203 +3.62711 3.67554 2.90554 0 +0 6.1942 3.0553 6.33652 +6.61939 5.93807 0 6.39917 +6.68876 4.54386 4.07897 0 +4.77916 0 3.464 0.566001 +4.22041 0 3.31122 1.19447 +>M01354 ZNF322 lnR0: 6.02 +3.39846 2.46206 0 3.78459 +0 2.05149 1.06128 1.05309 +4.08821 3.62711 0 2.66488 +2.3617 0 4.17923 2.28119 +5.32362 0 7.53651 5.56227 +3.78699 2.74665 3.81851 0 +1.96661 4.20132 0 4.32473 +2.80985 0.0921979 0 2.50798 +2.96566 2.00698 2.25073 0 +0 1.32369 3.52432 3.69876 +7.05059 0 6.27071 6.73182 +0 1.7173 0.746522 0.308311 +4.82274 0.610226 0 3.89898 +0 1.83075 1.69126 0.455855 +4.83816 4.76029 0 4.40633 +4.54781 0 3.29804 3.75914 +2.85719 0 4.04277 3.47452 +2.21023 2.04783 1.31145 0 +3.34768 2.18985 0 2.55407 +0.799987 1.05371 0 2.07562 +>M01355 ZNF335 lnR0: 7.188 +1.42809 4.30323 0 2.78392 +3.9233 3.10318 0 3.15331 +3.28562 0 1.83431 2.55587 +4.65442 1.28349 4.19332 0 +5.86709 4.097 0 3.30743 +3.13889 0.118131 1.81188 0 +5.97643 0 4.52512 4.40699 +5.34357 0 4.30323 1.02868 +0.729751 0.338346 -0.287732 0 +1.65872 0 0.618377 0.760706 +0.809136 0.679177 0 1.49046 +2.55587 0.834211 0 2.33566 +1.6385 0 2.99592 2.10779 +1.77009 2.44971 0 1.28942 +1.15089 0 1.45276 2.19123 +4.39945 2.05012 5.91876 0 +5.2383 4.04745 0 3.03767 +5.33574 0 5.45387 3.47963 +4.68241 0 6.5205 4.68241 +4.1291 3.40754 3.40754 0 +3.16477 2.57936 0 3.16477 +0 1.08005 2.8283 0.509536 +>M01356 ZNF431 lnR0: 7.772 +0 1.54402 0.621848 0.702796 +1.94489 0.493574 0 2.59382 +0 2.60705 0.722976 0.954405 +1.96098 0.0098184 -0.168986 0 +0 2.72974 1.07473 2.55966 +1.89974 0 1.97391 2.48793 +2.0554 0 2.87536 2.21429 +0 3.14371 0.101383 2.5732 +0 4.73074 2.29539 2.51784 +7.38512 0 5.35457 5.29035 +6.38364 0 5.51156 5.17322 +5.15459 3.27455 7.98289 0 +0 5.49127 4.62537 6.94259 +0 7.08633 5.10591 6.9682 +6.99641 5.22631 0 6.67763 +0 3.13719 5.38796 4.85885 +5.25245 0 6.88612 4.71033 +0 7.05702 4.08639 6.93889 +6.66654 7.51442 0 5.0971 +3.77413 7.44212 0 7.32399 +1.47302 0 1.28408 3.21255 +0 3.15008 1.3077 1.53975 +3.16555 0 1.2133 0.654325 diff --git a/conf/igenomes.config b/conf/igenomes.config index 3f11437..757f4bc 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -23,6 +23,7 @@ params { mito_name = "MT" macs_gsize = "2.7e9" blacklist = "${projectDir}/assets/blacklists/GRCh37-blacklist.bed" + pwms = "${projectDir}/assets/PWMs/Jaspar_Hocomoco_Kellis_human_PSEMs.txt" } 'GRCh38' { fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa" @@ -35,6 +36,7 @@ params { mito_name = "chrM" macs_gsize = "2.7e9" blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" + pwms = "${projectDir}/assets/PWMs/Jaspar_Hocomoco_Kellis_human_PSEMs.txt" } 'CHM13' { fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa" @@ -56,6 +58,7 @@ params { mito_name = "MT" macs_gsize = "1.87e9" blacklist = "${projectDir}/assets/blacklists/GRCm38-blacklist.bed" + pwms = "${projectDir}/assets/PWMs/Jaspar_Hocomoco_Kellis_mouse_PSEMs.txt" } 'TAIR10' { fasta = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa" @@ -290,6 +293,7 @@ params { mito_name = "chrM" macs_gsize = "2.7e9" blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" + pwms = "${projectDir}/assets/PWMs/Jaspar_Hocomoco_Kellis_human_PSEMs.txt" } 'hg19' { fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa" @@ -303,6 +307,7 @@ params { mito_name = "chrM" macs_gsize = "2.7e9" blacklist = "${projectDir}/assets/blacklists/hg19-blacklist.bed" + pwms = "${projectDir}/assets/PWMs/Jaspar_Hocomoco_Kellis_human_PSEMs.txt" } 'mm10' { fasta = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa" @@ -316,6 +321,7 @@ params { mito_name = "chrM" macs_gsize = "1.87e9" blacklist = "${projectDir}/assets/blacklists/mm10-blacklist.bed" + pwms = "${projectDir}/assets/PWMs/Jaspar_Hocomoco_Kellis_mouse_PSEMs.txt" } 'bosTau8' { fasta = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa" diff --git a/conf/modules.config b/conf/modules.config index 0a1733b..b666268 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -44,6 +44,7 @@ process { withName: ANNOTATE_SAMPLES { ext.args = {"'{print \$0 \"\\t\" \"${meta.id}\"}'"} + ext.prefix = {"${meta.id}.annotated"} } withName: CONCAT_SAMPLES { diff --git a/main.nf b/main.nf index 3459c57..0c1e1b5 100644 --- a/main.nf +++ b/main.nf @@ -33,6 +33,7 @@ include { PREPARE_GENOME } from './subworkflows/local/prepare_genome' params.fasta = getGenomeAttribute('fasta') params.gtf = getGenomeAttribute('gtf') params.blacklist = getGenomeAttribute('blacklist') +params.pwms = getGenomeAttribute('pwms') /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -52,12 +53,17 @@ workflow NFCORE_TFACTIVITY { ch_versions = Channel.empty() + ch_fasta = Channel.value(file(params.fasta)) + ch_gtf = Channel.value(file(params.gtf)) + ch_blacklist = Channel.value(file(params.blacklist)) + ch_pwms = Channel.value(file(params.pwms)) + // // SUBWORKFLOW: Prepare genome // PREPARE_GENOME ( - params.fasta, - params.gtf + ch_fasta, + ch_gtf ) ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions) @@ -67,9 +73,14 @@ workflow NFCORE_TFACTIVITY { // TFACTIVITY ( samplesheet, - ch_versions, + ch_fasta, + ch_gtf, + ch_blacklist, + ch_pwms, + params.window_size, + params.decay, params.merge_samples, - params.blacklist + ch_versions ) emit: diff --git a/modules/local/stare/main.nf b/modules/local/stare/main.nf new file mode 100644 index 0000000..a02e425 --- /dev/null +++ b/modules/local/stare/main.nf @@ -0,0 +1,31 @@ +process STARE { + tag "$meta.id" + label 'process_high' + + conda "bioconda::stare-abc" + container "biocontainers/stare-abc:1.0.4--haf6292c_1" + + input: + tuple val(meta), path(candidate_regions) + path(fasta) + path(gtf) + path(blacklist) + path(pwms) + val(window_size) + val(decay) + + output: + tuple val(meta), path("${meta.id}/Gene_TF_matrices/${meta.id}_TF_Gene_Affinities.txt"), emit: affinities + path "versions.yml" , emit: versions + + script: + """ + STARE.sh -c ${task.cpus} -a ${gtf} -g ${fasta} -p ${pwms} -b ${candidate_regions} -w ${window_size} -x ${blacklist} -e ${decay} -o ${meta.id} + gzip -fd ${meta.id}/Gene_TF_matrices/${meta.id}_TF_Gene_Affinities.txt.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + STARE: \$( STARE.sh --version ) + END_VERSIONS + """ +} \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 7560eea..29f9b8d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -16,6 +16,8 @@ params { // Pipeline options merge_samples = false min_peak_occurrence = 1 + window_size = 50000 + decay = true // References genome = null diff --git a/nextflow_schema.json b/nextflow_schema.json index 0d95a3f..2d6ce24 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -61,6 +61,20 @@ "description": "Minimum number of samples that a peak has to occur in to keep it while merging.", "fa_icon": "fas fa-compress-arrows-alt", "help_text": "If you have multiple samples with the same condition and assay and use the `--merge_samples` parameter, you can set this parameter to the minimum number of samples that a peak has to occur in to keep it while merging." + }, + "window_size": { + "type": "integer", + "default": 50000, + "description": "Size of the window to search for binding sites.", + "fa_icon": "fas fa-compress-arrows-alt", + "help_text": "Size of the window to search for binding sites. The default value is 50000." + }, + "decay": { + "type": "boolean", + "default": "true", + "description": "Use decay in STARE", + "fa_icon": "fas fa-compress-arrows-alt", + "help_text": "Use decay in STARE. The default value is `true`." } } }, @@ -106,6 +120,16 @@ "help_text": "This parameter is *mandatory* if `--genome` is not specified.", "fa_icon": "far fa-file-code" }, + "pwms": { + "type": "string", + "format": "file-path", + "exists": true, + "mimetype": "text/plain", + "pattern": "^\\S+\\.txt(\\.gz)?$", + "description": "Path to PWMs file.", + "help_text": "This parameter is *mandatory* if `--genome` is not specified.", + "fa_icon": "far fa-file-code" + }, "igenomes_ignore": { "type": "boolean", "description": "Do not load the iGenomes reference config.", diff --git a/subworkflows/local/peaks.nf b/subworkflows/local/peaks.nf index 1d518a6..ec1bd9d 100644 --- a/subworkflows/local/peaks.nf +++ b/subworkflows/local/peaks.nf @@ -2,6 +2,7 @@ include { GAWK as CLEAN_BED } from '../../modules/nf-core/gawk/main' include { BEDTOOLS_SORT as SORT_PEAKS } from '../../modules/nf-core/bedtools/sort/main' include { BEDTOOLS_SUBTRACT as BLACKLIST } from '../../modules/nf-core/bedtools/subtract/main' +include { STARE } from '../../modules/local/stare/main' // Subworkflows include { FOOTPRINTING } from './footprinting' @@ -11,8 +12,13 @@ workflow PEAKS { take: ch_peaks // channel: [ val(meta), [ peaks ] ] - merge_samples + fasta + gtf blacklist + pwms + window_size + decay + merge_samples main: @@ -36,10 +42,15 @@ workflow PEAKS { ch_versions = ch_versions.mix(SORT_PEAKS.out.versions) } - if (blacklist) { - BLACKLIST( ch_peaks.map{ meta, peaks -> [meta, peaks, blacklist] } ) - ch_peaks = BLACKLIST.out.bed - } + STARE( + ch_peaks, + fasta, + gtf, + blacklist, + pwms, + window_size, + decay + ) emit: diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index 51c82b6..d26ef95 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -12,12 +12,12 @@ workflow PREPARE_GENOME { ch_versions = Channel.empty() - ch_fasta = Channel.value([[id: 'fasta'], file(fasta)]) - ch_gtf = Channel.value([[id: 'gtf'], file(gtf)]) + ch_fasta_tuple = fasta.map { fasta -> [[id: 'fasta'], fasta] } + ch_gtf_tuple = gtf.map { gtf -> [[id: 'gtf'], gtf] } // Prepare gene map - EXTRACT_ID_SYMBOL_MAP(ch_gtf, [[], []]) + EXTRACT_ID_SYMBOL_MAP(ch_gtf_tuple, [[], []]) REMOVE_GENE_VERSIONS(EXTRACT_ID_SYMBOL_MAP.out.feature_annotation, []) ch_versions = ch_versions.mix( @@ -25,7 +25,7 @@ workflow PREPARE_GENOME { REMOVE_GENE_VERSIONS.out.versions ) - SAMTOOLS_FAIDX(ch_fasta, [[], []]) + SAMTOOLS_FAIDX(ch_fasta_tuple, [[], []]) ch_versions = ch_versions.mix( SAMTOOLS_FAIDX.out.versions diff --git a/workflows/tfactivity.nf b/workflows/tfactivity.nf index e5f4cd9..047d06c 100644 --- a/workflows/tfactivity.nf +++ b/workflows/tfactivity.nf @@ -23,9 +23,14 @@ workflow TFACTIVITY { take: ch_samplesheet // channel: samplesheet read in from --input - ch_versions - merge_samples + fasta + gtf blacklist + pwms + window_size + decay + merge_samples + ch_versions main: @@ -35,8 +40,13 @@ workflow TFACTIVITY { // ch_versions = ch_versions.mix(FASTQC.out.versions.first()) PEAKS( ch_samplesheet, - merge_samples, - blacklist + fasta, + gtf, + blacklist, + pwms, + window_size, + decay, + merge_samples ) ch_versions = ch_versions.mix(PEAKS.out.versions) From f3d324503f737eca8fc7e2450ace05cbe624dcf8 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 1 Mar 2024 20:54:18 +0100 Subject: [PATCH 011/206] Fix gene symbol map creation --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index b666268..6f49973 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -18,7 +18,7 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] - withName: 'PREPARE_GENOME:EXTRACT_ID_SYMBOL_MAP' { + withName: '.*:PREPARE_GENOME:EXTRACT_ID_SYMBOL_MAP' { ext.args = "-l \"gene_id,gene_name\"" } From f06a311dc9a5f3ecf839c4e6e5064371e8c26890 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 1 Mar 2024 21:23:15 +0100 Subject: [PATCH 012/206] Cleanup --- assets/PWMs/Jaspar_Hocomoco_Kellis_mouse_PSEMs.txt | 4 ++-- conf/modules.config | 6 ------ subworkflows/local/peaks.nf | 9 +++++++++ subworkflows/local/prepare_genome.nf | 10 +++------- 4 files changed, 14 insertions(+), 15 deletions(-) diff --git a/assets/PWMs/Jaspar_Hocomoco_Kellis_mouse_PSEMs.txt b/assets/PWMs/Jaspar_Hocomoco_Kellis_mouse_PSEMs.txt index 21d26dc..32ac37d 100644 --- a/assets/PWMs/Jaspar_Hocomoco_Kellis_mouse_PSEMs.txt +++ b/assets/PWMs/Jaspar_Hocomoco_Kellis_mouse_PSEMs.txt @@ -13,7 +13,7 @@ 5.00118 4.54008 0 4.01097 4.59839 4.13729 4.13729 0 5.0595 4.59839 0 5.0595 ->MA0009.1 TBXT lnR0: 0.764 +>MA0009.1 TBXT(MA0009.1) lnR0: 0.764 3.70208 0 1.67153 3.70208 4.24345 3.78234 4.77255 0 0 4.844 4.844 5.3051 @@ -5593,7 +5593,7 @@ 0 0.784889 1.49609 1.3326 0 0.878532 0.351887 1.23993 0 1.59853 0.345775 1.7867 ->M01026 TBXT lnR0: 8.94 +>M01026 TBXT(M01026) lnR0: 8.94 1.40118 1.13608 0.817305 0 3.0068 2.87366 2.21961 0 3.77574 3.39629 0.276195 0 diff --git a/conf/modules.config b/conf/modules.config index 6f49973..1fc54e8 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -22,12 +22,6 @@ process { ext.args = "-l \"gene_id,gene_name\"" } - withName: REMOVE_GENE_VERSIONS { - ext.args = {"'{sub(/\\.[0-9]+/, \"\", \$1); print \$1 \"\t\" \$2}'"} - ext.prefix = {"${meta.id}.no_version"} - ext.suffix = "tsv" - } - withName: CLEAN_BED { ext.args = {"'{print \$1 \"\\t\" \$2 \"\\t\" \$3}'"} ext.prefix = {"${meta.id}.clean"} diff --git a/subworkflows/local/peaks.nf b/subworkflows/local/peaks.nf index ec1bd9d..86a0260 100644 --- a/subworkflows/local/peaks.nf +++ b/subworkflows/local/peaks.nf @@ -32,6 +32,11 @@ workflow PEAKS { ch_peaks = FOOTPRINTING.out.footprinted_peaks + ch_versions = ch_versions.mix( + CLEAN_BED.out.versions, + FOOTPRINTING.out.versions + ) + if (merge_samples) { MERGE_SAMPLES(ch_peaks) ch_peaks = MERGE_SAMPLES.out.merged @@ -52,6 +57,10 @@ workflow PEAKS { decay ) + ch_versions = ch_versions.mix( + STARE.out.versions + ) + emit: versions = ch_versions // channel: [ versions.yml ] diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index d26ef95..5bf6bd2 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -1,5 +1,4 @@ include { ATLASGENEANNOTATIONMANIPULATION_GTF2FEATUREANNOTATION as EXTRACT_ID_SYMBOL_MAP } from '../../modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/main.nf' -include { GAWK as REMOVE_GENE_VERSIONS } from '../../modules/nf-core/gawk/main' include { SAMTOOLS_FAIDX } from '../../modules/nf-core/samtools/faidx/main' workflow PREPARE_GENOME { @@ -18,21 +17,18 @@ workflow PREPARE_GENOME { // Prepare gene map EXTRACT_ID_SYMBOL_MAP(ch_gtf_tuple, [[], []]) - REMOVE_GENE_VERSIONS(EXTRACT_ID_SYMBOL_MAP.out.feature_annotation, []) - ch_versions = ch_versions.mix( - EXTRACT_ID_SYMBOL_MAP.out.versions, - REMOVE_GENE_VERSIONS.out.versions - ) + // Prepare fasta index SAMTOOLS_FAIDX(ch_fasta_tuple, [[], []]) ch_versions = ch_versions.mix( + EXTRACT_ID_SYMBOL_MAP.out.versions, SAMTOOLS_FAIDX.out.versions ) emit: - gene_map = REMOVE_GENE_VERSIONS.out.output + gene_map = EXTRACT_ID_SYMBOL_MAP.out.feature_annotation fai = SAMTOOLS_FAIDX.out.fai versions = ch_versions // channel: [ versions.yml ] From a5d56dcb8cea0c6820d1598474456a10863f48a2 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 1 Mar 2024 21:34:57 +0100 Subject: [PATCH 013/206] Implement affinity mean calculation --- bin/combine_tables.py | 71 ++++++++++++++++++++++++++++ modules/local/combine_tables/main.nf | 31 ++++++++++++ subworkflows/local/peaks.nf | 17 +++++++ 3 files changed, 119 insertions(+) create mode 100755 bin/combine_tables.py create mode 100644 modules/local/combine_tables/main.nf diff --git a/bin/combine_tables.py b/bin/combine_tables.py new file mode 100755 index 0000000..a29c987 --- /dev/null +++ b/bin/combine_tables.py @@ -0,0 +1,71 @@ +#!/usr/bin/env python3 + +import argparse +import numpy as np +import pandas as pd + +# Define the command-line arguments +parser = argparse.ArgumentParser(description="Calculate statistics between two multiple files.") +parser.add_argument("-i", "--input", type=str, nargs='+', help="List of input file paths", required=True) +parser.add_argument("-o", "--output", type=str, help="Output file path", required=True) +parser.add_argument("-m", "--method", type=str, choices=["mean", "sum", "ratio"], default="mean", help="Calculation method (mean, sum, ratio)") +args = parser.parse_args() + +# Check if input and output paths are provided +if not args.input or not args.output: + parser.error("Input and output paths are required.") + +# Read all input files into a list of dataframes +dfs = [pd.read_csv(file, sep='\t', index_col=0) for file in args.input] + +if args.method == "sum": + index_union = dfs[0].index + for df in dfs[1:]: + index_union = index_union.union(df.index) + + # Add NA values for missing rows + dfs = [df.reindex(index_union) for df in dfs] +else: + index_intersection = dfs[0].index + for df in dfs[1:]: + index_intersection = index_intersection.intersection(df.index) + + print(f"Number of rows in intersection: {len(index_intersection)}") + # Keep row indices which are available in all dataframes + dfs = [df.loc[index_intersection] for df in dfs] + +# Check if all dataframes have the same dimensions +if not all(df.shape == dfs[0].shape for df in dfs): + raise ValueError(f"The input files must have the same dimensions. Got: {[df.shape for df in dfs]}") + +# Check if all dataframes have the same row names +if not all(df.index.equals(dfs[0].index) for df in dfs): + raise ValueError("The input files must have the same row names.") + +# Check if all dataframes have the same column names +if not all(df.columns.equals(dfs[0].columns) for df in dfs): + raise ValueError("The input files must have the same column names.") + +# Calculate the selected statistic +if args.method == "mean": + result = sum(dfs) / len(dfs) +elif args.method == "sum": + result = sum(dfs) +elif args.method == "ratio": + if len(dfs) != 2: + raise ValueError("The ratio method requires exactly two input files.") + + # Replace 0 values with minimal existing float value + dfs[1] = dfs[1].replace(0, np.finfo(float).eps) + + result = dfs[0] / dfs[1] + + print(f"Number of rows before dropping NA or inf values: {len(result)}") + + # Drop rows with NA or inf values (requirement for DYNAMITE) + result = result.replace([np.inf, -np.inf], np.nan).dropna() + + print(f"Number of rows after dropping NA or inf values: {len(result)}") + +# Write the result to a file +result.to_csv(args.output, sep='\t', index=True, quoting=0) \ No newline at end of file diff --git a/modules/local/combine_tables/main.nf b/modules/local/combine_tables/main.nf new file mode 100644 index 0000000..d93ab5d --- /dev/null +++ b/modules/local/combine_tables/main.nf @@ -0,0 +1,31 @@ +process COMBINE_TABLES { + tag "$meta.id" + label 'process_single' + + conda "conda-forge::mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6==fccb0c41a243c639e11dd1be7b74f563e624fcca-0" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0': + 'biocontainers/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0' }" + + input: + tuple val(meta), path(files) + val(method) + + output: + tuple val(meta), path("${prefix}.${extension}"), emit: combined + path "versions.yml" , emit: versions + + script: + prefix = task.ext.prefix ?: "${meta.id}" + extension = task.ext.extension ?: "tsv" + """ + combine_tables.py --input ${files} --method ${method} --output ${prefix}.${extension} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + python: \$(python --version | sed 's/Python //g') + pandas: \$(python -c "import pandas; print(pandas.__version__)") + numpy: \$(python -c "import numpy; print(numpy.__version__)") + END_VERSIONS + """ +} \ No newline at end of file diff --git a/subworkflows/local/peaks.nf b/subworkflows/local/peaks.nf index 86a0260..4418acf 100644 --- a/subworkflows/local/peaks.nf +++ b/subworkflows/local/peaks.nf @@ -3,6 +3,7 @@ include { GAWK as CLEAN_BED } from '../../modules/nf-core/gawk/mai include { BEDTOOLS_SORT as SORT_PEAKS } from '../../modules/nf-core/bedtools/sort/main' include { BEDTOOLS_SUBTRACT as BLACKLIST } from '../../modules/nf-core/bedtools/subtract/main' include { STARE } from '../../modules/local/stare/main' +include { COMBINE_TABLES as AFFINITY_MEAN } from '../../modules/local/combine_tables/main' // Subworkflows include { FOOTPRINTING } from './footprinting' @@ -57,6 +58,22 @@ workflow PEAKS { decay ) + ch_affinities = STARE.out.affinities + + if (!merge_samples) { + AFFINITY_MEAN(ch_affinities + .map { meta, affinities -> [meta.condition, meta.assay, affinities] } + .groupTuple(by: [0, 1]) + .map { condition, assay, affinities -> [[id: condition + "_" + assay, + condition: condition, + assay: assay], affinities] }, + "mean" + ) + + ch_affinities = AFFINITY_MEAN.out.combined + ch_versions = ch_versions.mix(AFFINITY_MEAN.out.versions) + } + ch_versions = ch_versions.mix( STARE.out.versions ) From ef78b0059a5dd4f5300ee60c6324320023a4d08a Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 1 Mar 2024 21:51:12 +0100 Subject: [PATCH 014/206] Implement calculation of affinity ratios --- subworkflows/local/peaks.nf | 21 ++++++++++++++++++++- workflows/tfactivity.nf | 10 +++++++++- 2 files changed, 29 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/peaks.nf b/subworkflows/local/peaks.nf index 4418acf..6d9540d 100644 --- a/subworkflows/local/peaks.nf +++ b/subworkflows/local/peaks.nf @@ -4,6 +4,7 @@ include { BEDTOOLS_SORT as SORT_PEAKS } from '../../modules/nf-core/bedtools include { BEDTOOLS_SUBTRACT as BLACKLIST } from '../../modules/nf-core/bedtools/subtract/main' include { STARE } from '../../modules/local/stare/main' include { COMBINE_TABLES as AFFINITY_MEAN } from '../../modules/local/combine_tables/main' +include { COMBINE_TABLES as AFFINITY_RATIO} from '../../modules/local/combine_tables/main' // Subworkflows include { FOOTPRINTING } from './footprinting' @@ -20,6 +21,7 @@ workflow PEAKS { window_size decay merge_samples + contrasts main: @@ -74,11 +76,28 @@ workflow PEAKS { ch_versions = ch_versions.mix(AFFINITY_MEAN.out.versions) } + ch_affinities_spread = ch_affinities + .map { meta, affinities -> [meta.condition, meta.assay, affinities] } + + ch_contrast_affinities = contrasts + .map {condition1, condition2 -> [condition2, condition1]} + .combine(ch_affinities_spread, by: 0) + .map {condition2, condition1, assay2, affinities2 -> [condition1, condition2, assay2, affinities2] } + .combine(ch_affinities_spread, by: 0) + .map {condition1, condition2, assay2, affinities2, assay1, affinities1 -> [condition1, condition2, assay1, affinities1, assay2, affinities2] } + .filter {condition1, condition2, assay1, affinities1, assay2, affinities2 -> assay1 == assay2} + .map {condition1, condition2, assay1, affinities1, assay2, affinities2 -> [condition1 + ":" + condition2, assay1, [affinities1, affinities2]] } + .map {contrast, assay, affinities -> [[id: contrast + "_" + assay, contrast: contrast, assay: assay], affinities] } + + AFFINITY_RATIO(ch_contrast_affinities, "ratio") + ch_versions = ch_versions.mix( - STARE.out.versions + STARE.out.versions, + AFFINITY_RATIO.out.versions, ) emit: + affinity_ratio = AFFINITY_RATIO.out.combined versions = ch_versions // channel: [ versions.yml ] } diff --git a/workflows/tfactivity.nf b/workflows/tfactivity.nf index 047d06c..b820957 100644 --- a/workflows/tfactivity.nf +++ b/workflows/tfactivity.nf @@ -38,6 +38,13 @@ workflow TFACTIVITY { // ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}) // ch_versions = ch_versions.mix(FASTQC.out.versions.first()) + + ch_conditions = ch_samplesheet.map { meta, peak_file -> meta.condition } + .toSortedList().flatten().unique() + + ch_contrasts = ch_conditions.combine(ch_conditions) + .filter { condition1, condition2 -> condition1 < condition2 } + PEAKS( ch_samplesheet, fasta, @@ -46,7 +53,8 @@ workflow TFACTIVITY { pwms, window_size, decay, - merge_samples + merge_samples, + ch_contrasts ) ch_versions = ch_versions.mix(PEAKS.out.versions) From 3c8438f3d913ffaee122c1aa392bcb7fcd2d7088 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 2 Mar 2024 08:54:45 +0100 Subject: [PATCH 015/206] Implement gene length extraction --- modules/local/gtftools/length/main.nf | 49 +++++++++++++++++++++++++++ subworkflows/local/prepare_genome.nf | 3 ++ 2 files changed, 52 insertions(+) create mode 100644 modules/local/gtftools/length/main.nf diff --git a/modules/local/gtftools/length/main.nf b/modules/local/gtftools/length/main.nf new file mode 100644 index 0000000..57333c1 --- /dev/null +++ b/modules/local/gtftools/length/main.nf @@ -0,0 +1,49 @@ +process GTFTOOLS_LENGTH { + tag "$meta.id" + label 'process_single' + + conda "bioconda:gtftools=0.9.0-0" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gtftools:0.9.0--pyh5e36f6f_0': + 'biocontainers/gtftools:0.9.0--pyh5e36f6f_0' }" + + input: + tuple val(meta), path(gtf) + + output: + tuple val(meta), path("${prefix}.${suffix}"), emit: lengths + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + prefix = task.ext.prefix ?: "${meta.id}" + suffix = task.ext.suffix ?: "txt" + """ + gtftools \\ + -l ${prefix}.${suffix} \\ + $gtf + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gtftools: \$(gtftools -v | sed 's/GTFtools version://') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + + // TODO nf-core: A stub section should mimic the execution of the original module as best as possible + // Have a look at the following examples: + // Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63 + // Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54 + """ + touch ${prefix}.${suffix} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gtftools: \$(gtftools -v | sed 's/GTFtools version://') + END_VERSIONS + """ +} diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index 5bf6bd2..55c85f6 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -1,4 +1,5 @@ include { ATLASGENEANNOTATIONMANIPULATION_GTF2FEATUREANNOTATION as EXTRACT_ID_SYMBOL_MAP } from '../../modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/main.nf' +include { GTFTOOLS_LENGTH } from '../../modules/local/gtftools/length/main' include { SAMTOOLS_FAIDX } from '../../modules/nf-core/samtools/faidx/main' workflow PREPARE_GENOME { @@ -17,6 +18,7 @@ workflow PREPARE_GENOME { // Prepare gene map EXTRACT_ID_SYMBOL_MAP(ch_gtf_tuple, [[], []]) + GTFTOOLS_LENGTH(ch_gtf_tuple) // Prepare fasta index @@ -29,6 +31,7 @@ workflow PREPARE_GENOME { emit: gene_map = EXTRACT_ID_SYMBOL_MAP.out.feature_annotation + gene_lengths = GTFTOOLS_LENGTH.out.lengths fai = SAMTOOLS_FAIDX.out.fai versions = ch_versions // channel: [ versions.yml ] From 95296817e3e40d907911a8ca2aa8c405139a8051 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 2 Mar 2024 12:04:16 +0100 Subject: [PATCH 016/206] Implement count merging --- assets/schema_counts_design.json | 38 +++++++++++++++++++++++++++ bin/combine_counts.py | 44 ++++++++++++++++++++++++++++++++ main.nf | 5 ++++ modules/local/counts/combine.nf | 29 +++++++++++++++++++++ nextflow.config | 2 ++ nextflow_schema.json | 21 +++++++++++++++ subworkflows/local/counts.nf | 31 ++++++++++++++++++++++ workflows/tfactivity.nf | 10 ++++++++ 8 files changed, 180 insertions(+) create mode 100644 assets/schema_counts_design.json create mode 100755 bin/combine_counts.py create mode 100644 modules/local/counts/combine.nf create mode 100644 subworkflows/local/counts.nf diff --git a/assets/schema_counts_design.json b/assets/schema_counts_design.json new file mode 100644 index 0000000..6d656f3 --- /dev/null +++ b/assets/schema_counts_design.json @@ -0,0 +1,38 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema", + "$id": "https://raw.githubusercontent.com/nf-core/tfactivity/master/assets/schema_counts_design.json", + "title": "nf-core/tfactivity pipeline - params.counts_design schema", + "description": "Schema for the file provided with params.counts_design", + "type": "array", + "items": { + "type": "object", + "properties": { + "sample": { + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "Sample name must be provided and cannot contain spaces", + "meta": ["id"] + }, + "condition": { + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "Condition name must be provided and cannot contain spaces", + "meta": ["condition"] + }, + "batch": { + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "Batch identifier cannot contain spaces", + "meta": ["batch"] + }, + "counts_file": { + "type": "string", + "format": "file-path", + "exists": true, + "pattern": "^\\S+\\.(csv|txt)$", + "errorMessage": "Counts file must be a .csv or .txt file" + } + }, + "required": ["sample", "condition"] + } +} diff --git a/bin/combine_counts.py b/bin/combine_counts.py new file mode 100755 index 0000000..120ce1e --- /dev/null +++ b/bin/combine_counts.py @@ -0,0 +1,44 @@ +#!/usr/bin/env python3 + +import pandas as pd +import argparse +import os + +parser = argparse.ArgumentParser(description="Create dataframe from count matrix and metadata") +parser.add_argument("--counts", type=str, help="Path to counts") +parser.add_argument("--metadata", type=str, help="Path to metadata") +parser.add_argument("--output", type=str, help="Path to output file") +args = parser.parse_args() + +metadata = pd.read_csv(args.metadata, index_col=0, header=0) + +if not os.path.exists(args.counts): + raise Exception("Counts input does not exist") + +if not os.path.isfile(args.counts): + raise Exception("Counts input is not a file") + +counts = pd.read_csv(args.counts, index_col=0, sep="\t", header=None) + +# If counts has no columns, add index name +if len(counts.columns) == 0: + counts.index.name = "gene_id" +else: + # Set first row as column names + counts.columns = counts.iloc[0] + # Remove first row + counts = counts.iloc[1:] + +for index, row in metadata.iterrows(): + if row["counts_file"]: + sample_df = pd.read_csv(row["counts_file"], header=None) + sample_counts = sample_df[0].to_list() + counts[index] = sample_counts + +samples = metadata.index.to_list() + +if not all([sample in counts.columns for sample in samples]): + raise Exception("Not all samples are in the counts matrix") + +counts.to_csv(args.output, sep="\t") +counts.index.to_series().to_csv("genes.txt", index=False, header=False) \ No newline at end of file diff --git a/main.nf b/main.nf index 0c1e1b5..af4dc25 100644 --- a/main.nf +++ b/main.nf @@ -57,6 +57,8 @@ workflow NFCORE_TFACTIVITY { ch_gtf = Channel.value(file(params.gtf)) ch_blacklist = Channel.value(file(params.blacklist)) ch_pwms = Channel.value(file(params.pwms)) + ch_counts = Channel.value(file(params.counts)) + ch_counts_design = Channel.value(file(params.counts_design)) // // SUBWORKFLOW: Prepare genome @@ -77,6 +79,9 @@ workflow NFCORE_TFACTIVITY { ch_gtf, ch_blacklist, ch_pwms, + PREPARE_GENOME.out.gene_lengths, + ch_counts, + ch_counts_design, params.window_size, params.decay, params.merge_samples, diff --git a/modules/local/counts/combine.nf b/modules/local/counts/combine.nf new file mode 100644 index 0000000..ccb6f96 --- /dev/null +++ b/modules/local/counts/combine.nf @@ -0,0 +1,29 @@ +process COMBINE_COUNTS { + tag "$meta.id" + label "process_low" + + conda "conda-forge::mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6==fccb0c41a243c639e11dd1be7b74f563e624fcca-0" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0': + 'biocontainers/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0' }" + + input: + tuple val(meta), path(counts), path(design) + path(extra_counts) + + output: + tuple val(meta), path("*.clean.tsv"), emit: counts + tuple val(meta), path("genes.txt") , emit: genes + path "versions.yml" , emit: versions + + script: + """ + combine_counts.py --counts ${counts} --metadata ${design} --output ${meta.id}.clean.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + python: \$(python --version | sed 's/Python //g') + pandas: \$(python -c "import pandas; print(pandas.__version__)") + END_VERSIONS + """ +} \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 29f9b8d..eabeff0 100644 --- a/nextflow.config +++ b/nextflow.config @@ -12,6 +12,8 @@ params { // TODO nf-core: Specify your pipeline's command line flags // Input options input = null + counts = null + counts_design = null // Pipeline options merge_samples = false diff --git a/nextflow_schema.json b/nextflow_schema.json index 2d6ce24..24572ac 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -23,6 +23,27 @@ "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/tfactivity/usage#samplesheet-input).", "fa_icon": "fas fa-file-csv" }, + "counts": { + "type": "string", + "format": "file-path", + "exists": true, + "mimetype": "text/csv", + "pattern": "^\\S+\\.(csv|txt)$", + "description": "Path to comma-separated file containing the counts for the samples in the experiment. Can also be a file containing just gene identifiers. In this case, count values need to be referenced in the counts_design file.", + "help_text": "You will need to create a counts file with the counts for the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with a header row. See [usage docs](https://nf-co.re/tfactivity/usage#counts-input).", + "fa_icon": "fas fa-file-csv" + }, + "counts_design": { + "type": "string", + "format": "file-path", + "exists": true, + "schema": "assets/schema_counts_design.json", + "mimetype": "text/csv", + "pattern": "^\\S+\\.csv$", + "description": "Path to comma-separated file containing information about the counts file.", + "help_text": "You will need to create a counts design file with information about the counts file in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/tfactivity/usage#counts-design-input).", + "fa_icon": "fas fa-file-csv" + }, "outdir": { "type": "string", "format": "directory-path", diff --git a/subworkflows/local/counts.nf b/subworkflows/local/counts.nf new file mode 100644 index 0000000..1edfecf --- /dev/null +++ b/subworkflows/local/counts.nf @@ -0,0 +1,31 @@ +include { COMBINE_COUNTS } from "../../modules/local/counts/combine" + +workflow COUNTS { + + take: + ch_gene_lengths + ch_counts + ch_counts_design + + main: + + ch_versions = Channel.empty() + + ch_extra_counts = ch_counts_design.splitCsv(header:true) + .filter{it["counts_file"]} + .map{it["counts_file"]}.collect() + + COMBINE_COUNTS( + ch_counts.combine(ch_counts_design).map{counts, design -> [[id: "counts"], counts, design]}, + ch_extra_counts + ) + + ch_combined_counts = COMBINE_COUNTS.out.counts + + versions = ch_versions.mix(COMBINE_COUNTS.out.versions) + + emit: + genes = COMBINE_COUNTS.out.genes + + versions = ch_versions // channel: [ versions.yml ] +} diff --git a/workflows/tfactivity.nf b/workflows/tfactivity.nf index b820957..baf209a 100644 --- a/workflows/tfactivity.nf +++ b/workflows/tfactivity.nf @@ -11,6 +11,7 @@ include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pi include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_tfactivity_pipeline' include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome' +include { COUNTS } from '../subworkflows/local/counts' include { PEAKS } from '../subworkflows/local/peaks' /* @@ -27,6 +28,9 @@ workflow TFACTIVITY { gtf blacklist pwms + gene_lengths + counts + counts_design window_size decay merge_samples @@ -45,6 +49,12 @@ workflow TFACTIVITY { ch_contrasts = ch_conditions.combine(ch_conditions) .filter { condition1, condition2 -> condition1 < condition2 } + COUNTS( + gene_lengths, + counts, + counts_design + ) + PEAKS( ch_samplesheet, fasta, From d52d58f72e74b0d1f46525b8d631b2b1ed097a83 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 2 Mar 2024 12:08:11 +0100 Subject: [PATCH 017/206] Add version capture of counts subworkflow --- workflows/tfactivity.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/tfactivity.nf b/workflows/tfactivity.nf index baf209a..23089cc 100644 --- a/workflows/tfactivity.nf +++ b/workflows/tfactivity.nf @@ -67,7 +67,7 @@ workflow TFACTIVITY { ch_contrasts ) - ch_versions = ch_versions.mix(PEAKS.out.versions) + ch_versions = ch_versions.mix(COUNTS.out.versions, PEAKS.out.versions) // // Collate and save software versions From 495bd9b6808ab587ea7f40c3227e9cbffc20f324 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 2 Mar 2024 13:47:18 +0100 Subject: [PATCH 018/206] Implement TPM calculation --- bin/calculate_tpm.py | 33 +++++++++++++++++++++++++++ bin/combine_counts.py | 15 ++++++++++++ main.nf | 1 + modules/local/counts/calculate_tpm.nf | 30 ++++++++++++++++++++++++ modules/local/counts/combine.nf | 3 ++- subworkflows/local/counts.nf | 10 +++++++- workflows/tfactivity.nf | 2 ++ 7 files changed, 92 insertions(+), 2 deletions(-) create mode 100755 bin/calculate_tpm.py create mode 100644 modules/local/counts/calculate_tpm.nf diff --git a/bin/calculate_tpm.py b/bin/calculate_tpm.py new file mode 100755 index 0000000..7102aef --- /dev/null +++ b/bin/calculate_tpm.py @@ -0,0 +1,33 @@ +#!/usr/bin/env python3 + +import pandas as pd +import argparse + +parser = argparse.ArgumentParser(description="Calculate TPM from count matrix and length information") +parser.add_argument("--counts", type=str, help="Path to counts") +parser.add_argument("--lengths", type=str, help="Path to gene lengths") +parser.add_argument("--output", type=str, help="Path to output file") +args = parser.parse_args() + +df_counts = pd.read_csv(args.counts, index_col=0, header=0, sep="\t") +df_lengths = pd.read_csv(args.lengths, index_col=0, header=0, sep="\t", usecols=["gene", "merged"]) +df_lengths.columns = ["length"] + +def remove_version(gene_id): + return gene_id.split(".")[0] + +df_lengths.index = df_lengths.index.map(remove_version) + +# Mean length for each gene (in kb) +df_lengths = df_lengths / 1e3 +df_lengths = df_lengths.groupby(df_lengths.index).mean() + +df_lengths = df_lengths.loc[df_counts.index] + +# Calculate TPM +df_rpk = df_counts.div(df_lengths["length"], axis=0) +df_scale = df_rpk.sum() / 1e6 +df_tpm = df_rpk.div(df_scale, axis=1) + +# Save to file +df_tpm.to_csv(args.output, sep="\t") \ No newline at end of file diff --git a/bin/combine_counts.py b/bin/combine_counts.py index 120ce1e..d4c31b6 100755 --- a/bin/combine_counts.py +++ b/bin/combine_counts.py @@ -7,10 +7,15 @@ parser = argparse.ArgumentParser(description="Create dataframe from count matrix and metadata") parser.add_argument("--counts", type=str, help="Path to counts") parser.add_argument("--metadata", type=str, help="Path to metadata") +parser.add_argument("--genes", type=str, help="Path to genes to include") parser.add_argument("--output", type=str, help="Path to output file") args = parser.parse_args() metadata = pd.read_csv(args.metadata, index_col=0, header=0) +df_genes = pd.read_csv(args.genes, sep="\t", index_col=0) + +def remove_version(gene_id): + return gene_id.split(".")[0] if not os.path.exists(args.counts): raise Exception("Counts input does not exist") @@ -40,5 +45,15 @@ if not all([sample in counts.columns for sample in samples]): raise Exception("Not all samples are in the counts matrix") +df_genes.index = df_genes.index.map(remove_version) +counts.index = counts.index.map(remove_version) + +counts = counts.groupby(counts.index).sum() + +gene_intersect = df_genes.index.intersection(counts.index) + +df_genes = df_genes.loc[gene_intersect] +counts = counts.loc[gene_intersect] + counts.to_csv(args.output, sep="\t") counts.index.to_series().to_csv("genes.txt", index=False, header=False) \ No newline at end of file diff --git a/main.nf b/main.nf index af4dc25..3c8f0e3 100644 --- a/main.nf +++ b/main.nf @@ -80,6 +80,7 @@ workflow NFCORE_TFACTIVITY { ch_blacklist, ch_pwms, PREPARE_GENOME.out.gene_lengths, + PREPARE_GENOME.out.gene_map, ch_counts, ch_counts_design, params.window_size, diff --git a/modules/local/counts/calculate_tpm.nf b/modules/local/counts/calculate_tpm.nf new file mode 100644 index 0000000..d5e567c --- /dev/null +++ b/modules/local/counts/calculate_tpm.nf @@ -0,0 +1,30 @@ +process CALCULATE_TPM { + tag "$meta.id" + label "process_low" + + conda "conda-forge::mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6==fccb0c41a243c639e11dd1be7b74f563e624fcca-0" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0': + 'biocontainers/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0' }" + + input: + tuple val(meta), path(counts) + tuple val(meta2), path(lengths) + + output: + tuple val(meta), path("*.tpm.tsv"), emit: tpm + + path "versions.yml" , emit: versions + + script: + """ + calculate_tpm.py --counts ${counts} --lengths ${lengths} --output ${meta.id}.tpm.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + python: \$(python --version | sed 's/Python //g') + pandas: \$(python -c "import pandas; print(pandas.__version__)") + numpy: \$(python -c "import numpy; print(numpy.__version__)") + END_VERSIONS + """ +} \ No newline at end of file diff --git a/modules/local/counts/combine.nf b/modules/local/counts/combine.nf index ccb6f96..aaf7c06 100644 --- a/modules/local/counts/combine.nf +++ b/modules/local/counts/combine.nf @@ -10,6 +10,7 @@ process COMBINE_COUNTS { input: tuple val(meta), path(counts), path(design) path(extra_counts) + tuple val(meta2), path(gene_map) output: tuple val(meta), path("*.clean.tsv"), emit: counts @@ -18,7 +19,7 @@ process COMBINE_COUNTS { script: """ - combine_counts.py --counts ${counts} --metadata ${design} --output ${meta.id}.clean.tsv + combine_counts.py --counts ${counts} --genes ${gene_map} --metadata ${design} --output ${meta.id}.clean.tsv cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/subworkflows/local/counts.nf b/subworkflows/local/counts.nf index 1edfecf..6f17075 100644 --- a/subworkflows/local/counts.nf +++ b/subworkflows/local/counts.nf @@ -1,9 +1,11 @@ include { COMBINE_COUNTS } from "../../modules/local/counts/combine" +include { CALCULATE_TPM } from "../../modules/local/counts/calculate_tpm" workflow COUNTS { take: ch_gene_lengths + gene_map ch_counts ch_counts_design @@ -17,7 +19,13 @@ workflow COUNTS { COMBINE_COUNTS( ch_counts.combine(ch_counts_design).map{counts, design -> [[id: "counts"], counts, design]}, - ch_extra_counts + ch_extra_counts, + gene_map + ) + + CALCULATE_TPM( + COMBINE_COUNTS.out.counts, + ch_gene_lengths ) ch_combined_counts = COMBINE_COUNTS.out.counts diff --git a/workflows/tfactivity.nf b/workflows/tfactivity.nf index 23089cc..aac23fd 100644 --- a/workflows/tfactivity.nf +++ b/workflows/tfactivity.nf @@ -29,6 +29,7 @@ workflow TFACTIVITY { blacklist pwms gene_lengths + gene_map counts counts_design window_size @@ -51,6 +52,7 @@ workflow TFACTIVITY { COUNTS( gene_lengths, + gene_map, counts, counts_design ) From ccdb8108981ead9fbc213df9140e47f9c4e3cb3f Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 2 Mar 2024 14:07:04 +0100 Subject: [PATCH 019/206] Implement count and TPM filtering --- bin/filter_genes.py | 38 +++++++++++++++++++++++++++ main.nf | 2 ++ modules/local/counts/filter_genes.nf | 39 ++++++++++++++++++++++++++++ nextflow.config | 2 ++ nextflow_schema.json | 14 ++++++++++ subworkflows/local/counts.nf | 16 ++++++++++-- workflows/tfactivity.nf | 6 ++++- 7 files changed, 114 insertions(+), 3 deletions(-) create mode 100755 bin/filter_genes.py create mode 100644 modules/local/counts/filter_genes.nf diff --git a/bin/filter_genes.py b/bin/filter_genes.py new file mode 100755 index 0000000..ae59ed4 --- /dev/null +++ b/bin/filter_genes.py @@ -0,0 +1,38 @@ +#!/usr/bin/env python3 + +import argparse +import pandas as pd + +# Define the command-line arguments +parser = argparse.ArgumentParser(description="Filter genes based on raw counts and TPM values.") +parser.add_argument("--counts", type=str, help="Path to counts") +parser.add_argument("--tpms", type=str, help="Path to TPM values") +parser.add_argument("--min_count", type=int, default=10, help="Minimum count value") +parser.add_argument("--min_tpm", type=float, default=1, help="Minimum TPM value") +parser.add_argument("--counts_output", type=str, help="Path to output counts") +parser.add_argument("--tpms_output", type=str, help="Path to output TPM values") +parser.add_argument("--genes_output", type=str, help="Path to output gene list") +args = parser.parse_args() + +# Read the input files +df_counts = pd.read_csv(args.counts, index_col=0, header=0, sep="\t") +df_tpms = pd.read_csv(args.tpms, index_col=0, header=0, sep="\t") + +# Filter based on sum of raw counts +df_counts = df_counts[df_counts.sum(axis=1) >= args.min_count] + +# Filter based on average TPM value +df_tpms = df_tpms[df_tpms.mean(axis=1) >= args.min_tpm] + +gene_intersection = df_counts.index.intersection(df_tpms.index) + +# Subset the dataframes +df_counts = df_counts.loc[gene_intersection] +df_tpms = df_tpms.loc[gene_intersection] + +# Write the output files +df_counts.to_csv(args.counts_output, sep="\t") +df_tpms.to_csv(args.tpms_output, sep="\t") + +with open(args.genes_output, "w") as f: + f.write("\n".join(gene_intersection)) \ No newline at end of file diff --git a/main.nf b/main.nf index 3c8f0e3..316cfdf 100644 --- a/main.nf +++ b/main.nf @@ -86,6 +86,8 @@ workflow NFCORE_TFACTIVITY { params.window_size, params.decay, params.merge_samples, + params.min_count, + params.min_tpm, ch_versions ) diff --git a/modules/local/counts/filter_genes.nf b/modules/local/counts/filter_genes.nf new file mode 100644 index 0000000..9b1a6fd --- /dev/null +++ b/modules/local/counts/filter_genes.nf @@ -0,0 +1,39 @@ +process FILTER_GENES { + tag "$meta.id" + label "process_low" + + conda "conda-forge::mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6==fccb0c41a243c639e11dd1be7b74f563e624fcca-0" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0': + 'biocontainers/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0' }" + + input: + tuple val(meta), path(counts) + tuple val(meta2), path(tpms) + val(min_count) + val(min_tpm) + + output: + tuple val(meta), path("*.counts_filtered.tsv") , emit: counts + tuple val(meta), path("*.tpm_filtered.tsv") , emit: tpms + tuple val(meta), path("*.genes_filtered.txt") , emit: genes + + path "versions.yml" , emit: versions + + script: + """ + filter_genes.py --counts ${counts} \\ + --tpms ${tpms} \\ + --min_count ${min_count} \\ + --min_tpm ${min_tpm} \\ + --counts_output ${meta.id}.counts_filtered.tsv \\ + --tpms_output ${meta.id}.tpm_filtered.tsv \\ + --genes_output ${meta.id}.genes_filtered.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + python: \$(python --version | sed 's/Python //g') + pandas: \$(python -c "import pandas; print(pandas.__version__)") + END_VERSIONS + """ +} \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index eabeff0..eb7260e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -20,6 +20,8 @@ params { min_peak_occurrence = 1 window_size = 50000 decay = true + min_count = 50 + min_tpm = 0 // References genome = null diff --git a/nextflow_schema.json b/nextflow_schema.json index 24572ac..5b3e7a3 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -96,6 +96,20 @@ "description": "Use decay in STARE", "fa_icon": "fas fa-compress-arrows-alt", "help_text": "Use decay in STARE. The default value is `true`." + }, + "min_count": { + "type": "integer", + "default": 50, + "description": "Minimum number of total counts to keep a gene in the analysis.", + "fa_icon": "fas fa-compress-arrows-alt", + "help_text": "Minimum number of total counts to keep a gene in the analysis. The default value is 50." + }, + "min_tpm": { + "type": "number", + "default": 0, + "description": "Minimum TPM to keep a gene in the analysis.", + "fa_icon": "fas fa-compress-arrows-alt", + "help_text": "Minimum TPM to keep a gene in the analysis. The default value is 0." } } }, diff --git a/subworkflows/local/counts.nf b/subworkflows/local/counts.nf index 6f17075..502b279 100644 --- a/subworkflows/local/counts.nf +++ b/subworkflows/local/counts.nf @@ -1,5 +1,6 @@ include { COMBINE_COUNTS } from "../../modules/local/counts/combine" include { CALCULATE_TPM } from "../../modules/local/counts/calculate_tpm" +include { FILTER_GENES } from "../../modules/local/counts/filter_genes" workflow COUNTS { @@ -8,6 +9,8 @@ workflow COUNTS { gene_map ch_counts ch_counts_design + min_count + min_tpm main: @@ -28,9 +31,18 @@ workflow COUNTS { ch_gene_lengths ) - ch_combined_counts = COMBINE_COUNTS.out.counts + FILTER_GENES( + COMBINE_COUNTS.out.counts, + CALCULATE_TPM.out.tpm, + min_count, + min_tpm + ) - versions = ch_versions.mix(COMBINE_COUNTS.out.versions) + versions = ch_versions.mix( + COMBINE_COUNTS.out.versions, + CALCULATE_TPM.out.versions, + FILTER_GENES.out.versions + ) emit: genes = COMBINE_COUNTS.out.genes diff --git a/workflows/tfactivity.nf b/workflows/tfactivity.nf index aac23fd..12745d0 100644 --- a/workflows/tfactivity.nf +++ b/workflows/tfactivity.nf @@ -35,6 +35,8 @@ workflow TFACTIVITY { window_size decay merge_samples + min_count + min_tpm ch_versions main: @@ -54,7 +56,9 @@ workflow TFACTIVITY { gene_lengths, gene_map, counts, - counts_design + counts_design, + min_count, + min_tpm ) PEAKS( From 5ac754ba4ae474c931e5f3d7b4546d68521113b3 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 2 Mar 2024 14:44:26 +0100 Subject: [PATCH 020/206] Implement DeSeq2 --- bin/filter_genes.py | 4 + bin/prepare_design.py | 21 + modules.json | 5 + modules/local/counts/prepare_design.nf | 27 + .../deseq2/differential/environment.yml | 7 + modules/nf-core/deseq2/differential/main.nf | 33 ++ modules/nf-core/deseq2/differential/meta.yml | 109 ++++ .../deseq2/differential/templates/deseq_de.R | 543 ++++++++++++++++++ subworkflows/local/counts.nf | 27 +- workflows/tfactivity.nf | 3 +- 10 files changed, 776 insertions(+), 3 deletions(-) create mode 100755 bin/prepare_design.py create mode 100644 modules/local/counts/prepare_design.nf create mode 100644 modules/nf-core/deseq2/differential/environment.yml create mode 100644 modules/nf-core/deseq2/differential/main.nf create mode 100644 modules/nf-core/deseq2/differential/meta.yml create mode 100755 modules/nf-core/deseq2/differential/templates/deseq_de.R diff --git a/bin/filter_genes.py b/bin/filter_genes.py index ae59ed4..6cd4148 100755 --- a/bin/filter_genes.py +++ b/bin/filter_genes.py @@ -30,6 +30,10 @@ df_counts = df_counts.loc[gene_intersection] df_tpms = df_tpms.loc[gene_intersection] +# Rename index to gene_id +df_counts.index.name = "gene_id" +df_tpms.index.name = "gene_id" + # Write the output files df_counts.to_csv(args.counts_output, sep="\t") df_tpms.to_csv(args.tpms_output, sep="\t") diff --git a/bin/prepare_design.py b/bin/prepare_design.py new file mode 100755 index 0000000..8aee562 --- /dev/null +++ b/bin/prepare_design.py @@ -0,0 +1,21 @@ +#!/usr/bin/env python3 + +import argparse +import pandas as pd + +# Define the command-line arguments +parser = argparse.ArgumentParser(description="Prepare design matrix for usage with DeSeq2.") +parser.add_argument("--input", type=str, help="Path to sample matrix") +parser.add_argument("--output", type=str, help="Path to output design matrix") +args = parser.parse_args() + +df = pd.read_csv(args.input, index_col=0, header=0) + +df.index.name = "experiment_accession" +df = df.drop("counts_file", axis=1) + +# Keep only columns with more than one unique value +df = df.loc[:, df.nunique() > 1] + +# Write the design matrix to a file +df.to_csv(args.output) \ No newline at end of file diff --git a/modules.json b/modules.json index ecf7fca..447169b 100644 --- a/modules.json +++ b/modules.json @@ -30,6 +30,11 @@ "git_sha": "9437e6053dccf4aafa022bfd6e7e9de67e625af8", "installed_by": ["modules"] }, + "deseq2/differential": { + "branch": "master", + "git_sha": "9326d73af3fbe2ee90d9ce0a737461a727c5118e", + "installed_by": ["modules"] + }, "fastqc": { "branch": "master", "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c", diff --git a/modules/local/counts/prepare_design.nf b/modules/local/counts/prepare_design.nf new file mode 100644 index 0000000..65a0234 --- /dev/null +++ b/modules/local/counts/prepare_design.nf @@ -0,0 +1,27 @@ +process PREPARE_DESIGN { + tag "$meta.id" + label "process_single" + + conda "conda-forge::mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6==fccb0c41a243c639e11dd1be7b74f563e624fcca-0" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0': + 'biocontainers/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0' }" + + input: + tuple val(meta), path(samplesheet) + + output: + tuple val(meta), path("*.design.csv"), emit: design + path "versions.yml" , emit: versions + + script: + """ + prepare_design.py --input ${samplesheet} --output ${meta.id}.design.csv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + python: \$(python --version | sed 's/Python //g') + pandas: \$(python -c "import pandas; print(pandas.__version__)") + END_VERSIONS + """ +} \ No newline at end of file diff --git a/modules/nf-core/deseq2/differential/environment.yml b/modules/nf-core/deseq2/differential/environment.yml new file mode 100644 index 0000000..0ab1d0b --- /dev/null +++ b/modules/nf-core/deseq2/differential/environment.yml @@ -0,0 +1,7 @@ +name: deseq2_differential +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bioconductor-deseq2=1.34.0 diff --git a/modules/nf-core/deseq2/differential/main.nf b/modules/nf-core/deseq2/differential/main.nf new file mode 100644 index 0000000..ab7bc06 --- /dev/null +++ b/modules/nf-core/deseq2/differential/main.nf @@ -0,0 +1,33 @@ +process DESEQ2_DIFFERENTIAL { + tag "$meta" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bioconductor-deseq2:1.34.0--r41hc247a5b_3' : + 'biocontainers/bioconductor-deseq2:1.34.0--r41hc247a5b_3' }" + + input: + tuple val(meta), val(contrast_variable), val(reference), val(target) + tuple val(meta2), path(samplesheet), path(counts) + tuple val(meta3), path(control_genes_file) + tuple val(meta4), path(transcript_lengths_file) + + output: + tuple val(meta), path("*.deseq2.results.tsv") , emit: results + tuple val(meta), path("*.deseq2.dispersion.png") , emit: dispersion_plot + tuple val(meta), path("*.dds.rld.rds") , emit: rdata + tuple val(meta), path("*.deseq2.sizefactors.tsv") , emit: size_factors + tuple val(meta), path("*.normalised_counts.tsv") , emit: normalised_counts + tuple val(meta), path("*.rlog.tsv") , optional: true, emit: rlog_counts + tuple val(meta), path("*.vst.tsv") , optional: true, emit: vst_counts + tuple val(meta), path("*.deseq2.model.txt") , emit: model + tuple val(meta), path("*.R_sessionInfo.log") , emit: session_info + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + template 'deseq_de.R' +} diff --git a/modules/nf-core/deseq2/differential/meta.yml b/modules/nf-core/deseq2/differential/meta.yml new file mode 100644 index 0000000..2b3e33b --- /dev/null +++ b/modules/nf-core/deseq2/differential/meta.yml @@ -0,0 +1,109 @@ +name: "deseq2_differential" +description: runs a differential expression analysis with DESeq2 +keywords: + - differential + - expression + - rna-seq + - deseq2 +tools: + - "deseq2": + description: "Differential gene expression analysis based on the negative binomial distribution" + homepage: "https://bioconductor.org/packages/release/bioc/html/DESeq2.html" + documentation: "https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html" + tool_dev_url: "https://github.com/mikelove/DESeq2" + doi: "10.1186/s13059-014-0550-8" + licence: ["LGPL >=3"] +input: + - meta: + type: map + description: | + Groovy Map containing contrast information. This can be used at the + workflow level to pass optional parameters to the module, e.g. + [ id:'contrast1', blocking:'patient' ] passed in as ext.args like: + '--blocking_variable $meta.blocking'. + - contrast_variable: + type: string + description: | + The column in the sample sheet that should be used to define groups for + comparison + - reference: + type: string + description: | + The value within the contrast_variable column of the sample sheet that + should be used to derive the reference samples + - target: + type: string + description: | + The value within the contrast_variable column of the sample sheet that + should be used to derive the target samples + - meta2: + type: map + description: | + Groovy map containing study-wide metadata related to the sample sheet + and matrix + - samplesheet: + type: file + description: | + CSV or TSV format sample sheet with sample metadata + - counts: + type: file + description: | + Raw TSV or CSV format expression matrix as output from the nf-core + RNA-seq workflow + - meta3: + type: file + description: | + Meta map describing control genes, e.g. [ id: 'ERCC' ] + - control_genes_file: + type: file + description: | + Text file listing control genes, one per line + - meta4: + type: map + description: | + Groovy map containing study-wide metadata related to the transcript + lengths file + - transcript_lengths_file: + type: file + description: | + Optional file of transcript lengths, with the same sample columns as + counts. If supplied, lengths will be supplied to DESeq2 to correct for + differences in average transcript lengths across samples. + +output: + - results: + type: file + description: TSV-format table of differential expression information as output by DESeq2 + pattern: "deseq2.results.tsv" + - dispersion_plot: + type: file + description: DESeq2 dispersion plot + pattern: "deseq2.dispersion.png" + - rdata: + type: file + description: Serialised DESeq2 object + pattern: "dds.rld.rds" + - sizefactors: + type: file + description: Size factors + pattern: "deseq2.sizefactors.tsv" + - normalised_counts: + type: file + description: TSV-format counts matrix, normalised to size factors + pattern: "normalised_counts.tsv" + - variance_stabilised_counts: + type: file + description: TSV-format counts matrix, normalised to size factors, with variance stabilisation applied + pattern: "variance_stabilised_counts.tsv" + - model: + type: file + description: TXT-format DESeq2 model + pattern: "deseq2.model.tsv" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@pinin4fjords" +maintainers: + - "@pinin4fjords" diff --git a/modules/nf-core/deseq2/differential/templates/deseq_de.R b/modules/nf-core/deseq2/differential/templates/deseq_de.R new file mode 100755 index 0000000..a1b3abc --- /dev/null +++ b/modules/nf-core/deseq2/differential/templates/deseq_de.R @@ -0,0 +1,543 @@ +#!/usr/bin/env Rscript + +################################################ +################################################ +## Functions ## +################################################ +################################################ + +#' Check for Non-Empty, Non-Whitespace String +#' +#' This function checks if the input is non-NULL and contains more than just whitespace. +#' It returns TRUE if the input is a non-empty, non-whitespace string, and FALSE otherwise. +#' +#' @param input A variable to check. +#' @return A logical value: TRUE if the input is a valid, non-empty, non-whitespace string; FALSE otherwise. +#' @examples +#' is_valid_string("Hello World") # Returns TRUE +#' is_valid_string(" ") # Returns FALSE +#' is_valid_string(NULL) # Returns FALSE + +is_valid_string <- function(input) { + !is.null(input) && nzchar(trimws(input)) +} + +#' Parse out options from a string without recourse to optparse +#' +#' @param x Long-form argument list like --opt1 val1 --opt2 val2 +#' +#' @return named list of options and values similar to optparse + +parse_args <- function(x){ + args_list <- unlist(strsplit(x, ' ?--')[[1]])[-1] + args_vals <- lapply(args_list, function(x) scan(text=x, what='character', quiet = TRUE)) + + # Ensure the option vectors are length 2 (key/ value) to catch empty ones + args_vals <- lapply(args_vals, function(z){ length(z) <- 2; z}) + + parsed_args <- structure(lapply(args_vals, function(x) x[2]), names = lapply(args_vals, function(x) x[1])) + parsed_args[! is.na(parsed_args)] +} + +#' Flexibly read CSV or TSV files +#' +#' @param file Input file +#' @param header Passed to read.delim() +#' @param row.names Passed to read.delim() +#' +#' @return output Data frame + +read_delim_flexible <- function(file, header = TRUE, row.names = NULL, check.names = TRUE){ + + ext <- tolower(tail(strsplit(basename(file), split = "\\\\.")[[1]], 1)) + + if (ext == "tsv" || ext == "txt") { + separator <- "\\t" + } else if (ext == "csv") { + separator <- "," + } else { + stop(paste("Unknown separator for", ext)) + } + + read.delim( + file, + sep = separator, + header = header, + row.names = row.names, + check.names = check.names + ) +} + +#' Round numeric dataframe columns to fixed decimal places by applying +#' formatting and converting back to numerics +#' +#' @param dataframe A data frame +#' @param columns Which columns to round (assumes all of them by default) +#' @param digits How many decimal places to round to? +#' +#' @return output Data frame + +round_dataframe_columns <- function(df, columns = NULL, digits = 8){ + if (is.null(columns)){ + columns <- colnames(df) + } + + df[,columns] <- format( + data.frame(df[, columns], check.names = FALSE), + nsmall = digits + ) + + # Convert columns back to numeric + + for (c in columns) { + df[[c]][grep("^ *NA\$", df[[c]])] <- NA + df[[c]] <- as.numeric(df[[c]]) + } + df +} + +################################################ +################################################ +## PARSE PARAMETERS FROM NEXTFLOW ## +################################################ +################################################ + +# I've defined these in a single array like this so that we could go back to an +# optparse-driven method in future with module bin/ directories, rather than +# the template + +# Set defaults and classes + +opt <- list( + output_prefix = ifelse('$task.ext.prefix' == 'null', '$meta.id', '$task.ext.prefix'), + count_file = '$counts', + sample_file = '$samplesheet', + contrast_variable = '$contrast_variable', + reference_level = '$reference', + target_level = '$target', + blocking_variables = NULL, + control_genes_file = '$control_genes_file', + transcript_lengths_file = '$transcript_lengths_file', + sizefactors_from_controls = FALSE, + gene_id_col = "gene_id", + sample_id_col = "experiment_accession", + subset_to_contrast_samples = FALSE, + exclude_samples_col = NULL, + exclude_samples_values = NULL, + test = "Wald", + fit_type = "parametric", + sf_type = 'ratio', + min_replicates_for_replace = 7, + use_t = FALSE, + lfc_threshold = 0, + alt_hypothesis = 'greaterAbs', + independent_filtering = TRUE, + p_adjust_method = 'BH', + alpha = 0.1, + minmu = 0.5, + vs_method = 'vst', # 'rlog', 'vst', or 'rlog,vst' + shrink_lfc = TRUE, + cores = 1, + vs_blind = TRUE, + vst_nsub = 1000 +) +opt_types <- lapply(opt, class) + +# Apply parameter overrides + +args_opt <- parse_args('$task.ext.args') +for ( ao in names(args_opt)){ + if (! ao %in% names(opt)){ + stop(paste("Invalid option:", ao)) + }else{ + + # Preserve classes from defaults where possible + if (! is.null(opt[[ao]])){ + args_opt[[ao]] <- as(args_opt[[ao]], opt_types[[ao]]) + } + opt[[ao]] <- args_opt[[ao]] + } +} + +# Check if required parameters have been provided + +required_opts <- c('contrast_variable', 'reference_level', 'target_level', 'output_prefix') +missing <- required_opts[!unlist(lapply(opt[required_opts], is_valid_string)) | !required_opts %in% names(opt)] + +if (length(missing) > 0){ + stop(paste("Missing required options:", paste(missing, collapse=', '))) +} + +# Check file inputs are valid + +for (file_input in c('count_file', 'sample_file')){ + if (! is_valid_string(opt[[file_input]])) { + stop(paste("Please provide", file_input), call. = FALSE) + } + + if (! file.exists(opt[[file_input]])){ + stop(paste0('Value of ', file_input, ': ', opt[[file_input]], ' is not a valid file')) + } +} + +################################################ +################################################ +## Finish loading libraries ## +################################################ +################################################ + +library(DESeq2) +library(BiocParallel) + +################################################ +################################################ +## READ IN COUNTS FILE AND SAMPLE METADATA ## +################################################ +################################################ + +count.table <- + read_delim_flexible( + file = opt\$count_file, + header = TRUE, + row.names = opt\$gene_id_col, + check.names = FALSE + ) +sample.sheet <- read_delim_flexible(file = opt\$sample_file) + +# Deal with spaces that may be in sample column +opt\$sample_id_col <- make.names(opt\$sample_id_col) + +if (! opt\$sample_id_col %in% colnames(sample.sheet)){ + stop(paste0("Specified sample ID column '", opt\$sample_id_col, "' is not in the sample sheet")) +} + +# Sample sheet can have duplicate rows for multiple sequencing runs, so uniqify +# before assigning row names + +sample.sheet <- sample.sheet[! duplicated(sample.sheet[[opt\$sample_id_col]]), ] +rownames(sample.sheet) <- sample.sheet[[opt\$sample_id_col]] + +# Check that all samples specified in the input sheet are present in the counts +# table. Assuming they are, subset and sort the count table to match the sample +# sheet + +missing_samples <- + sample.sheet[!rownames(sample.sheet) %in% colnames(count.table), opt\$sample_id_col] + +if (length(missing_samples) > 0) { + stop(paste( + length(missing_samples), + 'specified samples missing from count table:', + paste(missing_samples, collapse = ',') + )) +} else{ + # Save any non-count data, will gene metadata etc we might need later + noncount.table <- + count.table[, !colnames(count.table) %in% rownames(sample.sheet), drop = FALSE] + count.table <- count.table[, rownames(sample.sheet)] +} + +################################################ +################################################ +## CHECK CONTRAST SPECIFICATION ## +################################################ +################################################ + +contrast_variable <- make.names(opt\$contrast_variable) +blocking.vars <- c() + +if (!contrast_variable %in% colnames(sample.sheet)) { + stop( + paste0( + 'Chosen contrast variable \"', + contrast_variable, + '\" not in sample sheet' + ) + ) +} else if (any(!c(opt\$reflevel, opt\$treatlevel) %in% sample.sheet[[contrast_variable]])) { + stop( + paste( + 'Please choose reference and treatment levels that are present in the', + contrast_variable, + 'column of the sample sheet' + ) + ) +} else if (is_valid_string(opt\$blocking_variables)) { + blocking.vars = make.names(unlist(strsplit(opt\$blocking_variables, split = ';'))) + if (!all(blocking.vars %in% colnames(sample.sheet))) { + missing_block <- paste(blocking.vars[! blocking.vars %in% colnames(sample.sheet)], collapse = ',') + stop( + paste( + 'Blocking variables', missing_block, + 'do not correspond to sample sheet columns.' + ) + ) + } +} + +# Optionally, subset to only the samples involved in the contrast + +if (opt\$subset_to_contrast_samples){ + sample_selector <- sample.sheet[[contrast_variable]] %in% c(opt\$target_level, opt\$reference_level) + selected_samples <- sample.sheet[sample_selector, opt\$sample_id_col] + count.table <- count.table[, selected_samples] + sample.sheet <- sample.sheet[selected_samples, ] +} + +# Optionally, remove samples with specified values in a given field (probably +# don't use this as well as the above) + +if ((is_valid_string(opt\$exclude_samples_col)) && (is_valid_string(opt\$exclude_samples_values))){ + exclude_values = unlist(strsplit(opt\$exclude_samples_values, split = ';')) + + if (! opt\$exclude_samples_col %in% colnames(sample.sheet)){ + stop(paste(opt\$exclude_samples_col, ' specified to subset samples is not a valid sample sheet column')) + } + + print(paste0('Excluding samples with values of ', opt\$exclude_samples_values, ' in ', opt\$exclude_samples_col)) + sample_selector <- ! sample.sheet[[opt\$exclude_samples_col]] %in% exclude_values + + selected_samples <- sample.sheet[sample_selector, opt\$sample_id_col] + count.table <- count.table[, selected_samples] + sample.sheet <- sample.sheet[selected_samples, ] +} + +# Now specify the model. Use cell-means style so we can be explicit with the +# contrasts + +model <- '~ 0' + +if (is_valid_string(opt\$blocking_variables)) { + model <- paste(model, paste(blocking.vars, collapse = ' + '), sep=' + ') +} + +# Make sure all the appropriate variables are factors + +for (v in c(blocking.vars, contrast_variable)) { + sample.sheet[[v]] <- as.factor(sample.sheet[[v]]) +} + +# Variable of interest goes last, see +# https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#multi-factor-designs + +model <- paste(model, contrast_variable, sep = ' + ') + +################################################ +################################################ +## Run DESeq2 processes ## +################################################ +################################################ + +if (opt\$control_genes_file != ''){ + control_genes <- readLines(opt\$control_genes_file) + if (! opt\$sizefactors_from_controls){ + count.table <- count.table[setdiff(rownames(count.table), control_genes),] + } +} + +dds <- DESeqDataSetFromMatrix( + countData = round(count.table), + colData = sample.sheet, + design = as.formula(model) +) + +# Build in transcript lengths. Copying what tximport does here: +# https://github.com/thelovelab/DESeq2/blob/6947d5bc629015fb8ffb2453a91b71665a164483/R/AllClasses.R#L409 + +if (opt\$transcript_lengths_file != ''){ + lengths <- + read_delim_flexible( + file = opt\$transcript_lengths_file, + header = TRUE, + row.names = opt\$gene_id_col, + check.names = FALSE + ) + lengths <- lengths[rownames(count.table), colnames(count.table)] + dimnames(lengths) <- dimnames(dds) + assays(dds)[["avgTxLength"]] <- lengths +} + +if (opt\$control_genes_file != '' && opt\$sizefactors_from_controls){ + print(paste('Estimating size factors using', length(control_genes), 'control genes')) + dds <- estimateSizeFactors(dds, controlGenes=rownames(count.table) %in% control_genes) +} + +dds <- DESeq( + dds, + test = opt\$test, + fitType = opt\$fit_type, + minReplicatesForReplace = opt\$min_replicates_for_replace, + useT = opt\$use_t, + sfType = opt\$sf_type, + parallel=TRUE, BPPARAM=MulticoreParam(opt\$cores) +) + +comp.results <- + results( + dds, + lfcThreshold = opt\$lfc_threshold, + altHypothesis = opt\$alt_hypothesis, + independentFiltering = opt\$independent_filtering, + alpha = opt\$alpha, + pAdjustMethod = opt\$p_adjust_method, + minmu = opt\$minmu, + contrast = c( + contrast_variable, + c(opt\$target_level, opt\$reference_level) + ) + ) + +if (opt\$shrink_lfc){ + comp.results <- lfcShrink(dds, + type = 'ashr', + contrast = c( + contrast_variable, + c(opt\$target_level, opt\$reference_level) + ) + ) +} + +# See https://support.bioconductor.org/p/97676/ + +if (opt\$transcript_lengths_file != ''){ + size_factors = estimateSizeFactorsForMatrix(counts(dds) / assays(dds)[["avgTxLength"]]) +}else { + size_factors = sizeFactors(dds) +} + +################################################ +################################################ +## Generate outputs ## +################################################ +################################################ + +contrast.name <- + paste(opt\$target_level, opt\$reference_level, sep = "_vs_") +cat("Saving results for ", contrast.name, " ...\n", sep = "") + +# Differential expression table- note very limited rounding for consistency of +# results + +out_df <- cbind( + setNames(data.frame(rownames(comp.results)), opt\$gene_id_col), + round_dataframe_columns( + data.frame(comp.results[, !(colnames(comp.results) %in% opt\$gene_id_col)], check.names = FALSE) + ) +) +write.table( + out_df, + file = paste(opt\$output_prefix, 'deseq2.results.tsv', sep = '.'), + col.names = TRUE, + row.names = FALSE, + sep = '\t', + quote = FALSE +) + +# Dispersion plot + +png( + file = paste(opt\$output_prefix, 'deseq2.dispersion.png', sep = '.'), + width = 600, + height = 600 +) +plotDispEsts(dds) +dev.off() + +# R object for other processes to use + +saveRDS(dds, file = paste(opt\$output_prefix, 'dds.rld.rds', sep = '.')) + +# Size factors + +sf_df = data.frame( + sample = names(size_factors), + data.frame(size_factors, check.names = FALSE), + check.names = FALSE +) +colnames(sf_df) <- c('sample', 'sizeFactor') +write.table( + sf_df, + file = paste(opt\$output_prefix, 'deseq2.sizefactors.tsv', sep = '.'), + col.names = TRUE, + row.names = FALSE, + sep = '\t', + quote = FALSE +) + +# Write specified matrices + +out_df <- cbind( + setNames(data.frame(rownames(counts(dds))), opt\$gene_id_col), + data.frame(counts(dds, normalized = TRUE)[, !(colnames(counts(dds, normalized = TRUE)) %in% opt\$gene_id_col)], check.names = FALSE) +) +write.table( + out_df, + file = paste(opt\$output_prefix, 'normalised_counts.tsv', sep = '.'), + col.names = TRUE, + row.names = FALSE, + sep = '\t', + quote = FALSE +) + +# Note very limited rounding for consistency of results + +for (vs_method_name in strsplit(opt\$vs_method, ',')){ + if (vs_method_name == 'vst'){ + vs_mat <- vst(dds, blind = opt\$vs_blind, nsub = opt\$vst_nsub) + }else if (vs_method_name == 'rlog'){ + vs_mat <- rlog(dds, blind = opt\$vs_blind, fitType = opt\$fit_type) + } + + # Again apply the slight rounding and then restore numeric + + out_df <- cbind( + setNames(data.frame(rownames(counts(dds))), opt\$gene_id_col), + round_dataframe_columns( + data.frame(assay(vs_mat)[, !(colnames(assay(vs_mat)) %in% opt\$gene_id_col)], check.names = FALSE) + ) + ) + write.table( + out_df, + file = paste(opt\$output_prefix, vs_method_name, 'tsv', sep = '.'), + col.names = TRUE, + row.names = FALSE, + sep = '\t', + quote = FALSE + ) +} + +# Save model to file + +write(model, file=paste(opt\$output_prefix, 'deseq2.model.txt', sep = '.')) + +################################################ +################################################ +## R SESSION INFO ## +################################################ +################################################ + +sink(paste(opt\$output_prefix, "R_sessionInfo.log", sep = '.')) +print(sessionInfo()) +sink() + +################################################ +################################################ +## VERSIONS FILE ## +################################################ +################################################ + +r.version <- strsplit(version[['version.string']], ' ')[[1]][3] +deseq2.version <- as.character(packageVersion('DESeq2')) + +writeLines( + c( + '"${task.process}":', + paste(' r-base:', r.version), + paste(' bioconductor-deseq2:', deseq2.version) + ), +'versions.yml') + +################################################ +################################################ +################################################ +################################################ diff --git a/subworkflows/local/counts.nf b/subworkflows/local/counts.nf index 502b279..a7c6840 100644 --- a/subworkflows/local/counts.nf +++ b/subworkflows/local/counts.nf @@ -1,6 +1,8 @@ include { COMBINE_COUNTS } from "../../modules/local/counts/combine" include { CALCULATE_TPM } from "../../modules/local/counts/calculate_tpm" include { FILTER_GENES } from "../../modules/local/counts/filter_genes" +include { PREPARE_DESIGN } from "../../modules/local/counts/prepare_design" +include { DESEQ2_DIFFERENTIAL } from "../../modules/nf-core/deseq2/differential/main" workflow COUNTS { @@ -11,6 +13,7 @@ workflow COUNTS { ch_counts_design min_count min_tpm + contrasts main: @@ -38,14 +41,34 @@ workflow COUNTS { min_tpm ) + PREPARE_DESIGN(ch_counts_design.map{ design -> [[id: "design"], design]}) + + DESEQ2_DIFFERENTIAL( + Channel.value(["condition"]).combine(contrasts) + .map{ variable, reference, target -> + [[id: reference + ":" + target], variable, reference, target]}, + PREPARE_DESIGN.out.design + .map{ meta, design -> design } + .combine(FILTER_GENES.out.counts) + .map{design, meta, counts -> [meta, design, counts]}.collect(), + [[], []], + [[], []] + ) + versions = ch_versions.mix( COMBINE_COUNTS.out.versions, CALCULATE_TPM.out.versions, - FILTER_GENES.out.versions + FILTER_GENES.out.versions, + PREPARE_DESIGN.out.versions, + DESEQ2_DIFFERENTIAL.out.versions ) emit: - genes = COMBINE_COUNTS.out.genes + genes = FILTER_GENES.out.genes + raw_counts = FILTER_GENES.out.counts + tpms = CALCULATE_TPM.out.tpm + normalized = DESEQ2_DIFFERENTIAL.out.normalised_counts + differential = DESEQ2_DIFFERENTIAL.out.results versions = ch_versions // channel: [ versions.yml ] } diff --git a/workflows/tfactivity.nf b/workflows/tfactivity.nf index 12745d0..39d8193 100644 --- a/workflows/tfactivity.nf +++ b/workflows/tfactivity.nf @@ -58,7 +58,8 @@ workflow TFACTIVITY { counts, counts_design, min_count, - min_tpm + min_tpm, + ch_contrasts ) PEAKS( From 5ad6e1ef0601cfa1089baa94cad1b02c81f177bf Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 2 Mar 2024 15:57:35 +0100 Subject: [PATCH 021/206] Add DYNAMITE parameters --- main.nf | 6 ++++++ nextflow.config | 5 +++++ nextflow_schema.json | 28 ++++++++++++++++++++++++++++ subworkflows/local/counts.nf | 3 ++- subworkflows/local/dynamite.nf | 23 +++++++++++++++++++++++ subworkflows/local/peaks.nf | 16 +++++++++++----- workflows/tfactivity.nf | 19 +++++++++++++++++++ 7 files changed, 94 insertions(+), 6 deletions(-) create mode 100644 subworkflows/local/dynamite.nf diff --git a/main.nf b/main.nf index 316cfdf..23dcb21 100644 --- a/main.nf +++ b/main.nf @@ -88,6 +88,12 @@ workflow NFCORE_TFACTIVITY { params.merge_samples, params.min_count, params.min_tpm, + + params.dynamite_ofolds, + params.dynamite_ifolds, + params.dynamite_alpha, + params.dynamite_randomize, + ch_versions ) diff --git a/nextflow.config b/nextflow.config index eb7260e..7deaa18 100644 --- a/nextflow.config +++ b/nextflow.config @@ -23,6 +23,11 @@ params { min_count = 50 min_tpm = 0 + dynamite_ofolds = 3 + dynamite_ifolds = 6 + dynamite_alpha = 0.1 + dynamite_randomize = false + // References genome = null igenomes_base = 's3://ngi-igenomes/igenomes/' diff --git a/nextflow_schema.json b/nextflow_schema.json index 5b3e7a3..e215ef4 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -110,6 +110,34 @@ "description": "Minimum TPM to keep a gene in the analysis.", "fa_icon": "fas fa-compress-arrows-alt", "help_text": "Minimum TPM to keep a gene in the analysis. The default value is 0." + }, + "dynamite_ofolds": { + "type": "integer", + "default": 3, + "description": "Number of outer folds for dynamite.", + "fa_icon": "fas fa-compress-arrows-alt", + "help_text": "Number of outer folds for dynamite. The default value is 3." + }, + "dynamite_ifolds": { + "type": "integer", + "default": 6, + "description": "Number of inner folds for dynamite.", + "fa_icon": "fas fa-compress-arrows-alt", + "help_text": "Number of inner folds for dynamite. The default value is 6." + }, + "dynamite_alpha": { + "type": "number", + "default": 0.1, + "description": "Alpha value for dynamite.", + "fa_icon": "fas fa-compress-arrows-alt", + "help_text": "Alpha value for dynamite. The default value is 0.1." + }, + "dynamite_randomize": { + "type": "boolean", + "default": "false", + "description": "Randomize the data for dynamite.", + "fa_icon": "fas fa-compress-arrows-alt", + "help_text": "Randomize the data for dynamite. The default value is `false`." } } }, diff --git a/subworkflows/local/counts.nf b/subworkflows/local/counts.nf index a7c6840..82baeb5 100644 --- a/subworkflows/local/counts.nf +++ b/subworkflows/local/counts.nf @@ -46,7 +46,8 @@ workflow COUNTS { DESEQ2_DIFFERENTIAL( Channel.value(["condition"]).combine(contrasts) .map{ variable, reference, target -> - [[id: reference + ":" + target], variable, reference, target]}, + [[id: reference + ":" + target, condition1: reference, condition2: target], + variable, reference, target]}, PREPARE_DESIGN.out.design .map{ meta, design -> design } .combine(FILTER_GENES.out.counts) diff --git a/subworkflows/local/dynamite.nf b/subworkflows/local/dynamite.nf new file mode 100644 index 0000000..9615793 --- /dev/null +++ b/subworkflows/local/dynamite.nf @@ -0,0 +1,23 @@ + + +workflow DYNAMITE { + take: + ch_differential + ch_affinity_ratio + ofolds + ifolds + alpha + randomize + + main: + + ch_versions = Channel.empty() + + + + emit: + + + versions = ch_versions // channel: [ versions.yml ] +} + diff --git a/subworkflows/local/peaks.nf b/subworkflows/local/peaks.nf index 6d9540d..35043d7 100644 --- a/subworkflows/local/peaks.nf +++ b/subworkflows/local/peaks.nf @@ -82,12 +82,18 @@ workflow PEAKS { ch_contrast_affinities = contrasts .map {condition1, condition2 -> [condition2, condition1]} .combine(ch_affinities_spread, by: 0) - .map {condition2, condition1, assay2, affinities2 -> [condition1, condition2, assay2, affinities2] } + .map {condition2, condition1, assay2, affinities2 -> + [condition1, condition2, assay2, affinities2] } .combine(ch_affinities_spread, by: 0) - .map {condition1, condition2, assay2, affinities2, assay1, affinities1 -> [condition1, condition2, assay1, affinities1, assay2, affinities2] } - .filter {condition1, condition2, assay1, affinities1, assay2, affinities2 -> assay1 == assay2} - .map {condition1, condition2, assay1, affinities1, assay2, affinities2 -> [condition1 + ":" + condition2, assay1, [affinities1, affinities2]] } - .map {contrast, assay, affinities -> [[id: contrast + "_" + assay, contrast: contrast, assay: assay], affinities] } + .map {condition1, condition2, assay2, affinities2, assay1, affinities1 -> + [condition1, condition2, assay1, affinities1, assay2, affinities2] } + .filter {condition1, condition2, assay1, affinities1, assay2, affinities2 -> + assay1 == assay2} + .map {condition1, condition2, assay1, affinities1, assay2, affinities2 -> + [[id: condition1 + ":" + condition2 + "_" + assay1, + condition1: condition1, condition2: condition2, + assay: assay1], + [affinities1, affinities2]] } AFFINITY_RATIO(ch_contrast_affinities, "ratio") diff --git a/workflows/tfactivity.nf b/workflows/tfactivity.nf index 39d8193..1291127 100644 --- a/workflows/tfactivity.nf +++ b/workflows/tfactivity.nf @@ -13,6 +13,7 @@ include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_tfac include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome' include { COUNTS } from '../subworkflows/local/counts' include { PEAKS } from '../subworkflows/local/peaks' +include { DYNAMITE } from '../subworkflows/local/dynamite' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -35,8 +36,17 @@ workflow TFACTIVITY { window_size decay merge_samples + + // Counts min_count min_tpm + + // Dynamite + dynamite_ofolds + dynamite_ifolds + dynamite_alpha + dynamite_randomize + ch_versions main: @@ -74,6 +84,15 @@ workflow TFACTIVITY { ch_contrasts ) + DYNAMITE( + COUNTS.out.differential, + PEAKS.out.affinity_ratio, + dynamite_ofolds, + dynamite_ifolds, + dynamite_alpha, + dynamite_randomize + ) + ch_versions = ch_versions.mix(COUNTS.out.versions, PEAKS.out.versions) // From d8432d62396ddb1f9cb8c34c04dff338d8ca1fb5 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 2 Mar 2024 16:33:38 +0100 Subject: [PATCH 022/206] Implement dynamite data integration --- bin/dynamite_integrate.py | 30 +++++++++++++++++++++++ modules/local/dynamite/integrate_data.nf | 31 ++++++++++++++++++++++++ subworkflows/local/counts.nf | 5 +++- subworkflows/local/dynamite.nf | 12 ++++++++- subworkflows/local/peaks.nf | 1 + 5 files changed, 77 insertions(+), 2 deletions(-) create mode 100755 bin/dynamite_integrate.py create mode 100644 modules/local/dynamite/integrate_data.nf diff --git a/bin/dynamite_integrate.py b/bin/dynamite_integrate.py new file mode 100755 index 0000000..3957f5b --- /dev/null +++ b/bin/dynamite_integrate.py @@ -0,0 +1,30 @@ +#!/usr/bin/env python3 + +# Based on https://github.com/SchulzLab/TEPIC/blob/master/MachineLearningPipelines/DYNAMITE/Scripts/integrateData.py + +import pandas as pd +import argparse + +parser=argparse.ArgumentParser(prog="annotateTSS.py") +parser.add_argument("--affinities", type=str, help="TEPIC gene-TF scores") +parser.add_argument("--expression", type=str, help="DeSeq2 differential expression data") +parser.add_argument("--output", type=str, help="File to write the combined data to") +args=parser.parse_args() + +df_affinities = pd.read_csv(args.affinities, sep="\t", index_col=0) +df_expression = pd.read_csv(args.expression, sep="\t", index_col=0) + +def remove_version(gene_id): + return gene_id.split(".")[0] + +df_affinities.index = df_affinities.index.map(remove_version) +df_expression.index = df_expression.index.map(remove_version) + +gene_intersection = df_affinities.index.intersection(df_expression.index) + +df_affinities = df_affinities.loc[gene_intersection] +df_expression = df_expression.loc[gene_intersection] + +df_affinities["Expression"] = df_expression["log2FoldChange"] + +df_affinities.to_csv(args.output, sep="\t") \ No newline at end of file diff --git a/modules/local/dynamite/integrate_data.nf b/modules/local/dynamite/integrate_data.nf new file mode 100644 index 0000000..4d8d927 --- /dev/null +++ b/modules/local/dynamite/integrate_data.nf @@ -0,0 +1,31 @@ +process INTEGRATE_DATA { + tag "$meta.id" + label "process_single" + + conda "conda-forge::mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6==fccb0c41a243c639e11dd1be7b74f563e624fcca-0" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0': + 'biocontainers/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0' }" + + input: + tuple val(meta), path(differential_expression), path(affinity_ratio) + + output: + tuple val(meta), path("*.integrated.tsv"), emit: integrated + + path "versions.yml" , emit: versions + + script: + """ + dynamite_integrate.py \\ + --affinities ${affinity_ratio} \\ + --expression ${differential_expression} \\ + --output ${meta.id}.integrated.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + python: \$(python --version | sed 's/Python //g') + pandas: \$(python -c "import pandas; print(pandas.__version__)") + END_VERSIONS + """ +} \ No newline at end of file diff --git a/subworkflows/local/counts.nf b/subworkflows/local/counts.nf index 82baeb5..97dc1eb 100644 --- a/subworkflows/local/counts.nf +++ b/subworkflows/local/counts.nf @@ -46,7 +46,10 @@ workflow COUNTS { DESEQ2_DIFFERENTIAL( Channel.value(["condition"]).combine(contrasts) .map{ variable, reference, target -> - [[id: reference + ":" + target, condition1: reference, condition2: target], + [[id: reference + ":" + target, + contrast: reference + ":" + target, + condition1: reference, + condition2: target], variable, reference, target]}, PREPARE_DESIGN.out.design .map{ meta, design -> design } diff --git a/subworkflows/local/dynamite.nf b/subworkflows/local/dynamite.nf index 9615793..e334b6f 100644 --- a/subworkflows/local/dynamite.nf +++ b/subworkflows/local/dynamite.nf @@ -1,4 +1,4 @@ - +include { INTEGRATE_DATA } from '../../modules/local/dynamite/integrate_data' workflow DYNAMITE { take: @@ -13,6 +13,16 @@ workflow DYNAMITE { ch_versions = Channel.empty() + ch_combined = ch_differential.map{ meta, differential -> + [meta.condition1, meta.condition2, meta, differential]} + .combine(ch_affinity_ratio.map{ meta, affinity_ratio -> + [meta.condition1, meta.condition2, meta, affinity_ratio]}, by: [0,1]) + .map{ condition1, condition2, meta_differential, differential, meta_affinity, affinity_ratio -> + [meta_affinity, differential, affinity_ratio]} + + INTEGRATE_DATA(ch_combined) + + ch_versions = ch_versions.mix(INTEGRATE_DATA.out.versions) emit: diff --git a/subworkflows/local/peaks.nf b/subworkflows/local/peaks.nf index 35043d7..451b222 100644 --- a/subworkflows/local/peaks.nf +++ b/subworkflows/local/peaks.nf @@ -91,6 +91,7 @@ workflow PEAKS { assay1 == assay2} .map {condition1, condition2, assay1, affinities1, assay2, affinities2 -> [[id: condition1 + ":" + condition2 + "_" + assay1, + contrast: condition1 + ":" + condition2, condition1: condition1, condition2: condition2, assay: assay1], [affinities1, affinities2]] } From 2812f8febf0d569fd4b52017ec2ef94a87f099e5 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 2 Mar 2024 16:44:20 +0100 Subject: [PATCH 023/206] Rename DYNAMITE integration to preprocessing --- bin/{dynamite_integrate.py => dynamite_preprocess.py} | 3 ++- .../local/dynamite/{integrate_data.nf => preprocess.nf} | 8 ++++---- subworkflows/local/dynamite.nf | 6 +++--- 3 files changed, 9 insertions(+), 8 deletions(-) rename bin/{dynamite_integrate.py => dynamite_preprocess.py} (90%) rename modules/local/dynamite/{integrate_data.nf => preprocess.nf} (86%) diff --git a/bin/dynamite_integrate.py b/bin/dynamite_preprocess.py similarity index 90% rename from bin/dynamite_integrate.py rename to bin/dynamite_preprocess.py index 3957f5b..a2aea96 100755 --- a/bin/dynamite_integrate.py +++ b/bin/dynamite_preprocess.py @@ -25,6 +25,7 @@ def remove_version(gene_id): df_affinities = df_affinities.loc[gene_intersection] df_expression = df_expression.loc[gene_intersection] -df_affinities["Expression"] = df_expression["log2FoldChange"] +df_affinities["Expression"] = 0 +df_affinities.loc[df_expression["log2FoldChange"] > 0, "Expression"] = 1 df_affinities.to_csv(args.output, sep="\t") \ No newline at end of file diff --git a/modules/local/dynamite/integrate_data.nf b/modules/local/dynamite/preprocess.nf similarity index 86% rename from modules/local/dynamite/integrate_data.nf rename to modules/local/dynamite/preprocess.nf index 4d8d927..e016ade 100644 --- a/modules/local/dynamite/integrate_data.nf +++ b/modules/local/dynamite/preprocess.nf @@ -1,4 +1,4 @@ -process INTEGRATE_DATA { +process PREPROCESS { tag "$meta.id" label "process_single" @@ -11,16 +11,16 @@ process INTEGRATE_DATA { tuple val(meta), path(differential_expression), path(affinity_ratio) output: - tuple val(meta), path("*.integrated.tsv"), emit: integrated + tuple val(meta), path("*.preprocessed.tsv"), emit: output path "versions.yml" , emit: versions script: """ - dynamite_integrate.py \\ + dynamite_preprocess.py \\ --affinities ${affinity_ratio} \\ --expression ${differential_expression} \\ - --output ${meta.id}.integrated.tsv + --output ${meta.id}.preprocessed.tsv cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/subworkflows/local/dynamite.nf b/subworkflows/local/dynamite.nf index e334b6f..972e767 100644 --- a/subworkflows/local/dynamite.nf +++ b/subworkflows/local/dynamite.nf @@ -1,4 +1,4 @@ -include { INTEGRATE_DATA } from '../../modules/local/dynamite/integrate_data' +include { PREPROCESS } from '../../modules/local/dynamite/preprocess' workflow DYNAMITE { take: @@ -20,9 +20,9 @@ workflow DYNAMITE { .map{ condition1, condition2, meta_differential, differential, meta_affinity, affinity_ratio -> [meta_affinity, differential, affinity_ratio]} - INTEGRATE_DATA(ch_combined) + PREPROCESS(ch_combined) - ch_versions = ch_versions.mix(INTEGRATE_DATA.out.versions) + ch_versions = ch_versions.mix(PREPROCESS.out.versions) emit: From ed022ff7d3bbf505d983efe51e9c0f655c9807f6 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 2 Mar 2024 17:01:06 +0100 Subject: [PATCH 024/206] Implement DYNAMITE --- bin/DYNAMITE.R | 428 +++++++++++++++++++++++++++++ modules/local/dynamite/dynamite.nf | 32 +++ subworkflows/local/dynamite.nf | 5 +- 3 files changed, 464 insertions(+), 1 deletion(-) create mode 100755 bin/DYNAMITE.R create mode 100644 modules/local/dynamite/dynamite.nf diff --git a/bin/DYNAMITE.R b/bin/DYNAMITE.R new file mode 100755 index 0000000..4fd850d --- /dev/null +++ b/bin/DYNAMITE.R @@ -0,0 +1,428 @@ +#!/usr/bin/env Rscript + +args <- commandArgs(TRUE) +library('methods') +ggplotAvailable<-require("ggplot2") +gplotsAvailable<-require("gplots") +fontSize=.9 + +if(length(args) < 1) { + args <- c("--help") +} + +if("--help" %in% args) { + cat(" + Arguments: + --outDir= Output path (required) + --dataDir= Data directory (required) + --out_var= Name of the response variable (required) + --cores= Number of the cores to use (1 as default) + --alpha= Alpha parameter stepsize (0.1 as default) + --testsize= Size of test data (0.2 as default) + --Ofolds= Number of outer folds for model validation (3 as default) + --Ifolds= Number of inner cross validation folds (6 as default) + --balanced= Flag indicating whether the data should be balanced through downsampling (default TRUE) + --performance= Flag indicating whether performance measures should be computed (default TRUE) + --randomise= Flag indicating whether a model should be learned on randomised data (default FALSE) +") + q(save="no") +} + +#Processing command line arguments +parseArgs <- function(x) strsplit(sub("^--", "", x), "=") +argsDF <- as.data.frame(do.call("rbind", parseArgs(args))) +argsL <- as.list(as.character(argsDF$V2)) +names(argsL) <- argsDF$V1 + +#Checking required arguments +if(is.null(argsL$outDir)) { + cat("Error!\n\n Please specify an output directory \n\n ") +q(save="no") +} +argsL$outDir<-paste0(argsL$outDir,"/") + +if(is.null(argsL$dataDir)) { + cat("Error!\n\n Please specify the data directory \n\n ") +q(save="no") +} +argsL$dataDir<-paste0(argsL$dataDir,"/") + +if(is.null(argsL$out_var)) { + cat("Error!\n\n Please enter the name of the response variable \n\n ") +q(save="no") +} + +#Checking for optional arguments +if(is.null(argsL$cores)) { +argsL$cores<-20 +} +if(is.null(argsL$testsize)){ +argsL$testsize<-0.2 +} + +if(is.null(argsL$Ofolds)){ +argsL$Ofolds<-3 +} + +if(is.null(argsL$alpha)) { +argsL$alpha <-0.1 +} + +if(is.null(argsL$balanced)) { +argsL$balanced <-TRUE +} + +if(is.null(argsL$performance)) { +argsL$performance <-TRUE +} + + +if (is.null(argsL$Ifolds)){ +argsL$Ifolds <-6 +} + +if (is.null(argsL$randomise)){ +argsL$randomise <- FALSE +} + +#Creating output directory if necessary +dir.create(argsL$outDir,showWarning=FALSE,recursive=TRUE) + +permute<-function(x){ +s<-sample(length(x)) +x[s] +} + +#Loading required packages and initialising index variables +require(glmnet) +library("doMC") +i<-0 +k<-0 +counter<-0 +registerDoMC(argsL$cores) +#Checking the total number of samples +FileList<-list.files(path=argsL$dataDir) +print(paste("Samples to analyse:",as.character(length(FileList)),sep=" ")) +for(Sample in FileList){ + counter<-counter+1 + print(paste(as.character(counter),unlist(unlist(strsplit(Sample,".txt"))))) + } + +#Creating the header for the overview table +SampleOverview<-c("Name","Mean Test Accuracy","Var Test Accuracy","Mean F1_1","Var F1_1","Mean F1_2","Var F1_2","Mean Training Accuracy","Var Train Accuracy") + +#Declare elastic net functions +elaBinomial<-function(a,x,y,i){ + print(paste0("Learning model for alpha = ",a)) + elasticnet<-cv.glmnet(x, y, alpha=a,family="binomial",type.measure="class",parallel=TRUE,nfolds=i) + min(elasticnet$cvm) + } +elaMultinomial<-function(a,x,y,i){ + print(paste0("Learning model for alpha = ",a)) + elasticnet<-cv.glmnet(x, y, alpha=a,family="multinomial",type.measure="class",parallel=TRUE,nfolds=i) + min(elasticnet$cvm) + } + +coefficients<-vector("list",length(FileList)) + +# Data Preprocessing +for(Sample in FileList){ + # Process file names for plot title + name<-strsplit(Sample, ".",fixed=TRUE)[[1]][1] + print(paste0("Learning model for ",name)) + i<-i+1 + #Loading the data matrix + M<-read.table(paste(argsL$dataDir,Sample,sep="/"),header=TRUE,stringsAsFactors=FALSE,row.names=1) + #Removing features with standard deviation zero + SD<-apply(M,2,sd) + Feature_zero_SD<-as.vector(which(SD==0)) + if(length(Feature_zero_SD)>0){ + print("Warning! The following features are constant and will be removed from the feature matrix") + print(colnames(M)[Feature_zero_SD]) + M<-M[,-c(Feature_zero_SD)] + } + #Initialising FeatureNames, Test and Training Accuracy vectors and retrieving the column containing the response variable + FeatureName<-colnames(M) + Response_Variable_location<- grep(argsL$out_var,FeatureName) + TestAcc<-c(1:argsL$Ofolds) + TrainAcc<-c(1:argsL$Ofolds) + F1_1<-c(1:argsL$Ofolds) + F1_2<-c(1:argsL$Ofolds) + alphas=seq(0.0,1.0,as.numeric(argsL$alpha)) + coefficients[[i]]<-vector("list",as.numeric(argsL$Ofolds)) + #Normalising the data matrix + M[,-Response_Variable_location]<-log2(M[,-Response_Variable_location]+1) + M[,-Response_Variable_location]<-scale(M[,-Response_Variable_location],center=TRUE, scale=TRUE) + if (argsL$randomise == TRUE){ + MP<-apply(M[,-Response_Variable_location],2,permute) + M<-cbind(data.frame(scale(MP,center=TRUE, scale=TRUE)),M[,Response_Variable_location]) + colnames(M)<-FeatureName + } + + #Balancing the data set + if (argsL$balanced==TRUE){ + subM<-list(list()) + bM<-c() + index=0 + for (j in unique(M[,Response_Variable_location])){ + index<-index+1 + subM[[index]]<-M[which(M[,Response_Variable_location]==j),] + } + mSize=min(sapply(subM,dim)[1,]) + for (l in 1:length(subM)){ + rndselect=sample(x=nrow(subM[[l]]),size=mSize) + subM[[l]]=subM[[l]][rndselect,] + bM<-rbind(bM,subM[[l]]) + } + } + test_size<-1/as.numeric(argsL$testsize) + + if (argsL$performance){ + #Loop through the outer folds + for (k in 1:argsL$Ofolds){ + print(paste("Outer CV fold ",as.character(k),sep=" ")) + if (argsL$balanced==TRUE){ + #Balanced selection of test and training data + Test_Data<-c() + Train_Data<-c() + for (j in 1:length(subM)){ + rndselect=sample(x=nrow(subM[[j]]), size=mSize/test_size) + Test_Data<-rbind(Test_Data,subM[[j]][rndselect,]) + Train_Data<-rbind(Train_Data,subM[[j]][-rndselect,]) + } + }else{ + rndselect=sample(x=nrow(M),size=as.numeric(argsL$testsize)*nrow(M)) + Test_Data<-M[rndselect,] + Train_Data<-M[-rndselect,] + } + + #Split the features from response + x_train<-as.matrix(Train_Data[,-Response_Variable_location]) + x_test<-as.matrix(Test_Data[,-Response_Variable_location]) + y_train<-as.vector(unlist(Train_Data[,Response_Variable_location,drop=FALSE])) + y_test<-as.vector(unlist(Test_Data[,Response_Variable_location])) + + #Training model parameters in the inner cross validation + print(argsL$Ifolds) + if (length(unique(M[,Response_Variable_location]))==2){ + aError<-sapply(alphas,elaBinomial,x_train,y_train,as.numeric(argsL$Ifolds)) + }else{ + aError<-sapply(alphas,elaMultinomial,x_train,y_train,as.numeric(argsL$Ifolds)) + } + + #Determine best model and retrain it + index<-match(min(aError), aError) + print(paste0("Available alphas: ", alphas, " Errors: ", aError)) + print(paste0("Selected alpha: ", alphas[index])) + if (length(unique(M[,Response_Variable_location]))==2){ + elasticnet<-cv.glmnet(x_train, y_train,alpha=alphas[index],family="binomial",type.measure="class",parallel=TRUE,nfolds=as.numeric(argsL$Ifolds)) + }else{ + elasticnet<-cv.glmnet(x_train, y_train,alpha=alphas[index],family="multinomial",type.measure="class",parallel=TRUE,nfolds=as.numeric(argsL$Ifolds)) + } + + #Generating a plot visualising the model selection + svg(paste(paste0(argsL$outDir,"/Misclassification_vs_Lambda_Fold_",k,"_",name),"svg",sep=".")) + plot(elasticnet) + dev.off() + + #Applying the selected model to the test data + predict_test<-predict(elasticnet, x_test, s="lambda.min",type="class") + predict_train<-predict(elasticnet, x_train, s="lambda.min",type="class") + + #Printing and storing the performance table + tTest<-table(y_test,predict_test) + write.table(tTest,file=paste(argsL$outDir,"/Confusion-Matrix_",k,"_",name,".txt",sep=""),quote=FALSE,sep="\t",row.names=FALSE) + tTrain<-table(y_train,predict_train) + + #Storing Feature values + if (length(unique(M[,Response_Variable_location]))==2){ + coefficients[[i]][[k]]<-coef(elasticnet, s = "lambda.min") + }else{ + coefficients[[i]][[k]]<-c() + } + + #Calculating Accuracy measures + TestAcc[k]<-0 + TrainAcc[k]<-0 + F1_1[k]<-0 + F1_2[k]<-0 + for (index in 1:dim(tTest)[1]){ + TestAcc[k]<-TestAcc[k]+tTest[(index-1)*dim(tTest)[1]+index] + TrainAcc[k]<-TrainAcc[k]+tTrain[(index-1)*dim(tTest)[1]+index] + } + F1_1[k]<-(2*tTest[1])/(2*tTest[1]+tTest[2]+tTest[3]) + F1_2[k]<-(2*tTest[4])/(2*tTest[4]+tTest[2]+tTest[3]) + TestAcc[k]<-TestAcc[k]/sum(tTest) + TrainAcc[k]<-TrainAcc[k]/sum(tTrain) + } + + #Storing the mean performance values + sampleResult<-c(name,mean(TestAcc),var(TestAcc),mean(F1_1),var(F1_1),mean(F1_2),var(F1_2),mean(TrainAcc),var(TrainAcc)) + SampleOverview<-rbind(SampleOverview,sampleResult) + } + + #Learning one model on the full data set for feature analysis + print("Learning model on the entire data set") + if (argsL$balanced==TRUE){ + x_com<-as.matrix(bM[,-Response_Variable_location]) + y_com<-as.vector(unlist(bM[,Response_Variable_location,drop=FALSE])) + }else{ + x_com<-as.matrix(M[,-Response_Variable_location]) + y_com<-as.vector(unlist(M[,Response_Variable_location,drop=FALSE])) + } + aError=0 + if (length(unique(M[,Response_Variable_location]))==2){ + aError<-sapply(alphas,elaBinomial,x_com,y_com,as.numeric(argsL$Ifolds)) + }else{ + aError<-sapply(alphas,elaMultinomial,x_com,y_com,as.numeric(argsL$Ifolds)) + } + index<-match(min(aError), aError) + print(paste0("Available alphas: ", alphas, " Errors: ", aError)) + print(paste0("Selected alpha: ", alphas[index])) + if (length(unique(M[,Response_Variable_location]))==2){ + elasticnet<-cv.glmnet(x_com, y_com,alpha=alphas[index],family="binomial",type.measure="class",parallel=TRUE,nfolds=as.numeric(argsL$Ifolds)) + }else{ + elasticnet<-cv.glmnet(x_com, y_com,alpha=alphas[index],family="multinomial",type.measure="class",parallel=TRUE,nfolds=as.numeric(argsL$Ifolds)) + } + + #Store the feature values + if (length(unique(M[,Response_Variable_location]))>2){ + coefO<-coef(elasticnet,s="lambda.min") + for (j in names(coefO)){ + nf<-(coefO[j][[1]][,1])[-1] + nf2<-nf/max(abs(nf)) + nf3<-t(nf2) + nf3<-as.data.frame(nf3) + nf4<-t(rbind(colnames(nf3),nf3)) + colnames(nf4)<-c("TF","value") + nf4[,2]<-as.numeric(as.character(nf4[,2])) + nf4<-as.data.frame(nf4) + nf4[,2]<-as.numeric(as.character(nf4[,2])) + write.table(nf4,file=paste(argsL$outDir,paste("Class",j,"Regression_Coefficients_Entire_Data_Set.txt",sep="-"),sep='/'),quote=FALSE,sep="\t",row.names=FALSE) + nf4<-nf4[which(nf4$value >0.025),] + np<-c(1:length((nf4[,2]))) + np[which(nf4[,2]>0)]<-1 + np[which(nf4[,2]<=0)]<-0 + if (ggplotAvailable){ + ggplot2::ggplot(nf4,aes(x=reorder(TF,value),y=value,width=0.8,fill=np))+ + geom_bar(stat="identity")+ + theme_bw(10)+ylab("Normalised coefficient")+xlab("TF")+ + theme(axis.text.x=element_text(angle=45,hjust=1))+ + theme(strip.background = element_blank())+ + theme(legend.position="none") + ggsave(paste0(argsL$outDir,"Regression_Coefficients_Entire_Data_Set_Class",j,"_",name,".png"),width=min(50,5+(.3*length(nf4$TF))),height=5,limitsize=F) + } + } + }else{ + nf<-coef(elasticnet,s="lambda.min")[,1][-1] + nf2<-nf/max(abs(nf)) + nf3<-t(nf2) + nf3<-as.data.frame(nf3) + nf4<-t(rbind(colnames(nf3),nf3)) + colnames(nf4)<-c("TF","value") + nf4[,2]<-as.numeric(as.character(nf4[,2])) + nf4<-as.data.frame(nf4) + nf4[,2]<-as.numeric(as.character(nf4[,2])) + write.table(nf4,file=paste(argsL$outDir,paste0("Regression_Coefficients_Entire_Data_Set_",name,".txt"),sep='/'),quote=FALSE,sep="\t",row.names=FALSE) + nf4<-nf4[which(nf4$value !=0.0),] + np<-c(1:length((nf4[,2]))) + np[which(nf4[,2]>0)]<-1 + np[which(nf4[,2]<0)]<-0 + if (ggplotAvailable){ + ggplot2::ggplot(nf4,aes(x=reorder(TF,value),y=value,width=0.8,fill=np))+ + geom_bar(stat="identity")+ + theme_bw(10)+ylab("Normalised coefficient")+xlab("TF")+ + theme(axis.text.x=element_text(angle=45,hjust=1))+ + theme(strip.background = element_blank())+ + theme(legend.position="none") + ggsave(paste0(argsL$outDir,"Regression_Coefficients_Entire_Data_Set",name,".png"),width=min(50,5+(.3*length(nf4$TF))),height=5,limitsize=F) + } + } +} + + + +if (argsL$performance){ + print("Performance measures:") + print(paste("Mean Test Accuracy",mean(TestAcc),sep=" ")) + print(paste("Mean Training Accuracy",mean(TrainAcc),sep=" ")) + print(paste("Mean F1_1",mean(F1_1),sep=" ")) + print(paste("Mean F1_2",mean(F1_2),sep=" ")) + + for (i in 1:length(FileList)){ + featureMatrix<-c() + for (j in 1:length(coefficients[[i]])){ + if (length(coefficients[[i]][[j]]>1)){ + featureMatrix<-rbind(featureMatrix,coefficients[[i]][[j]][,1]) + } + } + if (length(featureMatrix > 1)){ + write.table(featureMatrix,paste(argsL$outDir,"Regression_Coefficients_Cross_Validation_",FileList[i],sep=""),quote=F,sep="\t",col.names=NA) + meanFeature<-apply(featureMatrix,2,median) + featureMatrix<-featureMatrix[,-1] + meanFeature<-meanFeature[-1] + featureMatrix<-featureMatrix[,which(meanFeature!=0.0)] + meanFeature<-meanFeature[which(meanFeature!=0.0)] + if(length(meanFeature) > 1){ + allFeatures<-featureMatrix[,order(meanFeature,decreasing=TRUE)] + meanFeatures<-meanFeature[order(meanFeature,decreasing=TRUE)] + all<-rbind(allFeatures,meanFeatures) + all<-all[,order(all[dim(all)[1],],decreasing=TRUE)] + row.names(all)<-c(paste("Fold ",c(1:(dim(all)[1]-1))),"Median") + if (gplotsAvailable){ + library("gplots") + svg(paste(argsL$outDir,"Regression_Coefficients_Cross_Validation_Heatmap_",unlist(unlist(strsplit(FileList[i],".txt")))[1],".svg",sep=""),width=min(54,7+(.3*length(meanFeature))),height=min(50,5+(.5*as.numeric(argsL$Ofolds)))) + if(any(allFeatures < 0)){ + allFeatures<-featureMatrix[,order(meanFeature,decreasing=TRUE)] + meanFeature<-meanFeature[order(meanFeature,decreasing=TRUE)] + all<-rbind(allFeatures,meanFeatures) + all<-all[,order(all[dim(all)[1],],decreasing=TRUE)] + row.names(all)<-c(paste("Fold ",c(1:(dim(all)[1]-1))),"Median") + heatmap.2(all,trace="none",col=bluered(250),srtCol=45,cexRow=fontSize,cexCol=fontSize,density.info="none",distfun = distF, dendrogram="none", margins=c(6,6),Colv=FALSE,Rowv=FALSE,key.xlab="Regression coefficient",keysize=0.9) + }else{ + allFeatures<-featureMatrix[,order(meanFeature,decreasing=TRUE)] + meanFeatures<-meanFeature[order(meanFeature,decreasing=TRUE)] + all<-rbind(allFeatures,meanFeatures) + all<-all[,order(all[dim(all)[1],],decreasing=TRUE)] + row.names(all)<-c(paste("Fold ",c(1:(dim(all)[1]-1))),"Median") + heatmap.2(all,trace="none",col=heat.colors(250),srtCol=45,cexRow=fontSize,cexCol=fontSize,density.info="none",distfun = distF, dendrogram="none", margins=c(6,6),Colv=FALSE,Rowv=FALSE,key.xlab="Regression coefficient",keysize=0.9) + } + dev.off() + } + }else{ + if (ggplotAvailable){ + library("ggplot2") + text<-"Mean regression coefficients are to small, a heatmap can not be shown." + ggplot()+annotate("text",x=4,y=25,size=8,label=text)+theme_void() + ggsave(filename=paste(argsL$outDir,"Regression_Coefficients_Cross_Validation_Heatmap_",unlist(unlist(strsplit(FileList[i],".txt")))[1],".png",sep=""),width=11,height=4) + } + } + } + } + #Generating summary output table + colnames(SampleOverview)<-SampleOverview[1,] + SampleOverview<-SampleOverview[-1,] + if(class(SampleOverview)=="matrix"){ + ggplotSampleOverview<-as.data.frame(rbind(cbind(SampleOverview[,1:3],rep("Test",length(SampleOverview[,1]))),cbind(SampleOverview[,c(1,8,9)],rep("Training",length(SampleOverview[,1]))),cbind(SampleOverview[,c(1,4,5)],rep("F1_1",length(SampleOverview[,1]))),cbind(SampleOverview[,c(1,6,7)],rep("F1_2",length(SampleOverview[,1]))))) + }else{ + ggplotSampleOverview<-as.data.frame(rbind(c(SampleOverview[1:3],"Test Accuracy"),c(SampleOverview[c(1,8,9)],"Trainings Accuracy"),c(SampleOverview[c(1,4,5)],"F1-Up"),c(SampleOverview[c(1,6,7)],"F1-Down"))) + } + + colnames(ggplotSampleOverview)<-c("Name","Mean","Variance","Measure") + row.names(ggplotSampleOverview)<-c(1:length(row.names(ggplotSampleOverview))) + ggplotSampleOverview[,2]<-as.numeric(as.character(ggplotSampleOverview[,2])) + ggplotSampleOverview[,3]<-as.numeric(as.character(ggplotSampleOverview[,3])) + write.table(ggplotSampleOverview,file=paste0(argsL$outDir,"/Performance_overview.txt"),quote=FALSE,sep='\t',row.names=FALSE) + if (ggplotAvailable){ + ggplot2::ggplot(ggplotSampleOverview,aes(x=Name,y=Mean,width=0.8,fill=Measure,group=Measure))+ + geom_bar(stat="identity",position="dodge")+ + theme_bw(22)+ylab("Value")+xlab("Sample")+ + theme(axis.text.x=element_text(angle=45,hjust=1))+ + scale_y_continuous(breaks=seq(0.0,1.0,0.05))+ + scale_fill_manual(values=c("red","blue","orange","black"))+ + coord_cartesian(ylim=c(0.0,1.0))+ + geom_errorbar(aes(ymin=Mean-sqrt(Variance),ymax=Mean+sqrt(Variance)),position=position_dodge(0.8),width=.4,size=.5)+ + theme(strip.background = element_blank()) + ggsave(paste0(argsL$outDir,"/Performance_Barplots.png"),width=20,height=20,units=c("cm")) + } +} diff --git a/modules/local/dynamite/dynamite.nf b/modules/local/dynamite/dynamite.nf new file mode 100644 index 0000000..98084c6 --- /dev/null +++ b/modules/local/dynamite/dynamite.nf @@ -0,0 +1,32 @@ +process DYNAMITE { + tag "$meta.id" + label "process_medium" + + conda "bioconda::bedtools conda-forge::gxx conda-forge::r-base conda-forge::r-gplots conda-forge::r-ggplot2 conda-forge::r-glmnet conda-forge::r-doMC conda-forge::r-reshape2 conda-forge::r-gridExtra pandas" + container "registry.hub.docker.com/bigdatainbiomedicine/inspect-tepic" + // TODO: Add more nf-core-like environment definition + + input: + tuple val(meta), path(data, stageAs: "input/classification.tsv") + val(ofolds) + val(ifolds) + val(alpha) + val(randomize) + + output: + tuple val(meta), path("${meta.id}_dynamite/Regression_Coefficients_Entire_Data_Set_classification.txt") + + script: + """ + DYNAMITE.R \\ + --dataDir=input \\ + --outDir="${meta.id}_dynamite" \\ + --out_var="Expression" \\ + --Ofolds=$ofolds \\ + --Ifolds=$ifolds \\ + --alpha=$alpha \\ + --performance=TRUE \\ + --randomise=$randomize \\ + --cores=$task.cpus + """ +} \ No newline at end of file diff --git a/subworkflows/local/dynamite.nf b/subworkflows/local/dynamite.nf index 972e767..2cd3766 100644 --- a/subworkflows/local/dynamite.nf +++ b/subworkflows/local/dynamite.nf @@ -1,4 +1,5 @@ -include { PREPROCESS } from '../../modules/local/dynamite/preprocess' +include { PREPROCESS } from '../../modules/local/dynamite/preprocess' +include { DYNAMITE as RUN_DYNAMITE } from '../../modules/local/dynamite/dynamite' workflow DYNAMITE { take: @@ -22,6 +23,8 @@ workflow DYNAMITE { PREPROCESS(ch_combined) + RUN_DYNAMITE(PREPROCESS.out.output, ofolds, ifolds, alpha, randomize) + ch_versions = ch_versions.mix(PREPROCESS.out.versions) From 57270089a42298536e9b3da12ed325c3d3423a45 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 2 Mar 2024 17:03:56 +0100 Subject: [PATCH 025/206] Remove artificial columns from DYNAMITE input --- bin/dynamite_preprocess.py | 2 ++ subworkflows/local/dynamite.nf | 1 + 2 files changed, 3 insertions(+) diff --git a/bin/dynamite_preprocess.py b/bin/dynamite_preprocess.py index a2aea96..9d7753f 100755 --- a/bin/dynamite_preprocess.py +++ b/bin/dynamite_preprocess.py @@ -25,6 +25,8 @@ def remove_version(gene_id): df_affinities = df_affinities.loc[gene_intersection] df_expression = df_expression.loc[gene_intersection] +df_affinities = df_affinities.drop(["NumPeaks", "AvgPeakDistance", "AvgPeakSize"], axis=1) + df_affinities["Expression"] = 0 df_affinities.loc[df_expression["log2FoldChange"] > 0, "Expression"] = 1 diff --git a/subworkflows/local/dynamite.nf b/subworkflows/local/dynamite.nf index 2cd3766..027625b 100644 --- a/subworkflows/local/dynamite.nf +++ b/subworkflows/local/dynamite.nf @@ -1,5 +1,6 @@ include { PREPROCESS } from '../../modules/local/dynamite/preprocess' include { DYNAMITE as RUN_DYNAMITE } from '../../modules/local/dynamite/dynamite' +include { GAWK as FILTER } from '../../modules/nf-core/gawk/main' workflow DYNAMITE { take: From 4a18f919348138b229d5dd05901c2645f10fbbf2 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 2 Mar 2024 17:09:47 +0100 Subject: [PATCH 026/206] Implement DYNAMITE filtering --- conf/modules.config | 6 ++++++ nextflow.config | 1 + nextflow_schema.json | 7 +++++++ subworkflows/local/dynamite.nf | 9 +++++++-- 4 files changed, 21 insertions(+), 2 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 1fc54e8..95d1b8b 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -54,6 +54,12 @@ process { ext.prefix = {"${meta.id}.merged"} } + withName: ".*DYNAMITE:FILTER" { + ext.args = {"'BEGIN{OFS=\"\\t\"} NR==1 || (\$2 >= ${params.dynamite_min_regression} || \$2 <= -${params.dynamite_min_regression} )'"} + ext.prefix = {"${meta.id}.filtered"} + ext.suffix = "tsv" + } + withName: CUSTOM_DUMPSOFTWAREVERSIONS { publishDir = [ path: { "${params.outdir}/pipeline_info" }, diff --git a/nextflow.config b/nextflow.config index 7deaa18..d0d0ad5 100644 --- a/nextflow.config +++ b/nextflow.config @@ -27,6 +27,7 @@ params { dynamite_ifolds = 6 dynamite_alpha = 0.1 dynamite_randomize = false + dynamite_min_regression = 0.1 // References genome = null diff --git a/nextflow_schema.json b/nextflow_schema.json index e215ef4..e6c2c5b 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -138,6 +138,13 @@ "description": "Randomize the data for dynamite.", "fa_icon": "fas fa-compress-arrows-alt", "help_text": "Randomize the data for dynamite. The default value is `false`." + }, + "dynamite_min_regression": { + "type": "number", + "default": 0.1, + "description": "Minimum regression value for dynamite.", + "fa_icon": "fas fa-compress-arrows-alt", + "help_text": "Minimum regression value for dynamite. The default value is 0.1." } } }, diff --git a/subworkflows/local/dynamite.nf b/subworkflows/local/dynamite.nf index 027625b..a389f64 100644 --- a/subworkflows/local/dynamite.nf +++ b/subworkflows/local/dynamite.nf @@ -26,11 +26,16 @@ workflow DYNAMITE { RUN_DYNAMITE(PREPROCESS.out.output, ofolds, ifolds, alpha, randomize) - ch_versions = ch_versions.mix(PREPROCESS.out.versions) + FILTER(RUN_DYNAMITE.out, []) + ch_versions = ch_versions.mix( + PREPROCESS.out.versions, + FILTER.out.versions + ) - emit: + emit: + FILTER.out.output versions = ch_versions // channel: [ versions.yml ] } From a7002c95905b86266116b818ff9ac2ce4fff5376 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 2 Mar 2024 17:10:25 +0100 Subject: [PATCH 027/206] Add DYNAMITE version capture --- workflows/tfactivity.nf | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/workflows/tfactivity.nf b/workflows/tfactivity.nf index 1291127..36d00ed 100644 --- a/workflows/tfactivity.nf +++ b/workflows/tfactivity.nf @@ -93,7 +93,11 @@ workflow TFACTIVITY { dynamite_randomize ) - ch_versions = ch_versions.mix(COUNTS.out.versions, PEAKS.out.versions) + ch_versions = ch_versions.mix( + COUNTS.out.versions, + PEAKS.out.versions, + DYNAMITE.out.versions + ) // // Collate and save software versions From f993045dbcb2fbfc50c0ed1d8f492e3d30aa96a2 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 2 Mar 2024 17:12:30 +0100 Subject: [PATCH 028/206] Remove fastQC and multiQC traces --- modules.json | 56 +++-- modules/nf-core/fastqc/environment.yml | 7 - modules/nf-core/fastqc/main.nf | 55 ----- modules/nf-core/fastqc/meta.yml | 57 ----- modules/nf-core/fastqc/tests/main.nf.test | 212 ------------------ .../nf-core/fastqc/tests/main.nf.test.snap | 88 -------- modules/nf-core/fastqc/tests/tags.yml | 2 - modules/nf-core/multiqc/environment.yml | 7 - modules/nf-core/multiqc/main.nf | 55 ----- modules/nf-core/multiqc/meta.yml | 58 ----- modules/nf-core/multiqc/tests/main.nf.test | 84 ------- .../nf-core/multiqc/tests/main.nf.test.snap | 41 ---- modules/nf-core/multiqc/tests/tags.yml | 2 - workflows/tfactivity.nf | 28 +-- 14 files changed, 35 insertions(+), 717 deletions(-) delete mode 100644 modules/nf-core/fastqc/environment.yml delete mode 100644 modules/nf-core/fastqc/main.nf delete mode 100644 modules/nf-core/fastqc/meta.yml delete mode 100644 modules/nf-core/fastqc/tests/main.nf.test delete mode 100644 modules/nf-core/fastqc/tests/main.nf.test.snap delete mode 100644 modules/nf-core/fastqc/tests/tags.yml delete mode 100644 modules/nf-core/multiqc/environment.yml delete mode 100644 modules/nf-core/multiqc/main.nf delete mode 100644 modules/nf-core/multiqc/meta.yml delete mode 100644 modules/nf-core/multiqc/tests/main.nf.test delete mode 100644 modules/nf-core/multiqc/tests/main.nf.test.snap delete mode 100644 modules/nf-core/multiqc/tests/tags.yml diff --git a/modules.json b/modules.json index 447169b..99029e2 100644 --- a/modules.json +++ b/modules.json @@ -8,52 +8,58 @@ "atlasgeneannotationmanipulation/gtf2featureannotation": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/merge": { "branch": "master", "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/sort": { "branch": "master", "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/subtract": { "branch": "master", "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cat/cat": { "branch": "master", "git_sha": "9437e6053dccf4aafa022bfd6e7e9de67e625af8", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "deseq2/differential": { "branch": "master", "git_sha": "9326d73af3fbe2ee90d9ce0a737461a727c5118e", - "installed_by": ["modules"] - }, - "fastqc": { - "branch": "master", - "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gawk": { "branch": "master", "git_sha": "dc3527855e7358c6d8400828754c0caa5f11698f", - "installed_by": ["modules"] - }, - "multiqc": { - "branch": "master", - "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/faidx": { "branch": "master", "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] } } }, @@ -62,20 +68,26 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfvalidation_plugin": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } } } -} +} \ No newline at end of file diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml deleted file mode 100644 index 1787b38..0000000 --- a/modules/nf-core/fastqc/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ -name: fastqc -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf deleted file mode 100644 index 9e19a74..0000000 --- a/modules/nf-core/fastqc/main.nf +++ /dev/null @@ -1,55 +0,0 @@ -process FASTQC { - tag "$meta.id" - label 'process_medium' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' : - 'biocontainers/fastqc:0.12.1--hdfd78af_0' }" - - input: - tuple val(meta), path(reads) - - output: - tuple val(meta), path("*.html"), emit: html - tuple val(meta), path("*.zip") , emit: zip - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - // Make list of old name and new name pairs to use for renaming in the bash while loop - def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] } - def rename_to = old_new_pairs*.join(' ').join(' ') - def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ') - """ - printf "%s %s\\n" $rename_to | while read old_name new_name; do - [ -f "\${new_name}" ] || ln -s \$old_name \$new_name - done - - fastqc \\ - $args \\ - --threads $task.cpus \\ - $renamed_files - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) - END_VERSIONS - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.html - touch ${prefix}.zip - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) - END_VERSIONS - """ -} diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml deleted file mode 100644 index ee5507e..0000000 --- a/modules/nf-core/fastqc/meta.yml +++ /dev/null @@ -1,57 +0,0 @@ -name: fastqc -description: Run FastQC on sequenced reads -keywords: - - quality control - - qc - - adapters - - fastq -tools: - - fastqc: - description: | - FastQC gives general quality metrics about your reads. - It provides information about the quality score distribution - across your reads, the per base sequence content (%A/C/G/T). - You get information about adapter contamination and other - overrepresented sequences. - homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ - documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ - licence: ["GPL-2.0-only"] -input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. -output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - html: - type: file - description: FastQC report - pattern: "*_{fastqc.html}" - - zip: - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@drpatelh" - - "@grst" - - "@ewels" - - "@FelixKrueger" -maintainers: - - "@drpatelh" - - "@grst" - - "@ewels" - - "@FelixKrueger" diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test deleted file mode 100644 index 70edae4..0000000 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ /dev/null @@ -1,212 +0,0 @@ -nextflow_process { - - name "Test Process FASTQC" - script "../main.nf" - process "FASTQC" - - tag "modules" - tag "modules_nfcore" - tag "fastqc" - - test("sarscov2 single-end [fastq]") { - - when { - process { - """ - input[0] = Channel.of([ - [ id: 'test', single_end:true ], - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - - // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. - // looks like this:
Mon 2 Oct 2023
test.gz
- // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_single") } - ) - } - } - - test("sarscov2 paired-end [fastq]") { - - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_paired") } - ) - } - } - - test("sarscov2 interleaved [fastq]") { - - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") } - ) - } - } - - test("sarscov2 paired-end [bam]") { - - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_bam") } - ) - } - } - - test("sarscov2 multiple [fastq]") { - - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, - { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, - { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][2]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][3]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_multiple") } - ) - } - } - - test("sarscov2 custom_prefix") { - - when { - process { - """ - input[0] = Channel.of([ - [ id:'mysample', single_end:true ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") } - ) - } - } - - test("sarscov2 single-end [fastq] - stub") { - - options "-stub" - - when { - process { - """ - input[0] = Channel.of([ - [ id: 'test', single_end:true ], - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out.html.collect { file(it[1]).getName() } + - process.out.zip.collect { file(it[1]).getName() } + - process.out.versions ).match("fastqc_stub") } - ) - } - } - -} diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap deleted file mode 100644 index 86f7c31..0000000 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ /dev/null @@ -1,88 +0,0 @@ -{ - "fastqc_versions_interleaved": { - "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-31T17:40:07.293713" - }, - "fastqc_stub": { - "content": [ - [ - "test.html", - "test.zip", - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-31T17:31:01.425198" - }, - "fastqc_versions_multiple": { - "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-31T17:40:55.797907" - }, - "fastqc_versions_bam": { - "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-31T17:40:26.795862" - }, - "fastqc_versions_single": { - "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-31T17:39:27.043675" - }, - "fastqc_versions_paired": { - "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-31T17:39:47.584191" - }, - "fastqc_versions_custom_prefix": { - "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-31T17:41:14.576531" - } -} \ No newline at end of file diff --git a/modules/nf-core/fastqc/tests/tags.yml b/modules/nf-core/fastqc/tests/tags.yml deleted file mode 100644 index 7834294..0000000 --- a/modules/nf-core/fastqc/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -fastqc: - - modules/nf-core/fastqc/** diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml deleted file mode 100644 index ca39fb6..0000000 --- a/modules/nf-core/multiqc/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ -name: multiqc -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - bioconda::multiqc=1.21 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf deleted file mode 100644 index 47ac352..0000000 --- a/modules/nf-core/multiqc/main.nf +++ /dev/null @@ -1,55 +0,0 @@ -process MULTIQC { - label 'process_single' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' : - 'biocontainers/multiqc:1.21--pyhdfd78af_0' }" - - input: - path multiqc_files, stageAs: "?/*" - path(multiqc_config) - path(extra_multiqc_config) - path(multiqc_logo) - - output: - path "*multiqc_report.html", emit: report - path "*_data" , emit: data - path "*_plots" , optional:true, emit: plots - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def config = multiqc_config ? "--config $multiqc_config" : '' - def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' - def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' - """ - multiqc \\ - --force \\ - $args \\ - $config \\ - $extra_config \\ - $logo \\ - . - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) - END_VERSIONS - """ - - stub: - """ - mkdir multiqc_data - touch multiqc_plots - touch multiqc_report.html - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) - END_VERSIONS - """ -} diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml deleted file mode 100644 index 45a9bc3..0000000 --- a/modules/nf-core/multiqc/meta.yml +++ /dev/null @@ -1,58 +0,0 @@ -name: multiqc -description: Aggregate results from bioinformatics analyses across many samples into a single report -keywords: - - QC - - bioinformatics tools - - Beautiful stand-alone HTML report -tools: - - multiqc: - description: | - MultiQC searches a given directory for analysis logs and compiles a HTML report. - It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. - homepage: https://multiqc.info/ - documentation: https://multiqc.info/docs/ - licence: ["GPL-3.0-or-later"] -input: - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC - - multiqc_config: - type: file - description: Optional config yml for MultiQC - pattern: "*.{yml,yaml}" - - extra_multiqc_config: - type: file - description: Second optional config yml for MultiQC. Will override common sections in multiqc_config. - pattern: "*.{yml,yaml}" - - multiqc_logo: - type: file - description: Optional logo file for MultiQC - pattern: "*.{png}" -output: - - report: - type: file - description: MultiQC report file - pattern: "multiqc_report.html" - - data: - type: directory - description: MultiQC data dir - pattern: "multiqc_data" - - plots: - type: file - description: Plots created by MultiQC - pattern: "*_data" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@abhi18av" - - "@bunop" - - "@drpatelh" - - "@jfy133" -maintainers: - - "@abhi18av" - - "@bunop" - - "@drpatelh" - - "@jfy133" diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test deleted file mode 100644 index f1c4242..0000000 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ /dev/null @@ -1,84 +0,0 @@ -nextflow_process { - - name "Test Process MULTIQC" - script "../main.nf" - process "MULTIQC" - - tag "modules" - tag "modules_nfcore" - tag "multiqc" - - test("sarscov2 single-end [fastqc]") { - - when { - process { - """ - input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) - input[1] = [] - input[2] = [] - input[3] = [] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, - { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("multiqc_versions_single") } - ) - } - - } - - test("sarscov2 single-end [fastqc] [config]") { - - when { - process { - """ - input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) - input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) - input[2] = [] - input[3] = [] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, - { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("multiqc_versions_config") } - ) - } - } - - test("sarscov2 single-end [fastqc] - stub") { - - options "-stub" - - when { - process { - """ - input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) - input[1] = [] - input[2] = [] - input[3] = [] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out.report.collect { file(it).getName() } + - process.out.data.collect { file(it).getName() } + - process.out.plots.collect { file(it).getName() } + - process.out.versions ).match("multiqc_stub") } - ) - } - - } -} diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap deleted file mode 100644 index bfebd80..0000000 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ /dev/null @@ -1,41 +0,0 @@ -{ - "multiqc_versions_single": { - "content": [ - [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-29T08:48:55.657331" - }, - "multiqc_stub": { - "content": [ - [ - "multiqc_report.html", - "multiqc_data", - "multiqc_plots", - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-29T08:49:49.071937" - }, - "multiqc_versions_config": { - "content": [ - [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-29T08:49:25.457567" - } -} \ No newline at end of file diff --git a/modules/nf-core/multiqc/tests/tags.yml b/modules/nf-core/multiqc/tests/tags.yml deleted file mode 100644 index bea6c0d..0000000 --- a/modules/nf-core/multiqc/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -multiqc: - - modules/nf-core/multiqc/** diff --git a/workflows/tfactivity.nf b/workflows/tfactivity.nf index 36d00ed..a02f4b8 100644 --- a/workflows/tfactivity.nf +++ b/workflows/tfactivity.nf @@ -51,11 +51,6 @@ workflow TFACTIVITY { main: - // ch_multiqc_files = Channel.empty() - - // ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}) - // ch_versions = ch_versions.mix(FASTQC.out.versions.first()) - ch_conditions = ch_samplesheet.map { meta, peak_file -> meta.condition } .toSortedList().flatten().unique() @@ -106,29 +101,8 @@ workflow TFACTIVITY { .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true) .set { ch_collated_versions } - // - // MODULE: MultiQC - // - // ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) - // ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty() - // ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty() - // summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") - // ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) - // ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) - // ch_methods_description = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description)) - // ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - // ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) - // ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false)) - - // MULTIQC ( - // ch_multiqc_files.collect(), - // ch_multiqc_config.toList(), - // ch_multiqc_custom_config.toList(), - // ch_multiqc_logo.toList() - // ) - emit: - multiqc_report = Channel.empty() // MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html + multiqc_report = Channel.empty() versions = ch_versions // channel: [ path(versions.yml) ] } From 41381a06381aa1d0e59db29ac7756556774ec920 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 2 Mar 2024 17:13:07 +0100 Subject: [PATCH 029/206] Rename DYNAMITE output --- subworkflows/local/dynamite.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/dynamite.nf b/subworkflows/local/dynamite.nf index a389f64..2ead542 100644 --- a/subworkflows/local/dynamite.nf +++ b/subworkflows/local/dynamite.nf @@ -35,7 +35,7 @@ workflow DYNAMITE { emit: - FILTER.out.output + regression_coefficients = FILTER.out.output versions = ch_versions // channel: [ versions.yml ] } From cdca486d6fe90ec8ee00cce08f32cbb16d5437a5 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 2 Mar 2024 17:59:34 +0100 Subject: [PATCH 030/206] Implement calculation of TF TG score --- bin/DYNAMITE.R | 2 +- bin/tf_tg_score.py | 51 ++++++++++++++++++++++++++++ modules/local/counts/combine.nf | 2 +- modules/local/ranking/tf_tg_score.nf | 32 +++++++++++++++++ nextflow.config | 2 +- nextflow_schema.json | 4 +-- subworkflows/local/peaks.nf | 4 +++ subworkflows/local/ranking.nf | 32 +++++++++++++++++ workflows/tfactivity.nf | 7 ++++ 9 files changed, 131 insertions(+), 5 deletions(-) create mode 100755 bin/tf_tg_score.py create mode 100644 modules/local/ranking/tf_tg_score.nf create mode 100644 subworkflows/local/ranking.nf diff --git a/bin/DYNAMITE.R b/bin/DYNAMITE.R index 4fd850d..bc98be4 100755 --- a/bin/DYNAMITE.R +++ b/bin/DYNAMITE.R @@ -132,7 +132,7 @@ for(Sample in FileList){ print(paste0("Learning model for ",name)) i<-i+1 #Loading the data matrix - M<-read.table(paste(argsL$dataDir,Sample,sep="/"),header=TRUE,stringsAsFactors=FALSE,row.names=1) + M<-read.table(paste(argsL$dataDir,Sample,sep="/"),header=TRUE,stringsAsFactors=FALSE,row.names=1,check.names=FALSE) #Removing features with standard deviation zero SD<-apply(M,2,sd) Feature_zero_SD<-as.vector(which(SD==0)) diff --git a/bin/tf_tg_score.py b/bin/tf_tg_score.py new file mode 100755 index 0000000..afe764c --- /dev/null +++ b/bin/tf_tg_score.py @@ -0,0 +1,51 @@ +#!/usr/bin/env python3 + +import pandas as pd +import argparse + +parser = argparse.ArgumentParser(description='Calculate TF-TG scores') +parser.add_argument('--differential', type=str, help='Differential expression file') +parser.add_argument('--affinities', type=str, help='Affinity file') +parser.add_argument('--regression_coefficients', type=str, help='Regression coefficients file') +parser.add_argument('--output', type=str, help='Output file') + +args = parser.parse_args() + +def remove_version(gene_id): + return gene_id.split(".")[0] + +df_differential = pd.read_csv(args.differential, sep='\t', index_col=0) +df_affinities = pd.read_csv(args.affinities, sep='\t', index_col=0) +df_coefficients = pd.read_csv(args.regression_coefficients, sep='\t', index_col=0) + +# Remove version from gene ids +df_differential.index = df_differential.index.map(remove_version) +df_affinities.index = df_affinities.index.map(remove_version) + +# Make sure genes are in common between the differential expression and affinities files +gene_intersection = df_differential.index.intersection(df_affinities.index) +assert len(gene_intersection) > 0, "No genes found in common between the differential expression and affinities files" + +df_affinities = df_affinities.loc[gene_intersection] +df_differential = df_differential.loc[gene_intersection] + +# Make sure TFs are in common between the affinities and coefficients files +tf_intersection = df_affinities.columns.intersection(df_coefficients.index) +assert len(tf_intersection) > 0, "No TFs found in common between the affinities and coefficients files" + +df_affinities = df_affinities[tf_intersection] +df_coefficients = df_coefficients.loc[tf_intersection] + + +# Calculate the TF-TG scores + +## Multiply the log2FC by the affinities +result = df_affinities \ + .mul(abs(df_differential["log2FoldChange"]), axis=0) \ + .mul(abs(df_coefficients["value"]), axis=1) + +## Make sure results are not empty +assert not result.empty, "No TF-TG scores were calculated" + +# Save the result +result.to_csv(args.output, sep='\t') \ No newline at end of file diff --git a/modules/local/counts/combine.nf b/modules/local/counts/combine.nf index aaf7c06..d457fba 100644 --- a/modules/local/counts/combine.nf +++ b/modules/local/counts/combine.nf @@ -1,6 +1,6 @@ process COMBINE_COUNTS { tag "$meta.id" - label "process_low" + label "process_single" conda "conda-forge::mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6==fccb0c41a243c639e11dd1be7b74f563e624fcca-0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/local/ranking/tf_tg_score.nf b/modules/local/ranking/tf_tg_score.nf new file mode 100644 index 0000000..f28d74a --- /dev/null +++ b/modules/local/ranking/tf_tg_score.nf @@ -0,0 +1,32 @@ +process TF_TG_SCORE { + tag "$meta.id" + label "process_single" + + conda "conda-forge::mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6==fccb0c41a243c639e11dd1be7b74f563e624fcca-0" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0': + 'biocontainers/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0' }" + + input: + tuple val(meta), path(differential), path(affinities), path(regression_coefficients) + + output: + tuple val(meta), path("*.score.tsv"), emit: counts + + path "versions.yml" , emit: versions + + script: + """ + tf_tg_score.py \\ + --differential ${differential} \\ + --affinities ${affinities} \\ + --regression_coefficients ${regression_coefficients} \\ + --output ${meta.id}.score.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + python: \$(python --version | sed 's/Python //g') + pandas: \$(python -c "import pandas; print(pandas.__version__)") + END_VERSIONS + """ +} \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index d0d0ad5..193f58a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -21,7 +21,7 @@ params { window_size = 50000 decay = true min_count = 50 - min_tpm = 0 + min_tpm = 1 dynamite_ofolds = 3 dynamite_ifolds = 6 diff --git a/nextflow_schema.json b/nextflow_schema.json index e6c2c5b..5146ef5 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -106,10 +106,10 @@ }, "min_tpm": { "type": "number", - "default": 0, + "default": 1, "description": "Minimum TPM to keep a gene in the analysis.", "fa_icon": "fas fa-compress-arrows-alt", - "help_text": "Minimum TPM to keep a gene in the analysis. The default value is 0." + "help_text": "Minimum TPM to keep a gene in the analysis. The default value is 1." }, "dynamite_ofolds": { "type": "integer", diff --git a/subworkflows/local/peaks.nf b/subworkflows/local/peaks.nf index 451b222..c6cce2b 100644 --- a/subworkflows/local/peaks.nf +++ b/subworkflows/local/peaks.nf @@ -5,6 +5,7 @@ include { BEDTOOLS_SUBTRACT as BLACKLIST } from '../../modules/nf-core/bedtools include { STARE } from '../../modules/local/stare/main' include { COMBINE_TABLES as AFFINITY_MEAN } from '../../modules/local/combine_tables/main' include { COMBINE_TABLES as AFFINITY_RATIO} from '../../modules/local/combine_tables/main' +include { COMBINE_TABLES as AFFINITY_SUM } from '../../modules/local/combine_tables/main' // Subworkflows include { FOOTPRINTING } from './footprinting' @@ -97,14 +98,17 @@ workflow PEAKS { [affinities1, affinities2]] } AFFINITY_RATIO(ch_contrast_affinities, "ratio") + AFFINITY_SUM(ch_contrast_affinities, "sum") ch_versions = ch_versions.mix( STARE.out.versions, AFFINITY_RATIO.out.versions, + AFFINITY_SUM.out.versions ) emit: affinity_ratio = AFFINITY_RATIO.out.combined + affinity_sum = AFFINITY_SUM.out.combined versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/local/ranking.nf b/subworkflows/local/ranking.nf new file mode 100644 index 0000000..6a75466 --- /dev/null +++ b/subworkflows/local/ranking.nf @@ -0,0 +1,32 @@ +include { TF_TG_SCORE } from '../../modules/local/ranking/tf_tg_score' + +workflow RANKING { + + take: + ch_differential + ch_affinities + ch_regression_coefficients + + main: + + ch_versions = Channel.empty() + + ch_combined = ch_differential.map{meta, differential -> + [meta.condition1, meta.condition2, differential]} + .combine(ch_affinities.map{meta, affinities -> + [meta.condition1, meta.condition2, meta.assay, affinities]}, by: [0, 1]) + .map{condition1, condition2, differential, assay, affinities -> + [condition1, condition2, assay, differential, affinities]} + .combine(ch_regression_coefficients.map{meta, regression_coefficients -> + [meta.condition1, meta.condition2, meta.assay, meta, regression_coefficients]}, by: [0, 1, 2]) + .map{condition1, condition2, assay, differential, affinities, meta, regression_coefficients -> + [meta, differential, affinities, regression_coefficients]} + + TF_TG_SCORE(ch_combined) + + emit: + + + versions = ch_versions // channel: [ versions.yml ] +} + diff --git a/workflows/tfactivity.nf b/workflows/tfactivity.nf index a02f4b8..ff3cd6e 100644 --- a/workflows/tfactivity.nf +++ b/workflows/tfactivity.nf @@ -14,6 +14,7 @@ include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome' include { COUNTS } from '../subworkflows/local/counts' include { PEAKS } from '../subworkflows/local/peaks' include { DYNAMITE } from '../subworkflows/local/dynamite' +include { RANKING } from '../subworkflows/local/ranking' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -88,6 +89,12 @@ workflow TFACTIVITY { dynamite_randomize ) + RANKING( + COUNTS.out.differential, + PEAKS.out.affinity_sum, + DYNAMITE.out.regression_coefficients + ) + ch_versions = ch_versions.mix( COUNTS.out.versions, PEAKS.out.versions, From afab053a745ea4546f6f7fe1fed0e8bb2a0526a8 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 2 Mar 2024 18:10:49 +0100 Subject: [PATCH 031/206] Implement ranking --- bin/ranking.py | 43 +++++++++++++++++++++++++++ main.nf | 2 ++ modules/local/counts/calculate_tpm.nf | 2 +- modules/local/counts/filter_genes.nf | 2 +- modules/local/ranking/ranking.nf | 30 +++++++++++++++++++ modules/local/ranking/tf_tg_score.nf | 2 +- nextflow.config | 2 ++ nextflow_schema.json | 7 +++++ subworkflows/local/ranking.nf | 6 +++- workflows/tfactivity.nf | 6 +++- 10 files changed, 97 insertions(+), 5 deletions(-) create mode 100755 bin/ranking.py create mode 100644 modules/local/ranking/ranking.nf diff --git a/bin/ranking.py b/bin/ranking.py new file mode 100755 index 0000000..ad4107b --- /dev/null +++ b/bin/ranking.py @@ -0,0 +1,43 @@ +#!/usr/bin/env python3 + +import argparse +import pandas as pd +import statistics as st +import scipy.stats as stats + +parser = argparse.ArgumentParser(description='Create TF ranking') +parser.add_argument('--input', type=str, help='Score file', required=True) +parser.add_argument('--alpha', type=float, help='Alpha value', required=True) +parser.add_argument('--output', type=str, help='Output file', required=True) + +args = parser.parse_args() + +df = pd.read_csv(args.input, sep='\t', header=0, index_col=0).T +df = df.dropna(axis=1, how='all') + +# Save whole content of the dataframe in a single, flattened list +background = df.values.flatten().tolist() +background_median = st.median(background) + +def mann_whitney_u(background, foreground): + _, p = stats.mannwhitneyu(background, foreground) + return p + +# Transform df to have the following columns: sum, mean, q95, q99, median, p-value +df['sum'] = df.sum(axis=1) +df['mean'] = df.mean(axis=1) +df['q95'] = df.quantile(0.95, axis=1) +df['q99'] = df.quantile(0.99, axis=1) +df['median'] = df.median(axis=1) +df['p-value'] = df.apply(lambda x: mann_whitney_u(background, x), axis=1) + +df = df[['sum', 'mean', 'q95', 'q99', 'median', 'p-value']] +df = df[(df['median'] > background_median) & (df['p-value'] < args.alpha)] + +df.sort_values(by=['median'], ascending=False, inplace=True) + +length = len(df.index) +df['rank'] = range(1, length + 1) +df['dcg'] = 1 - (df['rank'] - 1) / length + +df.to_csv(args.output, sep='\t') \ No newline at end of file diff --git a/main.nf b/main.nf index 23dcb21..6a37a4f 100644 --- a/main.nf +++ b/main.nf @@ -94,6 +94,8 @@ workflow NFCORE_TFACTIVITY { params.dynamite_alpha, params.dynamite_randomize, + params.alpha, + ch_versions ) diff --git a/modules/local/counts/calculate_tpm.nf b/modules/local/counts/calculate_tpm.nf index d5e567c..12df59c 100644 --- a/modules/local/counts/calculate_tpm.nf +++ b/modules/local/counts/calculate_tpm.nf @@ -1,6 +1,6 @@ process CALCULATE_TPM { tag "$meta.id" - label "process_low" + label "process_single" conda "conda-forge::mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6==fccb0c41a243c639e11dd1be7b74f563e624fcca-0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/local/counts/filter_genes.nf b/modules/local/counts/filter_genes.nf index 9b1a6fd..2127452 100644 --- a/modules/local/counts/filter_genes.nf +++ b/modules/local/counts/filter_genes.nf @@ -1,6 +1,6 @@ process FILTER_GENES { tag "$meta.id" - label "process_low" + label "process_single" conda "conda-forge::mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6==fccb0c41a243c639e11dd1be7b74f563e624fcca-0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/local/ranking/ranking.nf b/modules/local/ranking/ranking.nf new file mode 100644 index 0000000..e625822 --- /dev/null +++ b/modules/local/ranking/ranking.nf @@ -0,0 +1,30 @@ +process RANKING { + tag "$meta.id" + label "process_single" + + conda "bioconda::mulled-v2-cd5249a47f81a81b2e7785172c240f12497f55b4==c5c6cff7c28d3260400f938602ee600b1acf0323-0" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-cd5249a47f81a81b2e7785172c240f12497f55b4:c5c6cff7c28d3260400f938602ee600b1acf0323-0': + 'biocontainers/mulled-v2-cd5249a47f81a81b2e7785172c240f12497f55b4:c5c6cff7c28d3260400f938602ee600b1acf0323-0' }" + + input: + tuple val(meta), path(tf_tg_score) + val(alpha) + + output: + tuple val(meta), path("*.ranking.tsv"), emit: ranking + + path "versions.yml" , emit: versions + + script: + """ + ranking.py --input ${tf_tg_score} --alpha ${alpha} --output ${meta.id}.ranking.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + python: \$(python --version | sed 's/Python //g') + pandas: \$(python -c "import pandas; print(pandas.__version__)") + numpy: \$(python -c "import numpy; print(numpy.__version__)") + END_VERSIONS + """ +} \ No newline at end of file diff --git a/modules/local/ranking/tf_tg_score.nf b/modules/local/ranking/tf_tg_score.nf index f28d74a..a2b8955 100644 --- a/modules/local/ranking/tf_tg_score.nf +++ b/modules/local/ranking/tf_tg_score.nf @@ -11,7 +11,7 @@ process TF_TG_SCORE { tuple val(meta), path(differential), path(affinities), path(regression_coefficients) output: - tuple val(meta), path("*.score.tsv"), emit: counts + tuple val(meta), path("*.score.tsv"), emit: score path "versions.yml" , emit: versions diff --git a/nextflow.config b/nextflow.config index 193f58a..4841d3f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -29,6 +29,8 @@ params { dynamite_randomize = false dynamite_min_regression = 0.1 + alpha = 0.05 + // References genome = null igenomes_base = 's3://ngi-igenomes/igenomes/' diff --git a/nextflow_schema.json b/nextflow_schema.json index 5146ef5..a8ae259 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -145,6 +145,13 @@ "description": "Minimum regression value for dynamite.", "fa_icon": "fas fa-compress-arrows-alt", "help_text": "Minimum regression value for dynamite. The default value is 0.1." + }, + "alpha": { + "type": "number", + "default": 0.05, + "description": "Alpha value for the Mann-Whitney U test.", + "fa_icon": "fas fa-compress-arrows-alt", + "help_text": "Alpha value for the Mann-Whitney U test. The default value is 0.05." } } }, diff --git a/subworkflows/local/ranking.nf b/subworkflows/local/ranking.nf index 6a75466..2773dda 100644 --- a/subworkflows/local/ranking.nf +++ b/subworkflows/local/ranking.nf @@ -1,4 +1,5 @@ -include { TF_TG_SCORE } from '../../modules/local/ranking/tf_tg_score' +include { TF_TG_SCORE } from '../../modules/local/ranking/tf_tg_score' +include { RANKING as CREATE_RANKING } from '../../modules/local/ranking/ranking' workflow RANKING { @@ -6,6 +7,7 @@ workflow RANKING { ch_differential ch_affinities ch_regression_coefficients + alpha main: @@ -23,6 +25,8 @@ workflow RANKING { [meta, differential, affinities, regression_coefficients]} TF_TG_SCORE(ch_combined) + CREATE_RANKING(TF_TG_SCORE.out.score, alpha) + emit: diff --git a/workflows/tfactivity.nf b/workflows/tfactivity.nf index ff3cd6e..ba6f3f3 100644 --- a/workflows/tfactivity.nf +++ b/workflows/tfactivity.nf @@ -48,6 +48,9 @@ workflow TFACTIVITY { dynamite_alpha dynamite_randomize + // Ranking + alpha + ch_versions main: @@ -92,7 +95,8 @@ workflow TFACTIVITY { RANKING( COUNTS.out.differential, PEAKS.out.affinity_sum, - DYNAMITE.out.regression_coefficients + DYNAMITE.out.regression_coefficients, + alpha ) ch_versions = ch_versions.mix( From e03689ed6222ac6c6fbb3ed17c967eb5b06ecafb Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 2 Mar 2024 18:18:33 +0100 Subject: [PATCH 032/206] Clean up modules.config --- conf/modules.config | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 95d1b8b..3042899 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -13,7 +13,7 @@ process { publishDir = [ - path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, + path: { "${params.outdir}/all/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] @@ -60,21 +60,19 @@ process { ext.suffix = "tsv" } - withName: CUSTOM_DUMPSOFTWAREVERSIONS { + withName: ".*RANKING:CREATE_RANKING" { publishDir = [ - path: { "${params.outdir}/pipeline_info" }, + path: { "${params.outdir}/specific_ranking" }, mode: params.publish_dir_mode, - pattern: '*_versions.yml' + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] } - withName: 'MULTIQC' { - ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } + withName: CUSTOM_DUMPSOFTWAREVERSIONS { publishDir = [ - path: { "${params.outdir}/multiqc" }, + path: { "${params.outdir}/pipeline_info" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + pattern: '*_versions.yml' ] } - } From d75fa8c6bfd358f245ddbf25270b34516205a008 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 2 Mar 2024 18:52:55 +0100 Subject: [PATCH 033/206] Update README --- README.md | 48 +++++++++++++++++++---------- docs/images/mqc_fastqc_adapter.png | Bin 23458 -> 0 bytes docs/images/mqc_fastqc_counts.png | Bin 33918 -> 0 bytes docs/images/mqc_fastqc_quality.png | Bin 55769 -> 0 bytes docs/images/tfprio.jpeg | Bin 0 -> 571305 bytes 5 files changed, 31 insertions(+), 17 deletions(-) delete mode 100755 docs/images/mqc_fastqc_adapter.png delete mode 100755 docs/images/mqc_fastqc_counts.png delete mode 100755 docs/images/mqc_fastqc_quality.png create mode 100644 docs/images/tfprio.jpeg diff --git a/README.md b/README.md index 9408d37..b7b2690 100644 --- a/README.md +++ b/README.md @@ -19,28 +19,26 @@ ## Introduction -**nf-core/tfactivity** is a bioinformatics pipeline that ... +**nf-core/tfactivity** is a bioinformatics pipeline that can identify the most differentially active transcription factors (TFs) between multiple conditions. It takes a count matrix and open chromatin data (ATAC-seq, DNase-seq, HM-ChIP-seq) as input. It produces a ranking of transcription factors. +It is strongly based on the TF-Prioritizer, with the following workflow: - +![TF-Prioritizer workflow](docs/images/tfprio.jpeg) - - - -1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) -2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) +1. Identify accessible regions (can perform footprinting between close ChIP-seq peaks or take ATAC-seq peaks) +2. Calculate affinity scores for combinations of transcription factors and target genes (TGs) using [STARE](https://doi.org/10.1093/bioinformatics/btad062) +3. Identify differentially expressed genes between conditions +4. Utilize linear regression to identify the transcription factors that are most likely to be responsible for the differential gene expression +5. Calculate the TF-TG score based on: + 1. Differential expression of the target genes + 2. Affinity of the transcription factors to the target genes + 3. The regression coefficient of the transcription factors +6. Perform a Mann-Whitney U test and create a ranking of the transcription factors ## Usage > [!NOTE] > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. - +The `sample` column should match the columns in the expression matrix. The `condition` column is needs to match the `condition` column in the samplesheet. Additional covariates can be added to the design matrix and will be used in the differential expression analysis. Now, you can run the pipeline using: @@ -68,6 +78,9 @@ Now, you can run the pipeline using: nextflow run nf-core/tfactivity \ -profile \ --input samplesheet.csv \ + --genome GRCh38 \ + --counts \ + --counts_design design_matrix.csv \ --outdir ``` @@ -87,9 +100,10 @@ For more details about the output files and reports, please refer to the nf-core/tfactivity was originally written by Nico Trummer. + +If applicable, make list of people who have also contributed --> ## Contributions and Support diff --git a/docs/images/mqc_fastqc_adapter.png b/docs/images/mqc_fastqc_adapter.png deleted file mode 100755 index 361d0e47acfb424dea1f326590d1eb2f6dfa26b5..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 23458 zcmeFZ2UJtryD!S#x<#o93es(Ww4k)maRbte0-+a?-g^xY-3myTE`8G_KvA54)F1tn})nJ5u%TA4Y;^!^{48eL_}p#q-Umo0M|F1 z74+PQh^X8N|9_jcWbq~ zzn+tZC9B75nKdz=gQ8wo9GJ$P{D~3knlI_`-PRhCw34f1oYDLr^;oEbgxa#A^J%*2 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zx=>_qZ_#Fy|IKtllecIrN2BHYC*Bbp3Ep>G1*{44Z9dWOtODFTjvCqNP=~G}@@^)P zD5jR<=}E~B@u>gAbZP&`bb%STcEsQSr+&CR}n1rEJ?Hu^Up>x(uX_ zKXQ5eGdFMhV6;N&&f248XI+ohs~dqNzlyDm_SWuLyFi@sf=)k8c0Q?(qvp*bP2mTLCy7bZj literal 0 HcmV?d00001 From 47e6e85b18de82f970cc3b7ae8fb0c2da6b00ce2 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 2 Mar 2024 19:00:48 +0100 Subject: [PATCH 034/206] Update CITATIONS --- CITATIONS.md | 16 ++++++++++++---- README.md | 4 ++-- 2 files changed, 14 insertions(+), 6 deletions(-) diff --git a/CITATIONS.md b/CITATIONS.md index e7a20f9..6a0827a 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -10,13 +10,21 @@ ## Pipeline tools -- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) +- [DeSeq2](https://doi.org/10.1186/s13059-014-0550-8) - > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. + > Love, M.I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15, 550 (2014). -- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) +- [STARE](https://doi.org/10.1093/bioinformatics/btad062) - > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. + > Dennis Hecker, Fatemeh Behjati Ardakani, Alexander Karollus, Julien Gagneur, Marcel H Schulz, The adapted Activity-By-Contact model for enhancer–gene assignment and its application to single-cell data, Bioinformatics, Volume 39, Issue 2, February 2023 + +- [Bedtools](https://doi.org/10.1093%2Fbioinformatics%2Fbtq033) + + > Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28. PMID: 20110278; PMCID: PMC2832824. + +- [GTFtools](https://doi.org/10.1093/bioinformatics/btac561) + + > Hong-Dong Li, Cui-Xiang Lin, Jiantao Zheng, GTFtools: a software package for analyzing various features of gene models, Bioinformatics, Volume 38, Issue 20, 15 October 2022, Pages 4806–4808, ## Software packaging/containerisation tools diff --git a/README.md b/README.md index b7b2690..a7a6426 100644 --- a/README.md +++ b/README.md @@ -100,10 +100,10 @@ For more details about the output files and reports, please refer to the nf-core/tfactivity was originally written by Nico Trummer. - +- Markus Hoffmann +- Leon Hafner ## Contributions and Support From 3982b98d43dab97bde25cacd6e1a5b822b63844d Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 2 Mar 2024 19:02:29 +0100 Subject: [PATCH 035/206] Remove samtools traces --- modules.json | 7 --- .../nf-core/samtools/faidx/environment.yml | 8 --- modules/nf-core/samtools/faidx/main.nf | 50 --------------- modules/nf-core/samtools/faidx/meta.yml | 61 ------------------- subworkflows/local/prepare_genome.nf | 7 +-- 5 files changed, 1 insertion(+), 132 deletions(-) delete mode 100644 modules/nf-core/samtools/faidx/environment.yml delete mode 100644 modules/nf-core/samtools/faidx/main.nf delete mode 100644 modules/nf-core/samtools/faidx/meta.yml diff --git a/modules.json b/modules.json index 99029e2..19689a5 100644 --- a/modules.json +++ b/modules.json @@ -53,13 +53,6 @@ "installed_by": [ "modules" ] - }, - "samtools/faidx": { - "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": [ - "modules" - ] } } }, diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml deleted file mode 100644 index 3e95dd7..0000000 --- a/modules/nf-core/samtools/faidx/environment.yml +++ /dev/null @@ -1,8 +0,0 @@ -name: samtools_faidx -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf deleted file mode 100644 index cfe7ad9..0000000 --- a/modules/nf-core/samtools/faidx/main.nf +++ /dev/null @@ -1,50 +0,0 @@ -process SAMTOOLS_FAIDX { - tag "$fasta" - label 'process_single' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : - 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" - - input: - tuple val(meta), path(fasta) - tuple val(meta2), path(fai) - - output: - tuple val(meta), path ("*.{fa,fasta}") , emit: fa , optional: true - tuple val(meta), path ("*.fai") , emit: fai, optional: true - tuple val(meta), path ("*.gzi") , emit: gzi, optional: true - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - """ - samtools \\ - faidx \\ - $fasta \\ - $args - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS - """ - - stub: - def match = (task.ext.args =~ /-o(?:utput)?\s(.*)\s?/).findAll() - def fastacmd = match[0] ? "touch ${match[0][1]}" : '' - """ - ${fastacmd} - touch ${fasta}.fai - - cat <<-END_VERSIONS > versions.yml - - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS - """ -} diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml deleted file mode 100644 index e189af2..0000000 --- a/modules/nf-core/samtools/faidx/meta.yml +++ /dev/null @@ -1,61 +0,0 @@ -name: samtools_faidx -description: Index FASTA file -keywords: - - index - - fasta - - faidx -tools: - - samtools: - description: | - SAMtools is a set of utilities for interacting with and post-processing - short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. - These files are generated as output by short read aligners like BWA. - homepage: http://www.htslib.org/ - documentation: http://www.htslib.org/doc/samtools.html - doi: 10.1093/bioinformatics/btp352 - licence: ["MIT"] -input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: FASTA file - pattern: "*.{fa,fasta}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fai: - type: file - description: FASTA index file - pattern: "*.{fai}" -output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fai: - type: file - description: FASTA index file - pattern: "*.{fai}" - - gzi: - type: file - description: Optional gzip index file for compressed inputs - pattern: "*.gzi" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@drpatelh" - - "@ewels" - - "@phue" -maintainers: - - "@drpatelh" - - "@ewels" - - "@phue" diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index 55c85f6..c50bea0 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -1,6 +1,5 @@ include { ATLASGENEANNOTATIONMANIPULATION_GTF2FEATUREANNOTATION as EXTRACT_ID_SYMBOL_MAP } from '../../modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/main.nf' include { GTFTOOLS_LENGTH } from '../../modules/local/gtftools/length/main' -include { SAMTOOLS_FAIDX } from '../../modules/nf-core/samtools/faidx/main' workflow PREPARE_GENOME { @@ -20,19 +19,15 @@ workflow PREPARE_GENOME { EXTRACT_ID_SYMBOL_MAP(ch_gtf_tuple, [[], []]) GTFTOOLS_LENGTH(ch_gtf_tuple) - // Prepare fasta index - - SAMTOOLS_FAIDX(ch_fasta_tuple, [[], []]) ch_versions = ch_versions.mix( EXTRACT_ID_SYMBOL_MAP.out.versions, - SAMTOOLS_FAIDX.out.versions + GTFTOOLS_LENGTH.out.versions ) emit: gene_map = EXTRACT_ID_SYMBOL_MAP.out.feature_annotation gene_lengths = GTFTOOLS_LENGTH.out.lengths - fai = SAMTOOLS_FAIDX.out.fai versions = ch_versions // channel: [ versions.yml ] } From 53d99c703a6fe52afab47dc67637a1b982eea3d5 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 2 Mar 2024 19:05:11 +0100 Subject: [PATCH 036/206] Add developers --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index a7a6426..a901568 100644 --- a/README.md +++ b/README.md @@ -102,8 +102,8 @@ nf-core/tfactivity was originally written by Nico Trummer. We thank the following people for their extensive assistance in the development of this pipeline: -- Markus Hoffmann -- Leon Hafner +- [Markus Hoffmann](https://scholar.google.com/citations?user=_qXUS28AAAAJ) +- [Leon Hafner](https://www.linkedin.com/in/leon-hafner/) ## Contributions and Support From 2e099d3be5bd9c45fadd311456a462aaf47eba42 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 18 Mar 2024 14:37:49 +0100 Subject: [PATCH 037/206] Implement combining of rankings --- bin/combine_rankings.py | 20 ++++++++++++++++ conf/modules.config | 8 +++++++ modules/local/ranking/combine_rankings.nf | 29 +++++++++++++++++++++++ subworkflows/local/ranking.nf | 5 ++++ 4 files changed, 62 insertions(+) create mode 100755 bin/combine_rankings.py create mode 100644 modules/local/ranking/combine_rankings.nf diff --git a/bin/combine_rankings.py b/bin/combine_rankings.py new file mode 100755 index 0000000..965595e --- /dev/null +++ b/bin/combine_rankings.py @@ -0,0 +1,20 @@ +#!/usr/bin/env python3 + +import argparse +import pandas as pd + +parser = argparse.ArgumentParser(description='Combine TF rankings') +parser.add_argument('--input', type=str, nargs='+', help='Assay specific score files', required=True) +parser.add_argument('--output', type=str, help='Output file', required=True) + +args = parser.parse_args() + +dfs = [pd.read_csv(f, sep='\t', header=0, index_col=0) for f in args.input] +df = pd.concat([df[['dcg']] for df in dfs]) + +df = df.groupby(df.index).sum() +df.sort_values(by=['dcg'], ascending=False, inplace=True) + +df['rank'] = range(1, len(df.index) + 1) + +df.to_csv(args.output, sep='\t', index=True) \ No newline at end of file diff --git a/conf/modules.config b/conf/modules.config index 3042899..3297b7f 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -68,6 +68,14 @@ process { ] } + withName: COMBINE_RANKINGS { + publishDir = [ + path: { "${params.outdir}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + withName: CUSTOM_DUMPSOFTWAREVERSIONS { publishDir = [ path: { "${params.outdir}/pipeline_info" }, diff --git a/modules/local/ranking/combine_rankings.nf b/modules/local/ranking/combine_rankings.nf new file mode 100644 index 0000000..fe8b8a0 --- /dev/null +++ b/modules/local/ranking/combine_rankings.nf @@ -0,0 +1,29 @@ +process COMBINE_RANKINGS { + tag "$meta.id" + label "process_single" + + conda "bioconda::mulled-v2-cd5249a47f81a81b2e7785172c240f12497f55b4==c5c6cff7c28d3260400f938602ee600b1acf0323-0" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-cd5249a47f81a81b2e7785172c240f12497f55b4:c5c6cff7c28d3260400f938602ee600b1acf0323-0': + 'biocontainers/mulled-v2-cd5249a47f81a81b2e7785172c240f12497f55b4:c5c6cff7c28d3260400f938602ee600b1acf0323-0' }" + + input: + tuple val(meta), path(rankings) + + output: + tuple val(meta), path("combined.ranking.tsv"), emit: ranking + + path "versions.yml" , emit: versions + + script: + """ + combine_rankings.py --input ${rankings} --output combined.ranking.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + python: \$(python --version | sed 's/Python //g') + pandas: \$(python -c "import pandas; print(pandas.__version__)") + numpy: \$(python -c "import numpy; print(numpy.__version__)") + END_VERSIONS + """ +} \ No newline at end of file diff --git a/subworkflows/local/ranking.nf b/subworkflows/local/ranking.nf index 2773dda..3fc67cc 100644 --- a/subworkflows/local/ranking.nf +++ b/subworkflows/local/ranking.nf @@ -1,5 +1,6 @@ include { TF_TG_SCORE } from '../../modules/local/ranking/tf_tg_score' include { RANKING as CREATE_RANKING } from '../../modules/local/ranking/ranking' +include { COMBINE_RANKINGS } from '../../modules/local/ranking/combine_rankings' workflow RANKING { @@ -26,6 +27,10 @@ workflow RANKING { TF_TG_SCORE(ch_combined) CREATE_RANKING(TF_TG_SCORE.out.score, alpha) + COMBINE_RANKINGS(CREATE_RANKING.out.ranking .map{ meta, ranking -> ranking } + .collect() + .map{ rankings -> [[id: "all"], rankings]} + ) emit: From f3cdf71d6ffe92782e4f9f5ce40fc0d7a54a7bf1 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 18 Mar 2024 14:41:31 +0100 Subject: [PATCH 038/206] Add output for ranking subworkflow --- subworkflows/local/ranking.nf | 2 ++ 1 file changed, 2 insertions(+) diff --git a/subworkflows/local/ranking.nf b/subworkflows/local/ranking.nf index 3fc67cc..4b9fe5f 100644 --- a/subworkflows/local/ranking.nf +++ b/subworkflows/local/ranking.nf @@ -34,6 +34,8 @@ workflow RANKING { emit: + assay_specific = CREATE_RANKING.out.ranking + combined = COMBINE_RANKINGS.out.ranking versions = ch_versions // channel: [ versions.yml ] From 598e41faf319f3e04f26a8fce1534ee55384cc87 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 18 Mar 2024 14:45:52 +0100 Subject: [PATCH 039/206] Prettier --- README.md | 1 - assets/schema_input.json | 2 +- modules.json | 42 +++++++++++----------------------------- 3 files changed, 12 insertions(+), 33 deletions(-) diff --git a/README.md b/README.md index a901568..9ae973c 100644 --- a/README.md +++ b/README.md @@ -39,7 +39,6 @@ It is strongly based on the TF-Prioritizer, with the following workflow: > [!NOTE] > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. - First, prepare a samplesheet with your input data that looks as follows: `samplesheet.csv`: diff --git a/assets/schema_input.json b/assets/schema_input.json index e94c015..04a617d 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -30,7 +30,7 @@ "format": "file-path", "exists": true, "pattern": "^\\S+\\.(bed|broadPeak)$", - "errorMessage": "Peak file must be provided and must be a .bed or .broadPeak file", + "errorMessage": "Peak file must be provided and must be a .bed or .broadPeak file" }, "footprinting": { "type": "boolean", diff --git a/modules.json b/modules.json index 19689a5..7c5168c 100644 --- a/modules.json +++ b/modules.json @@ -8,51 +8,37 @@ "atlasgeneannotationmanipulation/gtf2featureannotation": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/merge": { "branch": "master", "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/sort": { "branch": "master", "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/subtract": { "branch": "master", "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cat/cat": { "branch": "master", "git_sha": "9437e6053dccf4aafa022bfd6e7e9de67e625af8", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "deseq2/differential": { "branch": "master", "git_sha": "9326d73af3fbe2ee90d9ce0a737461a727c5118e", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gawk": { "branch": "master", "git_sha": "dc3527855e7358c6d8400828754c0caa5f11698f", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -61,26 +47,20 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfvalidation_plugin": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } } } -} \ No newline at end of file +} From 1a646b2d9da617ca8ae9b132f48dbb79ac93c977 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 18 Mar 2024 14:50:41 +0100 Subject: [PATCH 040/206] Collect more version outputs --- subworkflows/local/peaks.nf | 1 - subworkflows/local/ranking.nf | 5 +++++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/peaks.nf b/subworkflows/local/peaks.nf index c6cce2b..f838164 100644 --- a/subworkflows/local/peaks.nf +++ b/subworkflows/local/peaks.nf @@ -1,7 +1,6 @@ // Modules include { GAWK as CLEAN_BED } from '../../modules/nf-core/gawk/main' include { BEDTOOLS_SORT as SORT_PEAKS } from '../../modules/nf-core/bedtools/sort/main' -include { BEDTOOLS_SUBTRACT as BLACKLIST } from '../../modules/nf-core/bedtools/subtract/main' include { STARE } from '../../modules/local/stare/main' include { COMBINE_TABLES as AFFINITY_MEAN } from '../../modules/local/combine_tables/main' include { COMBINE_TABLES as AFFINITY_RATIO} from '../../modules/local/combine_tables/main' diff --git a/subworkflows/local/ranking.nf b/subworkflows/local/ranking.nf index 4b9fe5f..25c46b4 100644 --- a/subworkflows/local/ranking.nf +++ b/subworkflows/local/ranking.nf @@ -32,6 +32,11 @@ workflow RANKING { .map{ rankings -> [[id: "all"], rankings]} ) + ch_versions = ch_versions.mix(TF_TG_SCORE.out.versions, + CREATE_RANKING.out.versions, + COMBINE_RANKINGS.out.versions + ) + emit: assay_specific = CREATE_RANKING.out.ranking From 15e9c8c8f0f0a312a7edfd4d773f7a6c6d39b31d Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 18 Mar 2024 14:16:21 +0000 Subject: [PATCH 041/206] Fix some linting checks --- bin/DYNAMITE.R | 615 ++++++++++++++++++++++++------------------------- 1 file changed, 307 insertions(+), 308 deletions(-) diff --git a/bin/DYNAMITE.R b/bin/DYNAMITE.R index bc98be4..f27c3d3 100755 --- a/bin/DYNAMITE.R +++ b/bin/DYNAMITE.R @@ -3,29 +3,29 @@ args <- commandArgs(TRUE) library('methods') ggplotAvailable<-require("ggplot2") -gplotsAvailable<-require("gplots") +gplotsAvailable<-require("gplots") fontSize=.9 if(length(args) < 1) { - args <- c("--help") + args <- c("--help") } - + if("--help" %in% args) { - cat(" - Arguments: - --outDir= Output path (required) - --dataDir= Data directory (required) - --out_var= Name of the response variable (required) - --cores= Number of the cores to use (1 as default) - --alpha= Alpha parameter stepsize (0.1 as default) - --testsize= Size of test data (0.2 as default) - --Ofolds= Number of outer folds for model validation (3 as default) - --Ifolds= Number of inner cross validation folds (6 as default) - --balanced= Flag indicating whether the data should be balanced through downsampling (default TRUE) - --performance= Flag indicating whether performance measures should be computed (default TRUE) - --randomise= Flag indicating whether a model should be learned on randomised data (default FALSE) -") - q(save="no") + cat(" + Arguments: + --outDir= Output path (required) + --dataDir= Data directory (required) + --out_var= Name of the response variable (required) + --cores= Number of the cores to use (1 as default) + --alpha= Alpha parameter stepsize (0.1 as default) + --testsize= Size of test data (0.2 as default) + --Ofolds= Number of outer folds for model validation (3 as default) + --Ifolds= Number of inner cross validation folds (6 as default) + --balanced= Flag indicating whether the data should be balanced through downsampling (default TRUE) + --performance= Flag indicating whether performance measures should be computed (default TRUE) + --randomise= Flag indicating whether a model should be learned on randomised data (default FALSE) +") + q(save="no") } #Processing command line arguments @@ -36,19 +36,19 @@ names(argsL) <- argsDF$V1 #Checking required arguments if(is.null(argsL$outDir)) { - cat("Error!\n\n Please specify an output directory \n\n ") -q(save="no") + cat("Error!\n\n Please specify an output directory \n\n ") + q(save="no") } argsL$outDir<-paste0(argsL$outDir,"/") if(is.null(argsL$dataDir)) { - cat("Error!\n\n Please specify the data directory \n\n ") + cat("Error!\n\n Please specify the data directory \n\n ") q(save="no") } argsL$dataDir<-paste0(argsL$dataDir,"/") if(is.null(argsL$out_var)) { - cat("Error!\n\n Please enter the name of the response variable \n\n ") + cat("Error!\n\n Please enter the name of the response variable \n\n ") q(save="no") } @@ -127,302 +127,301 @@ coefficients<-vector("list",length(FileList)) # Data Preprocessing for(Sample in FileList){ - # Process file names for plot title - name<-strsplit(Sample, ".",fixed=TRUE)[[1]][1] - print(paste0("Learning model for ",name)) - i<-i+1 - #Loading the data matrix - M<-read.table(paste(argsL$dataDir,Sample,sep="/"),header=TRUE,stringsAsFactors=FALSE,row.names=1,check.names=FALSE) - #Removing features with standard deviation zero - SD<-apply(M,2,sd) - Feature_zero_SD<-as.vector(which(SD==0)) - if(length(Feature_zero_SD)>0){ - print("Warning! The following features are constant and will be removed from the feature matrix") - print(colnames(M)[Feature_zero_SD]) - M<-M[,-c(Feature_zero_SD)] - } - #Initialising FeatureNames, Test and Training Accuracy vectors and retrieving the column containing the response variable - FeatureName<-colnames(M) - Response_Variable_location<- grep(argsL$out_var,FeatureName) - TestAcc<-c(1:argsL$Ofolds) - TrainAcc<-c(1:argsL$Ofolds) - F1_1<-c(1:argsL$Ofolds) - F1_2<-c(1:argsL$Ofolds) - alphas=seq(0.0,1.0,as.numeric(argsL$alpha)) - coefficients[[i]]<-vector("list",as.numeric(argsL$Ofolds)) - #Normalising the data matrix - M[,-Response_Variable_location]<-log2(M[,-Response_Variable_location]+1) - M[,-Response_Variable_location]<-scale(M[,-Response_Variable_location],center=TRUE, scale=TRUE) - if (argsL$randomise == TRUE){ - MP<-apply(M[,-Response_Variable_location],2,permute) - M<-cbind(data.frame(scale(MP,center=TRUE, scale=TRUE)),M[,Response_Variable_location]) - colnames(M)<-FeatureName - } - - #Balancing the data set - if (argsL$balanced==TRUE){ - subM<-list(list()) - bM<-c() - index=0 - for (j in unique(M[,Response_Variable_location])){ - index<-index+1 - subM[[index]]<-M[which(M[,Response_Variable_location]==j),] + # Process file names for plot title + name<-strsplit(Sample, ".",fixed=TRUE)[[1]][1] + print(paste0("Learning model for ",name)) + i<-i+1 + #Loading the data matrix + M<-read.table(paste(argsL$dataDir,Sample,sep="/"),header=TRUE,stringsAsFactors=FALSE,row.names=1,check.names=FALSE) + #Removing features with standard deviation zero + SD<-apply(M,2,sd) + Feature_zero_SD<-as.vector(which(SD==0)) + if(length(Feature_zero_SD)>0){ + print("Warning! The following features are constant and will be removed from the feature matrix") + print(colnames(M)[Feature_zero_SD]) + M<-M[,-c(Feature_zero_SD)] } - mSize=min(sapply(subM,dim)[1,]) - for (l in 1:length(subM)){ - rndselect=sample(x=nrow(subM[[l]]),size=mSize) - subM[[l]]=subM[[l]][rndselect,] - bM<-rbind(bM,subM[[l]]) + #Initialising FeatureNames, Test and Training Accuracy vectors and retrieving the column containing the response variable + FeatureName<-colnames(M) + Response_Variable_location<- grep(argsL$out_var,FeatureName) + TestAcc<-c(1:argsL$Ofolds) + TrainAcc<-c(1:argsL$Ofolds) + F1_1<-c(1:argsL$Ofolds) + F1_2<-c(1:argsL$Ofolds) + alphas=seq(0.0,1.0,as.numeric(argsL$alpha)) + coefficients[[i]]<-vector("list",as.numeric(argsL$Ofolds)) + #Normalising the data matrix + M[,-Response_Variable_location]<-log2(M[,-Response_Variable_location]+1) + M[,-Response_Variable_location]<-scale(M[,-Response_Variable_location],center=TRUE, scale=TRUE) + if (argsL$randomise == TRUE){ + MP<-apply(M[,-Response_Variable_location],2,permute) + M<-cbind(data.frame(scale(MP,center=TRUE, scale=TRUE)),M[,Response_Variable_location]) + colnames(M)<-FeatureName } - } - test_size<-1/as.numeric(argsL$testsize) - - if (argsL$performance){ - #Loop through the outer folds - for (k in 1:argsL$Ofolds){ - print(paste("Outer CV fold ",as.character(k),sep=" ")) - if (argsL$balanced==TRUE){ - #Balanced selection of test and training data - Test_Data<-c() - Train_Data<-c() - for (j in 1:length(subM)){ - rndselect=sample(x=nrow(subM[[j]]), size=mSize/test_size) - Test_Data<-rbind(Test_Data,subM[[j]][rndselect,]) - Train_Data<-rbind(Train_Data,subM[[j]][-rndselect,]) + + #Balancing the data set + if (argsL$balanced==TRUE){ + subM<-list(list()) + bM<-c() + index=0 + for (j in unique(M[,Response_Variable_location])){ + index<-index+1 + subM[[index]]<-M[which(M[,Response_Variable_location]==j),] + } + mSize=min(sapply(subM,dim)[1,]) + for (l in 1:length(subM)){ + rndselect=sample(x=nrow(subM[[l]]),size=mSize) + subM[[l]]=subM[[l]][rndselect,] + bM<-rbind(bM,subM[[l]]) } - }else{ - rndselect=sample(x=nrow(M),size=as.numeric(argsL$testsize)*nrow(M)) - Test_Data<-M[rndselect,] - Train_Data<-M[-rndselect,] - } - - #Split the features from response - x_train<-as.matrix(Train_Data[,-Response_Variable_location]) - x_test<-as.matrix(Test_Data[,-Response_Variable_location]) - y_train<-as.vector(unlist(Train_Data[,Response_Variable_location,drop=FALSE])) - y_test<-as.vector(unlist(Test_Data[,Response_Variable_location])) - - #Training model parameters in the inner cross validation - print(argsL$Ifolds) - if (length(unique(M[,Response_Variable_location]))==2){ - aError<-sapply(alphas,elaBinomial,x_train,y_train,as.numeric(argsL$Ifolds)) - }else{ - aError<-sapply(alphas,elaMultinomial,x_train,y_train,as.numeric(argsL$Ifolds)) - } - - #Determine best model and retrain it - index<-match(min(aError), aError) - print(paste0("Available alphas: ", alphas, " Errors: ", aError)) - print(paste0("Selected alpha: ", alphas[index])) - if (length(unique(M[,Response_Variable_location]))==2){ - elasticnet<-cv.glmnet(x_train, y_train,alpha=alphas[index],family="binomial",type.measure="class",parallel=TRUE,nfolds=as.numeric(argsL$Ifolds)) - }else{ - elasticnet<-cv.glmnet(x_train, y_train,alpha=alphas[index],family="multinomial",type.measure="class",parallel=TRUE,nfolds=as.numeric(argsL$Ifolds)) - } - - #Generating a plot visualising the model selection - svg(paste(paste0(argsL$outDir,"/Misclassification_vs_Lambda_Fold_",k,"_",name),"svg",sep=".")) - plot(elasticnet) - dev.off() - - #Applying the selected model to the test data - predict_test<-predict(elasticnet, x_test, s="lambda.min",type="class") - predict_train<-predict(elasticnet, x_train, s="lambda.min",type="class") - - #Printing and storing the performance table - tTest<-table(y_test,predict_test) - write.table(tTest,file=paste(argsL$outDir,"/Confusion-Matrix_",k,"_",name,".txt",sep=""),quote=FALSE,sep="\t",row.names=FALSE) - tTrain<-table(y_train,predict_train) - - #Storing Feature values - if (length(unique(M[,Response_Variable_location]))==2){ - coefficients[[i]][[k]]<-coef(elasticnet, s = "lambda.min") - }else{ - coefficients[[i]][[k]]<-c() - } - - #Calculating Accuracy measures - TestAcc[k]<-0 - TrainAcc[k]<-0 - F1_1[k]<-0 - F1_2[k]<-0 - for (index in 1:dim(tTest)[1]){ - TestAcc[k]<-TestAcc[k]+tTest[(index-1)*dim(tTest)[1]+index] - TrainAcc[k]<-TrainAcc[k]+tTrain[(index-1)*dim(tTest)[1]+index] - } - F1_1[k]<-(2*tTest[1])/(2*tTest[1]+tTest[2]+tTest[3]) - F1_2[k]<-(2*tTest[4])/(2*tTest[4]+tTest[2]+tTest[3]) - TestAcc[k]<-TestAcc[k]/sum(tTest) - TrainAcc[k]<-TrainAcc[k]/sum(tTrain) } + test_size<-1/as.numeric(argsL$testsize) + + if (argsL$performance){ + #Loop through the outer folds + for (k in 1:argsL$Ofolds){ + print(paste("Outer CV fold ",as.character(k),sep=" ")) + if (argsL$balanced==TRUE){ + #Balanced selection of test and training data + Test_Data<-c() + Train_Data<-c() + for (j in 1:length(subM)){ + rndselect=sample(x=nrow(subM[[j]]), size=mSize/test_size) + Test_Data<-rbind(Test_Data,subM[[j]][rndselect,]) + Train_Data<-rbind(Train_Data,subM[[j]][-rndselect,]) + } + }else{ + rndselect=sample(x=nrow(M),size=as.numeric(argsL$testsize)*nrow(M)) + Test_Data<-M[rndselect,] + Train_Data<-M[-rndselect,] + } + + #Split the features from response + x_train<-as.matrix(Train_Data[,-Response_Variable_location]) + x_test<-as.matrix(Test_Data[,-Response_Variable_location]) + y_train<-as.vector(unlist(Train_Data[,Response_Variable_location,drop=FALSE])) + y_test<-as.vector(unlist(Test_Data[,Response_Variable_location])) + + #Training model parameters in the inner cross validation + print(argsL$Ifolds) + if (length(unique(M[,Response_Variable_location]))==2){ + aError<-sapply(alphas,elaBinomial,x_train,y_train,as.numeric(argsL$Ifolds)) + }else{ + aError<-sapply(alphas,elaMultinomial,x_train,y_train,as.numeric(argsL$Ifolds)) + } + + #Determine best model and retrain it + index<-match(min(aError), aError) + print(paste0("Available alphas: ", alphas, " Errors: ", aError)) + print(paste0("Selected alpha: ", alphas[index])) + if (length(unique(M[,Response_Variable_location]))==2){ + elasticnet<-cv.glmnet(x_train, y_train,alpha=alphas[index],family="binomial",type.measure="class",parallel=TRUE,nfolds=as.numeric(argsL$Ifolds)) + }else{ + elasticnet<-cv.glmnet(x_train, y_train,alpha=alphas[index],family="multinomial",type.measure="class",parallel=TRUE,nfolds=as.numeric(argsL$Ifolds)) + } + + #Generating a plot visualising the model selection + svg(paste(paste0(argsL$outDir,"/Misclassification_vs_Lambda_Fold_",k,"_",name),"svg",sep=".")) + plot(elasticnet) + dev.off() + + #Applying the selected model to the test data + predict_test<-predict(elasticnet, x_test, s="lambda.min",type="class") + predict_train<-predict(elasticnet, x_train, s="lambda.min",type="class") + + #Printing and storing the performance table + tTest<-table(y_test,predict_test) + write.table(tTest,file=paste(argsL$outDir,"/Confusion-Matrix_",k,"_",name,".txt",sep=""),quote=FALSE,sep="\t",row.names=FALSE) + tTrain<-table(y_train,predict_train) + + #Storing Feature values + if (length(unique(M[,Response_Variable_location]))==2){ + coefficients[[i]][[k]]<-coef(elasticnet, s = "lambda.min") + }else{ + coefficients[[i]][[k]]<-c() + } + + #Calculating Accuracy measures + TestAcc[k]<-0 + TrainAcc[k]<-0 + F1_1[k]<-0 + F1_2[k]<-0 + for (index in 1:dim(tTest)[1]){ + TestAcc[k]<-TestAcc[k]+tTest[(index-1)*dim(tTest)[1]+index] + TrainAcc[k]<-TrainAcc[k]+tTrain[(index-1)*dim(tTest)[1]+index] + } + F1_1[k]<-(2*tTest[1])/(2*tTest[1]+tTest[2]+tTest[3]) + F1_2[k]<-(2*tTest[4])/(2*tTest[4]+tTest[2]+tTest[3]) + TestAcc[k]<-TestAcc[k]/sum(tTest) + TrainAcc[k]<-TrainAcc[k]/sum(tTrain) + } - #Storing the mean performance values - sampleResult<-c(name,mean(TestAcc),var(TestAcc),mean(F1_1),var(F1_1),mean(F1_2),var(F1_2),mean(TrainAcc),var(TrainAcc)) - SampleOverview<-rbind(SampleOverview,sampleResult) - } - - #Learning one model on the full data set for feature analysis - print("Learning model on the entire data set") - if (argsL$balanced==TRUE){ - x_com<-as.matrix(bM[,-Response_Variable_location]) - y_com<-as.vector(unlist(bM[,Response_Variable_location,drop=FALSE])) - }else{ - x_com<-as.matrix(M[,-Response_Variable_location]) - y_com<-as.vector(unlist(M[,Response_Variable_location,drop=FALSE])) - } - aError=0 - if (length(unique(M[,Response_Variable_location]))==2){ - aError<-sapply(alphas,elaBinomial,x_com,y_com,as.numeric(argsL$Ifolds)) - }else{ - aError<-sapply(alphas,elaMultinomial,x_com,y_com,as.numeric(argsL$Ifolds)) - } - index<-match(min(aError), aError) - print(paste0("Available alphas: ", alphas, " Errors: ", aError)) - print(paste0("Selected alpha: ", alphas[index])) - if (length(unique(M[,Response_Variable_location]))==2){ - elasticnet<-cv.glmnet(x_com, y_com,alpha=alphas[index],family="binomial",type.measure="class",parallel=TRUE,nfolds=as.numeric(argsL$Ifolds)) - }else{ - elasticnet<-cv.glmnet(x_com, y_com,alpha=alphas[index],family="multinomial",type.measure="class",parallel=TRUE,nfolds=as.numeric(argsL$Ifolds)) - } - - #Store the feature values - if (length(unique(M[,Response_Variable_location]))>2){ - coefO<-coef(elasticnet,s="lambda.min") - for (j in names(coefO)){ - nf<-(coefO[j][[1]][,1])[-1] - nf2<-nf/max(abs(nf)) - nf3<-t(nf2) - nf3<-as.data.frame(nf3) - nf4<-t(rbind(colnames(nf3),nf3)) - colnames(nf4)<-c("TF","value") - nf4[,2]<-as.numeric(as.character(nf4[,2])) - nf4<-as.data.frame(nf4) - nf4[,2]<-as.numeric(as.character(nf4[,2])) - write.table(nf4,file=paste(argsL$outDir,paste("Class",j,"Regression_Coefficients_Entire_Data_Set.txt",sep="-"),sep='/'),quote=FALSE,sep="\t",row.names=FALSE) - nf4<-nf4[which(nf4$value >0.025),] - np<-c(1:length((nf4[,2]))) - np[which(nf4[,2]>0)]<-1 - np[which(nf4[,2]<=0)]<-0 - if (ggplotAvailable){ - ggplot2::ggplot(nf4,aes(x=reorder(TF,value),y=value,width=0.8,fill=np))+ - geom_bar(stat="identity")+ - theme_bw(10)+ylab("Normalised coefficient")+xlab("TF")+ - theme(axis.text.x=element_text(angle=45,hjust=1))+ - theme(strip.background = element_blank())+ - theme(legend.position="none") - ggsave(paste0(argsL$outDir,"Regression_Coefficients_Entire_Data_Set_Class",j,"_",name,".png"),width=min(50,5+(.3*length(nf4$TF))),height=5,limitsize=F) - } + #Storing the mean performance values + sampleResult<-c(name,mean(TestAcc),var(TestAcc),mean(F1_1),var(F1_1),mean(F1_2),var(F1_2),mean(TrainAcc),var(TrainAcc)) + SampleOverview<-rbind(SampleOverview,sampleResult) } - }else{ - nf<-coef(elasticnet,s="lambda.min")[,1][-1] - nf2<-nf/max(abs(nf)) - nf3<-t(nf2) - nf3<-as.data.frame(nf3) - nf4<-t(rbind(colnames(nf3),nf3)) - colnames(nf4)<-c("TF","value") - nf4[,2]<-as.numeric(as.character(nf4[,2])) - nf4<-as.data.frame(nf4) - nf4[,2]<-as.numeric(as.character(nf4[,2])) - write.table(nf4,file=paste(argsL$outDir,paste0("Regression_Coefficients_Entire_Data_Set_",name,".txt"),sep='/'),quote=FALSE,sep="\t",row.names=FALSE) - nf4<-nf4[which(nf4$value !=0.0),] - np<-c(1:length((nf4[,2]))) - np[which(nf4[,2]>0)]<-1 - np[which(nf4[,2]<0)]<-0 - if (ggplotAvailable){ - ggplot2::ggplot(nf4,aes(x=reorder(TF,value),y=value,width=0.8,fill=np))+ - geom_bar(stat="identity")+ - theme_bw(10)+ylab("Normalised coefficient")+xlab("TF")+ - theme(axis.text.x=element_text(angle=45,hjust=1))+ - theme(strip.background = element_blank())+ - theme(legend.position="none") - ggsave(paste0(argsL$outDir,"Regression_Coefficients_Entire_Data_Set",name,".png"),width=min(50,5+(.3*length(nf4$TF))),height=5,limitsize=F) + + #Learning one model on the full data set for feature analysis + print("Learning model on the entire data set") + if (argsL$balanced==TRUE){ + x_com<-as.matrix(bM[,-Response_Variable_location]) + y_com<-as.vector(unlist(bM[,Response_Variable_location,drop=FALSE])) + }else{ + x_com<-as.matrix(M[,-Response_Variable_location]) + y_com<-as.vector(unlist(M[,Response_Variable_location,drop=FALSE])) + } + aError=0 + if (length(unique(M[,Response_Variable_location]))==2){ + aError<-sapply(alphas,elaBinomial,x_com,y_com,as.numeric(argsL$Ifolds)) + }else{ + aError<-sapply(alphas,elaMultinomial,x_com,y_com,as.numeric(argsL$Ifolds)) + } + index<-match(min(aError), aError) + print(paste0("Available alphas: ", alphas, " Errors: ", aError)) + print(paste0("Selected alpha: ", alphas[index])) + if (length(unique(M[,Response_Variable_location]))==2){ + elasticnet<-cv.glmnet(x_com, y_com,alpha=alphas[index],family="binomial",type.measure="class",parallel=TRUE,nfolds=as.numeric(argsL$Ifolds)) + }else{ + elasticnet<-cv.glmnet(x_com, y_com,alpha=alphas[index],family="multinomial",type.measure="class",parallel=TRUE,nfolds=as.numeric(argsL$Ifolds)) } - } -} + #Store the feature values + if (length(unique(M[,Response_Variable_location]))>2){ + coefO<-coef(elasticnet,s="lambda.min") + for (j in names(coefO)){ + nf<-(coefO[j][[1]][,1])[-1] + nf2<-nf/max(abs(nf)) + nf3<-t(nf2) + nf3<-as.data.frame(nf3) + nf4<-t(rbind(colnames(nf3),nf3)) + colnames(nf4)<-c("TF","value") + nf4[,2]<-as.numeric(as.character(nf4[,2])) + nf4<-as.data.frame(nf4) + nf4[,2]<-as.numeric(as.character(nf4[,2])) + write.table(nf4,file=paste(argsL$outDir,paste("Class",j,"Regression_Coefficients_Entire_Data_Set.txt",sep="-"),sep='/'),quote=FALSE,sep="\t",row.names=FALSE) + nf4<-nf4[which(nf4$value >0.025),] + np<-c(1:length((nf4[,2]))) + np[which(nf4[,2]>0)]<-1 + np[which(nf4[,2]<=0)]<-0 + if (ggplotAvailable){ + ggplot2::ggplot(nf4,aes(x=reorder(TF,value),y=value,width=0.8,fill=np))+ + geom_bar(stat="identity")+ + theme_bw(10)+ylab("Normalised coefficient")+xlab("TF")+ + theme(axis.text.x=element_text(angle=45,hjust=1))+ + theme(strip.background = element_blank())+ + theme(legend.position="none") + ggsave(paste0(argsL$outDir,"Regression_Coefficients_Entire_Data_Set_Class",j,"_",name,".png"),width=min(50,5+(.3*length(nf4$TF))),height=5,limitsize=F) + } + } + }else{ + nf<-coef(elasticnet,s="lambda.min")[,1][-1] + nf2<-nf/max(abs(nf)) + nf3<-t(nf2) + nf3<-as.data.frame(nf3) + nf4<-t(rbind(colnames(nf3),nf3)) + colnames(nf4)<-c("TF","value") + nf4[,2]<-as.numeric(as.character(nf4[,2])) + nf4<-as.data.frame(nf4) + nf4[,2]<-as.numeric(as.character(nf4[,2])) + write.table(nf4,file=paste(argsL$outDir,paste0("Regression_Coefficients_Entire_Data_Set_",name,".txt"),sep='/'),quote=FALSE,sep="\t",row.names=FALSE) + nf4<-nf4[which(nf4$value !=0.0),] + np<-c(1:length((nf4[,2]))) + np[which(nf4[,2]>0)]<-1 + np[which(nf4[,2]<0)]<-0 + if (ggplotAvailable){ + ggplot2::ggplot(nf4,aes(x=reorder(TF,value),y=value,width=0.8,fill=np))+ + geom_bar(stat="identity")+ + theme_bw(10)+ylab("Normalised coefficient")+xlab("TF")+ + theme(axis.text.x=element_text(angle=45,hjust=1))+ + theme(strip.background = element_blank())+ + theme(legend.position="none") + ggsave(paste0(argsL$outDir,"Regression_Coefficients_Entire_Data_Set",name,".png"),width=min(50,5+(.3*length(nf4$TF))),height=5,limitsize=F) + } + } +} if (argsL$performance){ - print("Performance measures:") - print(paste("Mean Test Accuracy",mean(TestAcc),sep=" ")) - print(paste("Mean Training Accuracy",mean(TrainAcc),sep=" ")) - print(paste("Mean F1_1",mean(F1_1),sep=" ")) - print(paste("Mean F1_2",mean(F1_2),sep=" ")) - - for (i in 1:length(FileList)){ - featureMatrix<-c() - for (j in 1:length(coefficients[[i]])){ - if (length(coefficients[[i]][[j]]>1)){ - featureMatrix<-rbind(featureMatrix,coefficients[[i]][[j]][,1]) - } - } - if (length(featureMatrix > 1)){ - write.table(featureMatrix,paste(argsL$outDir,"Regression_Coefficients_Cross_Validation_",FileList[i],sep=""),quote=F,sep="\t",col.names=NA) - meanFeature<-apply(featureMatrix,2,median) - featureMatrix<-featureMatrix[,-1] - meanFeature<-meanFeature[-1] - featureMatrix<-featureMatrix[,which(meanFeature!=0.0)] - meanFeature<-meanFeature[which(meanFeature!=0.0)] - if(length(meanFeature) > 1){ - allFeatures<-featureMatrix[,order(meanFeature,decreasing=TRUE)] - meanFeatures<-meanFeature[order(meanFeature,decreasing=TRUE)] - all<-rbind(allFeatures,meanFeatures) - all<-all[,order(all[dim(all)[1],],decreasing=TRUE)] - row.names(all)<-c(paste("Fold ",c(1:(dim(all)[1]-1))),"Median") - if (gplotsAvailable){ - library("gplots") - svg(paste(argsL$outDir,"Regression_Coefficients_Cross_Validation_Heatmap_",unlist(unlist(strsplit(FileList[i],".txt")))[1],".svg",sep=""),width=min(54,7+(.3*length(meanFeature))),height=min(50,5+(.5*as.numeric(argsL$Ofolds)))) - if(any(allFeatures < 0)){ - allFeatures<-featureMatrix[,order(meanFeature,decreasing=TRUE)] - meanFeature<-meanFeature[order(meanFeature,decreasing=TRUE)] - all<-rbind(allFeatures,meanFeatures) - all<-all[,order(all[dim(all)[1],],decreasing=TRUE)] - row.names(all)<-c(paste("Fold ",c(1:(dim(all)[1]-1))),"Median") - heatmap.2(all,trace="none",col=bluered(250),srtCol=45,cexRow=fontSize,cexCol=fontSize,density.info="none",distfun = distF, dendrogram="none", margins=c(6,6),Colv=FALSE,Rowv=FALSE,key.xlab="Regression coefficient",keysize=0.9) - }else{ - allFeatures<-featureMatrix[,order(meanFeature,decreasing=TRUE)] - meanFeatures<-meanFeature[order(meanFeature,decreasing=TRUE)] - all<-rbind(allFeatures,meanFeatures) - all<-all[,order(all[dim(all)[1],],decreasing=TRUE)] - row.names(all)<-c(paste("Fold ",c(1:(dim(all)[1]-1))),"Median") - heatmap.2(all,trace="none",col=heat.colors(250),srtCol=45,cexRow=fontSize,cexCol=fontSize,density.info="none",distfun = distF, dendrogram="none", margins=c(6,6),Colv=FALSE,Rowv=FALSE,key.xlab="Regression coefficient",keysize=0.9) - } - dev.off() - } - }else{ - if (ggplotAvailable){ - library("ggplot2") - text<-"Mean regression coefficients are to small, a heatmap can not be shown." - ggplot()+annotate("text",x=4,y=25,size=8,label=text)+theme_void() - ggsave(filename=paste(argsL$outDir,"Regression_Coefficients_Cross_Validation_Heatmap_",unlist(unlist(strsplit(FileList[i],".txt")))[1],".png",sep=""),width=11,height=4) - } - } - } - } - #Generating summary output table - colnames(SampleOverview)<-SampleOverview[1,] - SampleOverview<-SampleOverview[-1,] - if(class(SampleOverview)=="matrix"){ - ggplotSampleOverview<-as.data.frame(rbind(cbind(SampleOverview[,1:3],rep("Test",length(SampleOverview[,1]))),cbind(SampleOverview[,c(1,8,9)],rep("Training",length(SampleOverview[,1]))),cbind(SampleOverview[,c(1,4,5)],rep("F1_1",length(SampleOverview[,1]))),cbind(SampleOverview[,c(1,6,7)],rep("F1_2",length(SampleOverview[,1]))))) - }else{ - ggplotSampleOverview<-as.data.frame(rbind(c(SampleOverview[1:3],"Test Accuracy"),c(SampleOverview[c(1,8,9)],"Trainings Accuracy"),c(SampleOverview[c(1,4,5)],"F1-Up"),c(SampleOverview[c(1,6,7)],"F1-Down"))) - } + print("Performance measures:") + print(paste("Mean Test Accuracy",mean(TestAcc),sep=" ")) + print(paste("Mean Training Accuracy",mean(TrainAcc),sep=" ")) + print(paste("Mean F1_1",mean(F1_1),sep=" ")) + print(paste("Mean F1_2",mean(F1_2),sep=" ")) + + for (i in 1:length(FileList)){ + featureMatrix<-c() + for (j in 1:length(coefficients[[i]])){ + if (length(coefficients[[i]][[j]]>1)){ + featureMatrix<-rbind(featureMatrix,coefficients[[i]][[j]][,1]) + } + } + if (length(featureMatrix > 1)){ + write.table(featureMatrix,paste(argsL$outDir,"Regression_Coefficients_Cross_Validation_",FileList[i],sep=""),quote=F,sep="\t",col.names=NA) + meanFeature<-apply(featureMatrix,2,median) + featureMatrix<-featureMatrix[,-1] + meanFeature<-meanFeature[-1] + featureMatrix<-featureMatrix[,which(meanFeature!=0.0)] + meanFeature<-meanFeature[which(meanFeature!=0.0)] + if(length(meanFeature) > 1){ + allFeatures<-featureMatrix[,order(meanFeature,decreasing=TRUE)] + meanFeatures<-meanFeature[order(meanFeature,decreasing=TRUE)] + all<-rbind(allFeatures,meanFeatures) + all<-all[,order(all[dim(all)[1],],decreasing=TRUE)] + row.names(all)<-c(paste("Fold ",c(1:(dim(all)[1]-1))),"Median") + if (gplotsAvailable){ + library("gplots") + svg(paste(argsL$outDir,"Regression_Coefficients_Cross_Validation_Heatmap_",unlist(unlist(strsplit(FileList[i],".txt")))[1],".svg",sep=""),width=min(54,7+(.3*length(meanFeature))),height=min(50,5+(.5*as.numeric(argsL$Ofolds)))) + if(any(allFeatures < 0)){ + allFeatures<-featureMatrix[,order(meanFeature,decreasing=TRUE)] + meanFeature<-meanFeature[order(meanFeature,decreasing=TRUE)] + all<-rbind(allFeatures,meanFeatures) + all<-all[,order(all[dim(all)[1],],decreasing=TRUE)] + row.names(all)<-c(paste("Fold ",c(1:(dim(all)[1]-1))),"Median") + heatmap.2(all,trace="none",col=bluered(250),srtCol=45,cexRow=fontSize,cexCol=fontSize,density.info="none",distfun = distF, dendrogram="none", margins=c(6,6),Colv=FALSE,Rowv=FALSE,key.xlab="Regression coefficient",keysize=0.9) + }else{ + allFeatures<-featureMatrix[,order(meanFeature,decreasing=TRUE)] + meanFeatures<-meanFeature[order(meanFeature,decreasing=TRUE)] + all<-rbind(allFeatures,meanFeatures) + all<-all[,order(all[dim(all)[1],],decreasing=TRUE)] + row.names(all)<-c(paste("Fold ",c(1:(dim(all)[1]-1))),"Median") + heatmap.2(all,trace="none",col=heat.colors(250),srtCol=45,cexRow=fontSize,cexCol=fontSize,density.info="none",distfun = distF, dendrogram="none", margins=c(6,6),Colv=FALSE,Rowv=FALSE,key.xlab="Regression coefficient",keysize=0.9) + } + dev.off() + } + }else{ + if (ggplotAvailable){ + library("ggplot2") + text<-"Mean regression coefficients are to small, a heatmap can not be shown." + ggplot()+annotate("text",x=4,y=25,size=8,label=text)+theme_void() + ggsave(filename=paste(argsL$outDir,"Regression_Coefficients_Cross_Validation_Heatmap_",unlist(unlist(strsplit(FileList[i],".txt")))[1],".png",sep=""),width=11,height=4) + } + } + } + } + #Generating summary output table + colnames(SampleOverview)<-SampleOverview[1,] + SampleOverview<-SampleOverview[-1,] + if(class(SampleOverview)=="matrix"){ + ggplotSampleOverview<-as.data.frame(rbind(cbind(SampleOverview[,1:3],rep("Test",length(SampleOverview[,1]))),cbind(SampleOverview[,c(1,8,9)],rep("Training",length(SampleOverview[,1]))),cbind(SampleOverview[,c(1,4,5)],rep("F1_1",length(SampleOverview[,1]))),cbind(SampleOverview[,c(1,6,7)],rep("F1_2",length(SampleOverview[,1]))))) + }else{ + ggplotSampleOverview<-as.data.frame(rbind(c(SampleOverview[1:3],"Test Accuracy"),c(SampleOverview[c(1,8,9)],"Trainings Accuracy"),c(SampleOverview[c(1,4,5)],"F1-Up"),c(SampleOverview[c(1,6,7)],"F1-Down"))) + } - colnames(ggplotSampleOverview)<-c("Name","Mean","Variance","Measure") - row.names(ggplotSampleOverview)<-c(1:length(row.names(ggplotSampleOverview))) - ggplotSampleOverview[,2]<-as.numeric(as.character(ggplotSampleOverview[,2])) - ggplotSampleOverview[,3]<-as.numeric(as.character(ggplotSampleOverview[,3])) - write.table(ggplotSampleOverview,file=paste0(argsL$outDir,"/Performance_overview.txt"),quote=FALSE,sep='\t',row.names=FALSE) - if (ggplotAvailable){ - ggplot2::ggplot(ggplotSampleOverview,aes(x=Name,y=Mean,width=0.8,fill=Measure,group=Measure))+ - geom_bar(stat="identity",position="dodge")+ - theme_bw(22)+ylab("Value")+xlab("Sample")+ - theme(axis.text.x=element_text(angle=45,hjust=1))+ - scale_y_continuous(breaks=seq(0.0,1.0,0.05))+ - scale_fill_manual(values=c("red","blue","orange","black"))+ - coord_cartesian(ylim=c(0.0,1.0))+ - geom_errorbar(aes(ymin=Mean-sqrt(Variance),ymax=Mean+sqrt(Variance)),position=position_dodge(0.8),width=.4,size=.5)+ - theme(strip.background = element_blank()) - ggsave(paste0(argsL$outDir,"/Performance_Barplots.png"),width=20,height=20,units=c("cm")) - } + colnames(ggplotSampleOverview)<-c("Name","Mean","Variance","Measure") + row.names(ggplotSampleOverview)<-c(1:length(row.names(ggplotSampleOverview))) + ggplotSampleOverview[,2]<-as.numeric(as.character(ggplotSampleOverview[,2])) + ggplotSampleOverview[,3]<-as.numeric(as.character(ggplotSampleOverview[,3])) + write.table(ggplotSampleOverview,file=paste0(argsL$outDir,"/Performance_overview.txt"),quote=FALSE,sep='\t',row.names=FALSE) + if (ggplotAvailable){ + ggplot2::ggplot(ggplotSampleOverview,aes(x=Name,y=Mean,width=0.8,fill=Measure,group=Measure))+ + geom_bar(stat="identity",position="dodge")+ + theme_bw(22)+ylab("Value")+xlab("Sample")+ + theme(axis.text.x=element_text(angle=45,hjust=1))+ + scale_y_continuous(breaks=seq(0.0,1.0,0.05))+ + scale_fill_manual(values=c("red","blue","orange","black"))+ + coord_cartesian(ylim=c(0.0,1.0))+ + geom_errorbar(aes(ymin=Mean-sqrt(Variance),ymax=Mean+sqrt(Variance)),position=position_dodge(0.8),width=.4,size=.5)+ + theme(strip.background = element_blank()) + ggsave(paste0(argsL$outDir,"/Performance_Barplots.png"),width=20,height=20,units=c("cm")) + } } From 964fbd7999fcfa6979fc00f7034470dcfe95255c Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 18 Mar 2024 14:19:56 +0000 Subject: [PATCH 042/206] Fix python style checks --- bin/DYNAMITE.R | 22 +++++++++++----------- bin/calculate_tpm.py | 2 +- bin/combine_counts.py | 2 +- bin/combine_rankings.py | 2 +- bin/combine_tables.py | 6 +++--- bin/dynamite_preprocess.py | 2 +- bin/filter_genes.py | 2 +- bin/prepare_design.py | 2 +- bin/ranking.py | 2 +- bin/tf_tg_score.py | 2 +- 10 files changed, 22 insertions(+), 22 deletions(-) diff --git a/bin/DYNAMITE.R b/bin/DYNAMITE.R index f27c3d3..56eacf9 100755 --- a/bin/DYNAMITE.R +++ b/bin/DYNAMITE.R @@ -104,24 +104,24 @@ registerDoMC(argsL$cores) FileList<-list.files(path=argsL$dataDir) print(paste("Samples to analyse:",as.character(length(FileList)),sep=" ")) for(Sample in FileList){ - counter<-counter+1 - print(paste(as.character(counter),unlist(unlist(strsplit(Sample,".txt"))))) - } + counter<-counter+1 + print(paste(as.character(counter),unlist(unlist(strsplit(Sample,".txt"))))) + } #Creating the header for the overview table SampleOverview<-c("Name","Mean Test Accuracy","Var Test Accuracy","Mean F1_1","Var F1_1","Mean F1_2","Var F1_2","Mean Training Accuracy","Var Train Accuracy") #Declare elastic net functions elaBinomial<-function(a,x,y,i){ - print(paste0("Learning model for alpha = ",a)) - elasticnet<-cv.glmnet(x, y, alpha=a,family="binomial",type.measure="class",parallel=TRUE,nfolds=i) - min(elasticnet$cvm) - } + print(paste0("Learning model for alpha = ",a)) + elasticnet<-cv.glmnet(x, y, alpha=a,family="binomial",type.measure="class",parallel=TRUE,nfolds=i) + min(elasticnet$cvm) + } elaMultinomial<-function(a,x,y,i){ - print(paste0("Learning model for alpha = ",a)) - elasticnet<-cv.glmnet(x, y, alpha=a,family="multinomial",type.measure="class",parallel=TRUE,nfolds=i) - min(elasticnet$cvm) - } + print(paste0("Learning model for alpha = ",a)) + elasticnet<-cv.glmnet(x, y, alpha=a,family="multinomial",type.measure="class",parallel=TRUE,nfolds=i) + min(elasticnet$cvm) + } coefficients<-vector("list",length(FileList)) diff --git a/bin/calculate_tpm.py b/bin/calculate_tpm.py index 7102aef..1da3926 100755 --- a/bin/calculate_tpm.py +++ b/bin/calculate_tpm.py @@ -30,4 +30,4 @@ def remove_version(gene_id): df_tpm = df_rpk.div(df_scale, axis=1) # Save to file -df_tpm.to_csv(args.output, sep="\t") \ No newline at end of file +df_tpm.to_csv(args.output, sep="\t") diff --git a/bin/combine_counts.py b/bin/combine_counts.py index d4c31b6..8d27905 100755 --- a/bin/combine_counts.py +++ b/bin/combine_counts.py @@ -56,4 +56,4 @@ def remove_version(gene_id): counts = counts.loc[gene_intersect] counts.to_csv(args.output, sep="\t") -counts.index.to_series().to_csv("genes.txt", index=False, header=False) \ No newline at end of file +counts.index.to_series().to_csv("genes.txt", index=False, header=False) diff --git a/bin/combine_rankings.py b/bin/combine_rankings.py index 965595e..04ef996 100755 --- a/bin/combine_rankings.py +++ b/bin/combine_rankings.py @@ -17,4 +17,4 @@ df['rank'] = range(1, len(df.index) + 1) -df.to_csv(args.output, sep='\t', index=True) \ No newline at end of file +df.to_csv(args.output, sep='\t', index=True) diff --git a/bin/combine_tables.py b/bin/combine_tables.py index a29c987..2da10ee 100755 --- a/bin/combine_tables.py +++ b/bin/combine_tables.py @@ -29,7 +29,7 @@ index_intersection = dfs[0].index for df in dfs[1:]: index_intersection = index_intersection.intersection(df.index) - + print(f"Number of rows in intersection: {len(index_intersection)}") # Keep row indices which are available in all dataframes dfs = [df.loc[index_intersection] for df in dfs] @@ -54,7 +54,7 @@ elif args.method == "ratio": if len(dfs) != 2: raise ValueError("The ratio method requires exactly two input files.") - + # Replace 0 values with minimal existing float value dfs[1] = dfs[1].replace(0, np.finfo(float).eps) @@ -68,4 +68,4 @@ print(f"Number of rows after dropping NA or inf values: {len(result)}") # Write the result to a file -result.to_csv(args.output, sep='\t', index=True, quoting=0) \ No newline at end of file +result.to_csv(args.output, sep='\t', index=True, quoting=0) diff --git a/bin/dynamite_preprocess.py b/bin/dynamite_preprocess.py index 9d7753f..ed5c3a6 100755 --- a/bin/dynamite_preprocess.py +++ b/bin/dynamite_preprocess.py @@ -30,4 +30,4 @@ def remove_version(gene_id): df_affinities["Expression"] = 0 df_affinities.loc[df_expression["log2FoldChange"] > 0, "Expression"] = 1 -df_affinities.to_csv(args.output, sep="\t") \ No newline at end of file +df_affinities.to_csv(args.output, sep="\t") diff --git a/bin/filter_genes.py b/bin/filter_genes.py index 6cd4148..d7dd958 100755 --- a/bin/filter_genes.py +++ b/bin/filter_genes.py @@ -39,4 +39,4 @@ df_tpms.to_csv(args.tpms_output, sep="\t") with open(args.genes_output, "w") as f: - f.write("\n".join(gene_intersection)) \ No newline at end of file + f.write("\n".join(gene_intersection)) diff --git a/bin/prepare_design.py b/bin/prepare_design.py index 8aee562..3456896 100755 --- a/bin/prepare_design.py +++ b/bin/prepare_design.py @@ -18,4 +18,4 @@ df = df.loc[:, df.nunique() > 1] # Write the design matrix to a file -df.to_csv(args.output) \ No newline at end of file +df.to_csv(args.output) diff --git a/bin/ranking.py b/bin/ranking.py index ad4107b..24bfc1f 100755 --- a/bin/ranking.py +++ b/bin/ranking.py @@ -40,4 +40,4 @@ def mann_whitney_u(background, foreground): df['rank'] = range(1, length + 1) df['dcg'] = 1 - (df['rank'] - 1) / length -df.to_csv(args.output, sep='\t') \ No newline at end of file +df.to_csv(args.output, sep='\t') diff --git a/bin/tf_tg_score.py b/bin/tf_tg_score.py index afe764c..cba7eb3 100755 --- a/bin/tf_tg_score.py +++ b/bin/tf_tg_score.py @@ -48,4 +48,4 @@ def remove_version(gene_id): assert not result.empty, "No TF-TG scores were calculated" # Save the result -result.to_csv(args.output, sep='\t') \ No newline at end of file +result.to_csv(args.output, sep='\t') From fd19ac3c5c12ae6244194b8cf5acb0a180d763a2 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 18 Mar 2024 14:25:57 +0000 Subject: [PATCH 043/206] Fix more style problems --- modules/local/combine_tables/main.nf | 8 ++++---- modules/local/counts/calculate_tpm.nf | 2 +- modules/local/counts/combine.nf | 2 +- modules/local/counts/filter_genes.nf | 2 +- modules/local/counts/prepare_design.nf | 2 +- modules/local/dynamite/dynamite.nf | 6 +++--- modules/local/dynamite/preprocess.nf | 2 +- modules/local/gtftools/length/main.nf | 2 +- modules/local/ranking/combine_rankings.nf | 2 +- modules/local/ranking/ranking.nf | 2 +- modules/local/ranking/tf_tg_score.nf | 10 +++++----- modules/local/stare/main.nf | 4 ++-- subworkflows/local/counts.nf | 2 +- subworkflows/local/dynamite.nf | 7 +++---- subworkflows/local/footprinting.nf | 9 ++++----- subworkflows/local/peaks.nf | 6 +++--- subworkflows/local/ranking.nf | 7 +++---- workflows/tfactivity.nf | 2 +- 18 files changed, 37 insertions(+), 40 deletions(-) diff --git a/modules/local/combine_tables/main.nf b/modules/local/combine_tables/main.nf index d93ab5d..575b0a6 100644 --- a/modules/local/combine_tables/main.nf +++ b/modules/local/combine_tables/main.nf @@ -6,15 +6,15 @@ process COMBINE_TABLES { container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0': 'biocontainers/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0' }" - + input: tuple val(meta), path(files) val(method) - + output: tuple val(meta), path("${prefix}.${extension}"), emit: combined path "versions.yml" , emit: versions - + script: prefix = task.ext.prefix ?: "${meta.id}" extension = task.ext.extension ?: "tsv" @@ -28,4 +28,4 @@ process COMBINE_TABLES { numpy: \$(python -c "import numpy; print(numpy.__version__)") END_VERSIONS """ -} \ No newline at end of file +} diff --git a/modules/local/counts/calculate_tpm.nf b/modules/local/counts/calculate_tpm.nf index 12df59c..11289ff 100644 --- a/modules/local/counts/calculate_tpm.nf +++ b/modules/local/counts/calculate_tpm.nf @@ -27,4 +27,4 @@ process CALCULATE_TPM { numpy: \$(python -c "import numpy; print(numpy.__version__)") END_VERSIONS """ -} \ No newline at end of file +} diff --git a/modules/local/counts/combine.nf b/modules/local/counts/combine.nf index d457fba..28a6203 100644 --- a/modules/local/counts/combine.nf +++ b/modules/local/counts/combine.nf @@ -27,4 +27,4 @@ process COMBINE_COUNTS { pandas: \$(python -c "import pandas; print(pandas.__version__)") END_VERSIONS """ -} \ No newline at end of file +} diff --git a/modules/local/counts/filter_genes.nf b/modules/local/counts/filter_genes.nf index 2127452..171d436 100644 --- a/modules/local/counts/filter_genes.nf +++ b/modules/local/counts/filter_genes.nf @@ -36,4 +36,4 @@ process FILTER_GENES { pandas: \$(python -c "import pandas; print(pandas.__version__)") END_VERSIONS """ -} \ No newline at end of file +} diff --git a/modules/local/counts/prepare_design.nf b/modules/local/counts/prepare_design.nf index 65a0234..02cc254 100644 --- a/modules/local/counts/prepare_design.nf +++ b/modules/local/counts/prepare_design.nf @@ -24,4 +24,4 @@ process PREPARE_DESIGN { pandas: \$(python -c "import pandas; print(pandas.__version__)") END_VERSIONS """ -} \ No newline at end of file +} diff --git a/modules/local/dynamite/dynamite.nf b/modules/local/dynamite/dynamite.nf index 98084c6..355ab1c 100644 --- a/modules/local/dynamite/dynamite.nf +++ b/modules/local/dynamite/dynamite.nf @@ -12,10 +12,10 @@ process DYNAMITE { val(ifolds) val(alpha) val(randomize) - + output: tuple val(meta), path("${meta.id}_dynamite/Regression_Coefficients_Entire_Data_Set_classification.txt") - + script: """ DYNAMITE.R \\ @@ -29,4 +29,4 @@ process DYNAMITE { --randomise=$randomize \\ --cores=$task.cpus """ -} \ No newline at end of file +} diff --git a/modules/local/dynamite/preprocess.nf b/modules/local/dynamite/preprocess.nf index e016ade..c731f1d 100644 --- a/modules/local/dynamite/preprocess.nf +++ b/modules/local/dynamite/preprocess.nf @@ -28,4 +28,4 @@ process PREPROCESS { pandas: \$(python -c "import pandas; print(pandas.__version__)") END_VERSIONS """ -} \ No newline at end of file +} diff --git a/modules/local/gtftools/length/main.nf b/modules/local/gtftools/length/main.nf index 57333c1..c114dcc 100644 --- a/modules/local/gtftools/length/main.nf +++ b/modules/local/gtftools/length/main.nf @@ -33,7 +33,7 @@ process GTFTOOLS_LENGTH { stub: def args = task.ext.args ?: '' - + // TODO nf-core: A stub section should mimic the execution of the original module as best as possible // Have a look at the following examples: // Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63 diff --git a/modules/local/ranking/combine_rankings.nf b/modules/local/ranking/combine_rankings.nf index fe8b8a0..4dfd3f4 100644 --- a/modules/local/ranking/combine_rankings.nf +++ b/modules/local/ranking/combine_rankings.nf @@ -26,4 +26,4 @@ process COMBINE_RANKINGS { numpy: \$(python -c "import numpy; print(numpy.__version__)") END_VERSIONS """ -} \ No newline at end of file +} diff --git a/modules/local/ranking/ranking.nf b/modules/local/ranking/ranking.nf index e625822..c66b29f 100644 --- a/modules/local/ranking/ranking.nf +++ b/modules/local/ranking/ranking.nf @@ -27,4 +27,4 @@ process RANKING { numpy: \$(python -c "import numpy; print(numpy.__version__)") END_VERSIONS """ -} \ No newline at end of file +} diff --git a/modules/local/ranking/tf_tg_score.nf b/modules/local/ranking/tf_tg_score.nf index a2b8955..47d0d71 100644 --- a/modules/local/ranking/tf_tg_score.nf +++ b/modules/local/ranking/tf_tg_score.nf @@ -18,10 +18,10 @@ process TF_TG_SCORE { script: """ tf_tg_score.py \\ - --differential ${differential} \\ - --affinities ${affinities} \\ - --regression_coefficients ${regression_coefficients} \\ - --output ${meta.id}.score.tsv + --differential ${differential} \\ + --affinities ${affinities} \\ + --regression_coefficients ${regression_coefficients} \\ + --output ${meta.id}.score.tsv cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -29,4 +29,4 @@ process TF_TG_SCORE { pandas: \$(python -c "import pandas; print(pandas.__version__)") END_VERSIONS """ -} \ No newline at end of file +} diff --git a/modules/local/stare/main.nf b/modules/local/stare/main.nf index a02e425..cef44d9 100644 --- a/modules/local/stare/main.nf +++ b/modules/local/stare/main.nf @@ -4,7 +4,7 @@ process STARE { conda "bioconda::stare-abc" container "biocontainers/stare-abc:1.0.4--haf6292c_1" - + input: tuple val(meta), path(candidate_regions) path(fasta) @@ -28,4 +28,4 @@ process STARE { STARE: \$( STARE.sh --version ) END_VERSIONS """ -} \ No newline at end of file +} diff --git a/subworkflows/local/counts.nf b/subworkflows/local/counts.nf index 97dc1eb..1ded31b 100644 --- a/subworkflows/local/counts.nf +++ b/subworkflows/local/counts.nf @@ -45,7 +45,7 @@ workflow COUNTS { DESEQ2_DIFFERENTIAL( Channel.value(["condition"]).combine(contrasts) - .map{ variable, reference, target -> + .map{ variable, reference, target -> [[id: reference + ":" + target, contrast: reference + ":" + target, condition1: reference, diff --git a/subworkflows/local/dynamite.nf b/subworkflows/local/dynamite.nf index 2ead542..906a55a 100644 --- a/subworkflows/local/dynamite.nf +++ b/subworkflows/local/dynamite.nf @@ -15,13 +15,13 @@ workflow DYNAMITE { ch_versions = Channel.empty() - ch_combined = ch_differential.map{ meta, differential -> + ch_combined = ch_differential.map{ meta, differential -> [meta.condition1, meta.condition2, meta, differential]} - .combine(ch_affinity_ratio.map{ meta, affinity_ratio -> + .combine(ch_affinity_ratio.map{ meta, affinity_ratio -> [meta.condition1, meta.condition2, meta, affinity_ratio]}, by: [0,1]) .map{ condition1, condition2, meta_differential, differential, meta_affinity, affinity_ratio -> [meta_affinity, differential, affinity_ratio]} - + PREPROCESS(ch_combined) RUN_DYNAMITE(PREPROCESS.out.output, ofolds, ifolds, alpha, randomize) @@ -39,4 +39,3 @@ workflow DYNAMITE { versions = ch_versions // channel: [ versions.yml ] } - diff --git a/subworkflows/local/footprinting.nf b/subworkflows/local/footprinting.nf index d3c047f..12dbabc 100644 --- a/subworkflows/local/footprinting.nf +++ b/subworkflows/local/footprinting.nf @@ -10,8 +10,8 @@ workflow FOOTPRINTING { ch_versions = Channel.empty() - ch_footprint_split = ch_peaks.branch{ - meta, peaks -> + ch_footprint_split = ch_peaks.branch{ + meta, peaks -> footprinting: meta.footprinting as_is: !meta.footprinting } @@ -19,8 +19,8 @@ workflow FOOTPRINTING { BEDTOOLS_MERGE( ch_footprint_split.footprinting ) ch_include_original_split = BEDTOOLS_MERGE.out.bed - .branch{ - meta, bed -> + .branch{ + meta, bed -> include: meta.include_original subtract: !meta.include_original } @@ -43,4 +43,3 @@ workflow FOOTPRINTING { versions = ch_versions // channel: [ versions.yml ] } - diff --git a/subworkflows/local/peaks.nf b/subworkflows/local/peaks.nf index f838164..aaa5fe5 100644 --- a/subworkflows/local/peaks.nf +++ b/subworkflows/local/peaks.nf @@ -67,8 +67,8 @@ workflow PEAKS { .map { meta, affinities -> [meta.condition, meta.assay, affinities] } .groupTuple(by: [0, 1]) .map { condition, assay, affinities -> [[id: condition + "_" + assay, - condition: condition, - assay: assay], affinities] }, + condition: condition, + assay: assay], affinities] }, "mean" ) @@ -95,7 +95,7 @@ workflow PEAKS { condition1: condition1, condition2: condition2, assay: assay1], [affinities1, affinities2]] } - + AFFINITY_RATIO(ch_contrast_affinities, "ratio") AFFINITY_SUM(ch_contrast_affinities, "sum") diff --git a/subworkflows/local/ranking.nf b/subworkflows/local/ranking.nf index 25c46b4..c632cfb 100644 --- a/subworkflows/local/ranking.nf +++ b/subworkflows/local/ranking.nf @@ -14,7 +14,7 @@ workflow RANKING { ch_versions = Channel.empty() - ch_combined = ch_differential.map{meta, differential -> + ch_combined = ch_differential.map{meta, differential -> [meta.condition1, meta.condition2, differential]} .combine(ch_affinities.map{meta, affinities -> [meta.condition1, meta.condition2, meta.assay, affinities]}, by: [0, 1]) @@ -33,8 +33,8 @@ workflow RANKING { ) ch_versions = ch_versions.mix(TF_TG_SCORE.out.versions, - CREATE_RANKING.out.versions, - COMBINE_RANKINGS.out.versions + CREATE_RANKING.out.versions, + COMBINE_RANKINGS.out.versions ) @@ -45,4 +45,3 @@ workflow RANKING { versions = ch_versions // channel: [ versions.yml ] } - diff --git a/workflows/tfactivity.nf b/workflows/tfactivity.nf index ba6f3f3..387b23e 100644 --- a/workflows/tfactivity.nf +++ b/workflows/tfactivity.nf @@ -57,7 +57,7 @@ workflow TFACTIVITY { ch_conditions = ch_samplesheet.map { meta, peak_file -> meta.condition } .toSortedList().flatten().unique() - + ch_contrasts = ch_conditions.combine(ch_conditions) .filter { condition1, condition2 -> condition1 < condition2 } From 0526a75239c06d8d4cabf58f32c83cdd3d91144d Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 18 Mar 2024 15:09:45 +0000 Subject: [PATCH 044/206] Convert counts to symbols --- bin/calculate_tpm.py | 8 ++++---- bin/combine_counts.py | 16 ++++++++++------ main.nf | 2 ++ modules/local/counts/calculate_tpm.nf | 3 ++- modules/local/counts/combine.nf | 3 ++- nextflow.config | 2 ++ subworkflows/local/counts.nf | 7 +++++-- workflows/tfactivity.nf | 4 +++- 8 files changed, 30 insertions(+), 15 deletions(-) diff --git a/bin/calculate_tpm.py b/bin/calculate_tpm.py index 1da3926..ed263d1 100755 --- a/bin/calculate_tpm.py +++ b/bin/calculate_tpm.py @@ -6,17 +6,17 @@ parser = argparse.ArgumentParser(description="Calculate TPM from count matrix and length information") parser.add_argument("--counts", type=str, help="Path to counts") parser.add_argument("--lengths", type=str, help="Path to gene lengths") +parser.add_argument("--gene_map", type=str, help="Path to geneID - symbol mapping file") parser.add_argument("--output", type=str, help="Path to output file") args = parser.parse_args() df_counts = pd.read_csv(args.counts, index_col=0, header=0, sep="\t") df_lengths = pd.read_csv(args.lengths, index_col=0, header=0, sep="\t", usecols=["gene", "merged"]) df_lengths.columns = ["length"] +df_genes = pd.read_csv(args.gene_map, sep="\t", index_col=0) -def remove_version(gene_id): - return gene_id.split(".")[0] - -df_lengths.index = df_lengths.index.map(remove_version) +conversion_dict = df_genes["gene_name"].to_dict() +df_lengths.index = df_lengths.index.map(conversion_dict).str.upper() # Mean length for each gene (in kb) df_lengths = df_lengths / 1e3 diff --git a/bin/combine_counts.py b/bin/combine_counts.py index 8d27905..6e0ce21 100755 --- a/bin/combine_counts.py +++ b/bin/combine_counts.py @@ -7,12 +7,13 @@ parser = argparse.ArgumentParser(description="Create dataframe from count matrix and metadata") parser.add_argument("--counts", type=str, help="Path to counts") parser.add_argument("--metadata", type=str, help="Path to metadata") -parser.add_argument("--genes", type=str, help="Path to genes to include") +parser.add_argument("--gene_map", type=str, help="Path to geneID - symbol mapping file") +parser.add_argument("--agg_method", type=str, help="Aggregation method for counts", choices=["sum", "mean", "max"], default="sum") parser.add_argument("--output", type=str, help="Path to output file") args = parser.parse_args() metadata = pd.read_csv(args.metadata, index_col=0, header=0) -df_genes = pd.read_csv(args.genes, sep="\t", index_col=0) +df_genes = pd.read_csv(args.gene_map, sep="\t", index_col=0) def remove_version(gene_id): return gene_id.split(".")[0] @@ -48,12 +49,15 @@ def remove_version(gene_id): df_genes.index = df_genes.index.map(remove_version) counts.index = counts.index.map(remove_version) -counts = counts.groupby(counts.index).sum() +# Map gene ids to gene symbols +conversion_dict = df_genes["gene_name"].to_dict() +counts.index = counts.index.map(lambda x: conversion_dict.get(x, x)).str.upper() -gene_intersect = df_genes.index.intersection(counts.index) +# Keep only count values for genes which are present in the gene symbol mapping file +existing_symbols = df_genes["gene_name"].str.upper().to_list() +counts = counts[counts.index.isin(existing_symbols)] -df_genes = df_genes.loc[gene_intersect] -counts = counts.loc[gene_intersect] +counts = counts.groupby(counts.index).agg(args.agg_method) counts.to_csv(args.output, sep="\t") counts.index.to_series().to_csv("genes.txt", index=False, header=False) diff --git a/main.nf b/main.nf index 6a37a4f..408e1b4 100644 --- a/main.nf +++ b/main.nf @@ -86,8 +86,10 @@ workflow NFCORE_TFACTIVITY { params.window_size, params.decay, params.merge_samples, + params.min_count, params.min_tpm, + params.expression_aggregation, params.dynamite_ofolds, params.dynamite_ifolds, diff --git a/modules/local/counts/calculate_tpm.nf b/modules/local/counts/calculate_tpm.nf index 11289ff..bc54430 100644 --- a/modules/local/counts/calculate_tpm.nf +++ b/modules/local/counts/calculate_tpm.nf @@ -10,6 +10,7 @@ process CALCULATE_TPM { input: tuple val(meta), path(counts) tuple val(meta2), path(lengths) + tuple val(meta3), path(gene_map) output: tuple val(meta), path("*.tpm.tsv"), emit: tpm @@ -18,7 +19,7 @@ process CALCULATE_TPM { script: """ - calculate_tpm.py --counts ${counts} --lengths ${lengths} --output ${meta.id}.tpm.tsv + calculate_tpm.py --counts ${counts} --lengths ${lengths} --gene_map ${gene_map} --output ${meta.id}.tpm.tsv cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/local/counts/combine.nf b/modules/local/counts/combine.nf index 28a6203..b04f864 100644 --- a/modules/local/counts/combine.nf +++ b/modules/local/counts/combine.nf @@ -11,6 +11,7 @@ process COMBINE_COUNTS { tuple val(meta), path(counts), path(design) path(extra_counts) tuple val(meta2), path(gene_map) + val(agg_method) output: tuple val(meta), path("*.clean.tsv"), emit: counts @@ -19,7 +20,7 @@ process COMBINE_COUNTS { script: """ - combine_counts.py --counts ${counts} --genes ${gene_map} --metadata ${design} --output ${meta.id}.clean.tsv + combine_counts.py --counts ${counts} --agg_method ${agg_method} --gene_map ${gene_map} --metadata ${design} --output ${meta.id}.clean.tsv cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/nextflow.config b/nextflow.config index 4841d3f..560cccc 100644 --- a/nextflow.config +++ b/nextflow.config @@ -22,6 +22,8 @@ params { decay = true min_count = 50 min_tpm = 1 + expression_aggregation = 'sum' + affinity_aggregation = 'max' dynamite_ofolds = 3 dynamite_ifolds = 6 diff --git a/subworkflows/local/counts.nf b/subworkflows/local/counts.nf index 1ded31b..dea4de1 100644 --- a/subworkflows/local/counts.nf +++ b/subworkflows/local/counts.nf @@ -14,6 +14,7 @@ workflow COUNTS { min_count min_tpm contrasts + agg_method main: @@ -26,12 +27,14 @@ workflow COUNTS { COMBINE_COUNTS( ch_counts.combine(ch_counts_design).map{counts, design -> [[id: "counts"], counts, design]}, ch_extra_counts, - gene_map + gene_map, + agg_method ) CALCULATE_TPM( COMBINE_COUNTS.out.counts, - ch_gene_lengths + ch_gene_lengths, + gene_map ) FILTER_GENES( diff --git a/workflows/tfactivity.nf b/workflows/tfactivity.nf index 387b23e..6564f21 100644 --- a/workflows/tfactivity.nf +++ b/workflows/tfactivity.nf @@ -41,6 +41,7 @@ workflow TFACTIVITY { // Counts min_count min_tpm + expression_agg_method // Dynamite dynamite_ofolds @@ -68,7 +69,8 @@ workflow TFACTIVITY { counts_design, min_count, min_tpm, - ch_contrasts + ch_contrasts, + expression_agg_method ) PEAKS( From 15494c533fcafb8a42cc1cefea2beb73ee1f45a0 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 18 Mar 2024 16:05:37 +0000 Subject: [PATCH 045/206] Use gene symbols everywhere --- bin/aggregate_synonyms.py | 27 +++++++++++++++ bin/filter_pwms.py | 33 +++++++++++++++++++ main.nf | 3 ++ modules/local/peaks/aggregate_synonyms.nf | 31 +++++++++++++++++ modules/local/peaks/filter_pwms.nf | 29 ++++++++++++++++ .../local/{stare/main.nf => peaks/stare.nf} | 2 +- nextflow.config | 4 ++- nextflow_schema.json | 28 ++++++++++++++++ subworkflows/local/counts.nf | 12 +++++++ subworkflows/local/peaks.nf | 21 ++++++++++-- workflows/tfactivity.nf | 12 +++++-- 11 files changed, 195 insertions(+), 7 deletions(-) create mode 100755 bin/aggregate_synonyms.py create mode 100755 bin/filter_pwms.py create mode 100644 modules/local/peaks/aggregate_synonyms.nf create mode 100644 modules/local/peaks/filter_pwms.nf rename modules/local/{stare/main.nf => peaks/stare.nf} (96%) diff --git a/bin/aggregate_synonyms.py b/bin/aggregate_synonyms.py new file mode 100755 index 0000000..10a0c2e --- /dev/null +++ b/bin/aggregate_synonyms.py @@ -0,0 +1,27 @@ +#!/usr/bin/env python3 + +import pandas as pd +import argparse + +parser = argparse.ArgumentParser(description="Aggregate affinities across synonym genes and TFs") +parser.add_argument("--input", type=str, help="Path to affinities") +parser.add_argument("--gene_map", type=str, help="Path to geneID - symbol mapping file") +parser.add_argument("--agg_method", type=str, help="Method to aggregate affinities", choices=["mean", "max", "sum"], default="max") +parser.add_argument("--output", type=str, help="Path to output file") +args = parser.parse_args() + +df_affinities = pd.read_csv(args.input, index_col=0, header=0, sep="\t") +df_genes = pd.read_csv(args.gene_map, sep="\t", index_col=0) + +conversion_dict = df_genes["gene_name"].to_dict() +df_affinities.index = df_affinities.index.map(conversion_dict).str.upper() + +# Aggregate across genes +df_affinities = df_affinities.groupby(df_affinities.index).agg(args.agg_method) + +# Aggregate across TFs +df_affinities.columns = df_affinities.columns.str.replace(r"\(.*\)", "").str.strip() +df_affinities = df_affinities.groupby(df_affinities.columns, axis=1).agg(args.agg_method) + +# Save to file +df_affinities.to_csv(args.output, sep="\t") diff --git a/bin/filter_pwms.py b/bin/filter_pwms.py new file mode 100755 index 0000000..f2320c6 --- /dev/null +++ b/bin/filter_pwms.py @@ -0,0 +1,33 @@ +#!/usr/bin/env python3 + +import argparse + +parser = argparse.ArgumentParser(description="Filter PWMs based on genes.") +parser.add_argument("--input", type=str, help="Path to input PWMs") +parser.add_argument("--genes", type=str, help="Path to genes") +parser.add_argument("--output", type=str, help="Path to output PWMs") + +args = parser.parse_args() + +with open(args.genes, "r") as f: + legal_genes = set([gene.rstrip("\n") for gene in f.readlines()]) + +f_input = open(args.input, "r") +f_output = open(args.output, "w") + +legal = True + +for line in f_input: + if legal and not line.startswith(">"): + f_output.write(line) + else: + splitted = line.split("\t") + group = splitted[1] + genes = group.split("::") + legal = any(gene in legal_genes for gene in genes) + + if legal: + f_output.write(line) + +f_input.close() +f_output.close() diff --git a/main.nf b/main.nf index 408e1b4..7825404 100644 --- a/main.nf +++ b/main.nf @@ -86,10 +86,13 @@ workflow NFCORE_TFACTIVITY { params.window_size, params.decay, params.merge_samples, + params.affinity_aggregation, params.min_count, params.min_tpm, params.expression_aggregation, + params.min_count_tf, + params.min_tpm_tf, params.dynamite_ofolds, params.dynamite_ifolds, diff --git a/modules/local/peaks/aggregate_synonyms.nf b/modules/local/peaks/aggregate_synonyms.nf new file mode 100644 index 0000000..b69aa54 --- /dev/null +++ b/modules/local/peaks/aggregate_synonyms.nf @@ -0,0 +1,31 @@ +process AGGREGATE_SYNONYMS { + tag "$meta.id" + label "process_single" + + conda "bioconda::mulled-v2-cd5249a47f81a81b2e7785172c240f12497f55b4==c5c6cff7c28d3260400f938602ee600b1acf0323-0" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-cd5249a47f81a81b2e7785172c240f12497f55b4:c5c6cff7c28d3260400f938602ee600b1acf0323-0': + 'biocontainers/mulled-v2-cd5249a47f81a81b2e7785172c240f12497f55b4:c5c6cff7c28d3260400f938602ee600b1acf0323-0' }" + + input: + tuple val(meta), path(affinities) + tuple val(meta2), path(gene_map) + val(agg_method) + + output: + tuple val(meta), path("${meta.id}.agg_affinities.tsv"), emit: affinities + + path "versions.yml" , emit: versions + + script: + """ + aggregate_synonyms.py --input ${affinities} --gene_map ${gene_map} --agg_method ${agg_method} --output ${meta.id}.agg_affinities.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + python: \$(python --version | sed 's/Python //g') + pandas: \$(python -c "import pandas; print(pandas.__version__)") + numpy: \$(python -c "import numpy; print(numpy.__version__)") + END_VERSIONS + """ +} diff --git a/modules/local/peaks/filter_pwms.nf b/modules/local/peaks/filter_pwms.nf new file mode 100644 index 0000000..35178fd --- /dev/null +++ b/modules/local/peaks/filter_pwms.nf @@ -0,0 +1,29 @@ +process FILTER_PWMS { + tag "$meta.id" + label "process_single" + + conda "conda-forge::mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6==fccb0c41a243c639e11dd1be7b74f563e624fcca-0" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0': + 'biocontainers/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0' }" + + input: + tuple val(meta), path(genes) + path(pwms) + + output: + tuple val(meta), path("pwms.txt") , emit: pwms + + path "versions.yml" , emit: versions + + script: + """ + filter_pwms.py --input ${pwms} --genes ${genes} --output pwms.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + python: \$(python --version | sed 's/Python //g') + pandas: \$(python -c "import pandas; print(pandas.__version__)") + END_VERSIONS + """ +} diff --git a/modules/local/stare/main.nf b/modules/local/peaks/stare.nf similarity index 96% rename from modules/local/stare/main.nf rename to modules/local/peaks/stare.nf index cef44d9..0b73c8f 100644 --- a/modules/local/stare/main.nf +++ b/modules/local/peaks/stare.nf @@ -10,7 +10,7 @@ process STARE { path(fasta) path(gtf) path(blacklist) - path(pwms) + tuple val(meta2), path(pwms) val(window_size) val(decay) diff --git a/nextflow.config b/nextflow.config index 560cccc..188dec0 100644 --- a/nextflow.config +++ b/nextflow.config @@ -22,7 +22,9 @@ params { decay = true min_count = 50 min_tpm = 1 - expression_aggregation = 'sum' + min_count_tf = 50 + min_tpm_tf = 1 + expression_aggregation = 'mean' affinity_aggregation = 'max' dynamite_ofolds = 3 diff --git a/nextflow_schema.json b/nextflow_schema.json index a8ae259..8931c07 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -97,6 +97,20 @@ "fa_icon": "fas fa-compress-arrows-alt", "help_text": "Use decay in STARE. The default value is `true`." }, + "expression_aggregation": { + "type": "string", + "default": "mean", + "description": "Method to aggregate expression values.", + "fa_icon": "fas fa-compress-arrows-alt", + "help_text": "Method to aggregate expression values. The default value is `mean`." + }, + "affinity_aggregation": { + "type": "string", + "default": "max", + "description": "Method to aggregate affinity values.", + "fa_icon": "fas fa-compress-arrows-alt", + "help_text": "Method to aggregate affinity values. The default value is `max`." + }, "min_count": { "type": "integer", "default": 50, @@ -111,6 +125,20 @@ "fa_icon": "fas fa-compress-arrows-alt", "help_text": "Minimum TPM to keep a gene in the analysis. The default value is 1." }, + "min_count_tf": { + "type": "integer", + "default": 50, + "description": "Minimum number of total counts to keep a transcription factor in the analysis.", + "fa_icon": "fas fa-compress-arrows-alt", + "help_text": "Minimum number of total counts to keep a transcription factor in the analysis. The default value is 50." + }, + "min_tpm_tf": { + "type": "number", + "default": 1, + "description": "Minimum TPM to keep a transcription factor in the analysis.", + "fa_icon": "fas fa-compress-arrows-alt", + "help_text": "Minimum TPM to keep a transcription factor in the analysis. The default value is 1." + }, "dynamite_ofolds": { "type": "integer", "default": 3, diff --git a/subworkflows/local/counts.nf b/subworkflows/local/counts.nf index dea4de1..5fdbfb1 100644 --- a/subworkflows/local/counts.nf +++ b/subworkflows/local/counts.nf @@ -1,6 +1,7 @@ include { COMBINE_COUNTS } from "../../modules/local/counts/combine" include { CALCULATE_TPM } from "../../modules/local/counts/calculate_tpm" include { FILTER_GENES } from "../../modules/local/counts/filter_genes" +include { FILTER_GENES as FILTER_TFS } from "../../modules/local/counts/filter_genes" include { PREPARE_DESIGN } from "../../modules/local/counts/prepare_design" include { DESEQ2_DIFFERENTIAL } from "../../modules/nf-core/deseq2/differential/main" @@ -15,6 +16,8 @@ workflow COUNTS { min_tpm contrasts agg_method + min_count_tf + min_tpm_tf main: @@ -44,6 +47,13 @@ workflow COUNTS { min_tpm ) + FILTER_TFS( + COMBINE_COUNTS.out.counts.map{ meta, counts -> [[id: "TFs"], counts]}, + CALCULATE_TPM.out.tpm, + min_count_tf, + min_tpm_tf + ) + PREPARE_DESIGN(ch_counts_design.map{ design -> [[id: "design"], design]}) DESEQ2_DIFFERENTIAL( @@ -66,6 +76,7 @@ workflow COUNTS { COMBINE_COUNTS.out.versions, CALCULATE_TPM.out.versions, FILTER_GENES.out.versions, + FILTER_TFS.out.versions, PREPARE_DESIGN.out.versions, DESEQ2_DIFFERENTIAL.out.versions ) @@ -73,6 +84,7 @@ workflow COUNTS { emit: genes = FILTER_GENES.out.genes raw_counts = FILTER_GENES.out.counts + tfs = FILTER_TFS.out.genes tpms = CALCULATE_TPM.out.tpm normalized = DESEQ2_DIFFERENTIAL.out.normalised_counts differential = DESEQ2_DIFFERENTIAL.out.results diff --git a/subworkflows/local/peaks.nf b/subworkflows/local/peaks.nf index aaa5fe5..7bea07e 100644 --- a/subworkflows/local/peaks.nf +++ b/subworkflows/local/peaks.nf @@ -1,7 +1,9 @@ // Modules include { GAWK as CLEAN_BED } from '../../modules/nf-core/gawk/main' include { BEDTOOLS_SORT as SORT_PEAKS } from '../../modules/nf-core/bedtools/sort/main' -include { STARE } from '../../modules/local/stare/main' +include { FILTER_PWMS } from '../../modules/local/peaks/filter_pwms' +include { STARE } from '../../modules/local/peaks/stare' +include { AGGREGATE_SYNONYMS } from '../../modules/local/peaks/aggregate_synonyms' include { COMBINE_TABLES as AFFINITY_MEAN } from '../../modules/local/combine_tables/main' include { COMBINE_TABLES as AFFINITY_RATIO} from '../../modules/local/combine_tables/main' include { COMBINE_TABLES as AFFINITY_SUM } from '../../modules/local/combine_tables/main' @@ -22,6 +24,9 @@ workflow PEAKS { decay merge_samples contrasts + tfs + gene_map + agg_method main: @@ -50,12 +55,14 @@ workflow PEAKS { ch_versions = ch_versions.mix(SORT_PEAKS.out.versions) } + FILTER_PWMS(tfs, pwms) + STARE( ch_peaks, fasta, gtf, blacklist, - pwms, + FILTER_PWMS.out.pwms.collect(), window_size, decay ) @@ -76,7 +83,13 @@ workflow PEAKS { ch_versions = ch_versions.mix(AFFINITY_MEAN.out.versions) } - ch_affinities_spread = ch_affinities + AGGREGATE_SYNONYMS( + ch_affinities, + gene_map, + agg_method + ) + + ch_affinities_spread = AGGREGATE_SYNONYMS.out.affinities .map { meta, affinities -> [meta.condition, meta.assay, affinities] } ch_contrast_affinities = contrasts @@ -100,7 +113,9 @@ workflow PEAKS { AFFINITY_SUM(ch_contrast_affinities, "sum") ch_versions = ch_versions.mix( + FILTER_PWMS.out.versions, STARE.out.versions, + AGGREGATE_SYNONYMS.out.versions, AFFINITY_RATIO.out.versions, AFFINITY_SUM.out.versions ) diff --git a/workflows/tfactivity.nf b/workflows/tfactivity.nf index 6564f21..2f3f0fd 100644 --- a/workflows/tfactivity.nf +++ b/workflows/tfactivity.nf @@ -37,11 +37,14 @@ workflow TFACTIVITY { window_size decay merge_samples + affinity_agg_method // Counts min_count min_tpm expression_agg_method + min_count_tf + min_tpm_tf // Dynamite dynamite_ofolds @@ -70,7 +73,9 @@ workflow TFACTIVITY { min_count, min_tpm, ch_contrasts, - expression_agg_method + expression_agg_method, + min_count_tf, + min_tpm_tf ) PEAKS( @@ -82,7 +87,10 @@ workflow TFACTIVITY { window_size, decay, merge_samples, - ch_contrasts + ch_contrasts, + COUNTS.out.tfs, + gene_map, + affinity_agg_method ) DYNAMITE( From 3a8c7568bd360ebc8c6ac6ac57e68aa0b47b3a95 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 23 Mar 2024 08:25:31 +0100 Subject: [PATCH 046/206] Init angular project --- modules/local/report/create/app/.editorconfig | 16 + modules/local/report/create/app/.gitignore | 42 + .../report/create/app/.vscode/extensions.json | 4 + .../report/create/app/.vscode/launch.json | 20 + .../report/create/app/.vscode/tasks.json | 42 + modules/local/report/create/app/README.md | 27 + modules/local/report/create/app/angular.json | 101 + .../local/report/create/app/package-lock.json | 12370 ++++++++++++++++ modules/local/report/create/app/package.json | 38 + .../create/app/src/app/app.component.html | 336 + .../create/app/src/app/app.component.scss | 0 .../create/app/src/app/app.component.spec.ts | 29 + .../create/app/src/app/app.component.ts | 13 + .../report/create/app/src/app/app.config.ts | 8 + .../report/create/app/src/app/app.routes.ts | 3 + .../report/create/app/src/assets/.gitkeep | 0 .../local/report/create/app/src/favicon.ico | Bin 0 -> 15086 bytes .../local/report/create/app/src/index.html | 13 + modules/local/report/create/app/src/main.ts | 6 + .../local/report/create/app/src/styles.scss | 1 + .../local/report/create/app/tsconfig.app.json | 14 + modules/local/report/create/app/tsconfig.json | 32 + .../report/create/app/tsconfig.spec.json | 14 + modules/local/report/create/main.nf | 12 + 24 files changed, 13141 insertions(+) create mode 100644 modules/local/report/create/app/.editorconfig create mode 100644 modules/local/report/create/app/.gitignore create mode 100644 modules/local/report/create/app/.vscode/extensions.json create mode 100644 modules/local/report/create/app/.vscode/launch.json create mode 100644 modules/local/report/create/app/.vscode/tasks.json create mode 100644 modules/local/report/create/app/README.md create mode 100644 modules/local/report/create/app/angular.json create mode 100644 modules/local/report/create/app/package-lock.json create mode 100644 modules/local/report/create/app/package.json create mode 100644 modules/local/report/create/app/src/app/app.component.html create mode 100644 modules/local/report/create/app/src/app/app.component.scss create mode 100644 modules/local/report/create/app/src/app/app.component.spec.ts create mode 100644 modules/local/report/create/app/src/app/app.component.ts create mode 100644 modules/local/report/create/app/src/app/app.config.ts create mode 100644 modules/local/report/create/app/src/app/app.routes.ts create mode 100644 modules/local/report/create/app/src/assets/.gitkeep create mode 100644 modules/local/report/create/app/src/favicon.ico create mode 100644 modules/local/report/create/app/src/index.html create mode 100644 modules/local/report/create/app/src/main.ts create mode 100644 modules/local/report/create/app/src/styles.scss create mode 100644 modules/local/report/create/app/tsconfig.app.json create mode 100644 modules/local/report/create/app/tsconfig.json create mode 100644 modules/local/report/create/app/tsconfig.spec.json create mode 100644 modules/local/report/create/main.nf diff --git a/modules/local/report/create/app/.editorconfig b/modules/local/report/create/app/.editorconfig new file mode 100644 index 0000000..59d9a3a --- /dev/null +++ b/modules/local/report/create/app/.editorconfig @@ -0,0 +1,16 @@ +# Editor configuration, see https://editorconfig.org +root = true + +[*] +charset = utf-8 +indent_style = space +indent_size = 2 +insert_final_newline = true +trim_trailing_whitespace = true + +[*.ts] +quote_type = single + +[*.md] +max_line_length = off +trim_trailing_whitespace = false diff --git a/modules/local/report/create/app/.gitignore b/modules/local/report/create/app/.gitignore new file mode 100644 index 0000000..0711527 --- /dev/null +++ b/modules/local/report/create/app/.gitignore @@ -0,0 +1,42 @@ +# See http://help.github.com/ignore-files/ for more about ignoring files. + +# Compiled output +/dist +/tmp +/out-tsc +/bazel-out + +# Node +/node_modules +npm-debug.log +yarn-error.log + +# IDEs and editors +.idea/ +.project +.classpath +.c9/ +*.launch +.settings/ +*.sublime-workspace + +# Visual Studio Code +.vscode/* +!.vscode/settings.json +!.vscode/tasks.json +!.vscode/launch.json +!.vscode/extensions.json +.history/* + +# Miscellaneous +/.angular/cache +.sass-cache/ +/connect.lock +/coverage +/libpeerconnection.log +testem.log +/typings + +# System files +.DS_Store +Thumbs.db diff --git a/modules/local/report/create/app/.vscode/extensions.json b/modules/local/report/create/app/.vscode/extensions.json new file mode 100644 index 0000000..77b3745 --- /dev/null +++ b/modules/local/report/create/app/.vscode/extensions.json @@ -0,0 +1,4 @@ +{ + // For more information, visit: https://go.microsoft.com/fwlink/?linkid=827846 + "recommendations": ["angular.ng-template"] +} diff --git a/modules/local/report/create/app/.vscode/launch.json b/modules/local/report/create/app/.vscode/launch.json new file mode 100644 index 0000000..925af83 --- /dev/null +++ b/modules/local/report/create/app/.vscode/launch.json @@ -0,0 +1,20 @@ +{ + // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387 + "version": "0.2.0", + "configurations": [ + { + "name": "ng serve", + "type": "chrome", + "request": "launch", + "preLaunchTask": "npm: start", + "url": "http://localhost:4200/" + }, + { + "name": "ng test", + "type": "chrome", + "request": "launch", + "preLaunchTask": "npm: test", + "url": "http://localhost:9876/debug.html" + } + ] +} diff --git a/modules/local/report/create/app/.vscode/tasks.json b/modules/local/report/create/app/.vscode/tasks.json new file mode 100644 index 0000000..a298b5b --- /dev/null +++ b/modules/local/report/create/app/.vscode/tasks.json @@ -0,0 +1,42 @@ +{ + // For more information, visit: https://go.microsoft.com/fwlink/?LinkId=733558 + "version": "2.0.0", + "tasks": [ + { + "type": "npm", + "script": "start", + "isBackground": true, + "problemMatcher": { + "owner": "typescript", + "pattern": "$tsc", + "background": { + "activeOnStart": true, + "beginsPattern": { + "regexp": "(.*?)" + }, + "endsPattern": { + "regexp": "bundle generation complete" + } + } + } + }, + { + "type": "npm", + "script": "test", + "isBackground": true, + "problemMatcher": { + "owner": "typescript", + "pattern": "$tsc", + "background": { + "activeOnStart": true, + "beginsPattern": { + "regexp": "(.*?)" + }, + "endsPattern": { + "regexp": "bundle generation complete" + } + } + } + } + ] +} diff --git a/modules/local/report/create/app/README.md b/modules/local/report/create/app/README.md new file mode 100644 index 0000000..209eaef --- /dev/null +++ b/modules/local/report/create/app/README.md @@ -0,0 +1,27 @@ +# App + +This project was generated with [Angular CLI](https://github.com/angular/angular-cli) version 17.3.1. + +## Development server + +Run `ng serve` for a dev server. Navigate to `http://localhost:4200/`. The application will automatically reload if you change any of the source files. + +## Code scaffolding + +Run `ng generate component component-name` to generate a new component. You can also use `ng generate directive|pipe|service|class|guard|interface|enum|module`. + +## Build + +Run `ng build` to build the project. The build artifacts will be stored in the `dist/` directory. + +## Running unit tests + +Run `ng test` to execute the unit tests via [Karma](https://karma-runner.github.io). + +## Running end-to-end tests + +Run `ng e2e` to execute the end-to-end tests via a platform of your choice. To use this command, you need to first add a package that implements end-to-end testing capabilities. + +## Further help + +To get more help on the Angular CLI use `ng help` or go check out the [Angular CLI Overview and Command Reference](https://angular.io/cli) page. diff --git a/modules/local/report/create/app/angular.json b/modules/local/report/create/app/angular.json new file mode 100644 index 0000000..09c35f7 --- /dev/null +++ b/modules/local/report/create/app/angular.json @@ -0,0 +1,101 @@ +{ + "$schema": "./node_modules/@angular/cli/lib/config/schema.json", + "version": 1, + "newProjectRoot": "projects", + "projects": { + "app": { + "projectType": "application", + "schematics": { + "@schematics/angular:component": { + "style": "scss" + } + }, + "root": "", + "sourceRoot": "src", + "prefix": "app", + "architect": { + "build": { + "builder": "@angular-devkit/build-angular:application", + "options": { + "outputPath": "dist/app", + "index": "src/index.html", + "browser": 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development", + "test": "ng test" + }, + "private": true, + "dependencies": { + "@angular/animations": "^17.3.0", + "@angular/common": "^17.3.0", + "@angular/compiler": "^17.3.0", + "@angular/core": "^17.3.0", + "@angular/forms": "^17.3.0", + "@angular/platform-browser": "^17.3.0", + "@angular/platform-browser-dynamic": "^17.3.0", + "@angular/router": "^17.3.0", + "rxjs": "~7.8.0", + "tslib": "^2.3.0", + "zone.js": "~0.14.3" + }, + "devDependencies": { + "@angular-devkit/build-angular": "^17.3.1", + "@angular/cli": "^17.3.1", + "@angular/compiler-cli": "^17.3.0", + "@types/jasmine": "~5.1.0", + "jasmine-core": "~5.1.0", + "karma": "~6.4.0", + "karma-chrome-launcher": "~3.2.0", + "karma-coverage": "~2.2.0", + "karma-jasmine": "~5.1.0", + "karma-jasmine-html-reporter": "~2.1.0", + "typescript": "~5.4.2" + } +} diff --git a/modules/local/report/create/app/src/app/app.component.html b/modules/local/report/create/app/src/app/app.component.html new file mode 100644 index 0000000..36093e1 --- /dev/null +++ b/modules/local/report/create/app/src/app/app.component.html @@ -0,0 +1,336 @@ + + + + + + + + + + + +

 + + + + + + + + + + + diff --git a/modules/local/report/create/app/src/app/app.component.scss b/modules/local/report/create/app/src/app/app.component.scss new file mode 100644 index 0000000..e69de29 diff --git a/modules/local/report/create/app/src/app/app.component.spec.ts b/modules/local/report/create/app/src/app/app.component.spec.ts new file mode 100644 index 0000000..44771e7 --- /dev/null +++ b/modules/local/report/create/app/src/app/app.component.spec.ts @@ -0,0 +1,29 @@ +import { TestBed } from '@angular/core/testing'; +import { AppComponent } from './app.component'; + +describe('AppComponent', () => { + beforeEach(async () => { + await TestBed.configureTestingModule({ + imports: [AppComponent], + }).compileComponents(); + }); + + it('should create the app', () => { + const fixture = TestBed.createComponent(AppComponent); + const app = fixture.componentInstance; + expect(app).toBeTruthy(); + }); + + it(`should have the 'app' title`, () => { + const fixture = TestBed.createComponent(AppComponent); + const app = fixture.componentInstance; + expect(app.title).toEqual('app'); + }); + + it('should render title', () => { + const fixture = TestBed.createComponent(AppComponent); + fixture.detectChanges(); + const compiled = fixture.nativeElement as HTMLElement; + expect(compiled.querySelector('h1')?.textContent).toContain('Hello, app'); + }); +}); diff --git a/modules/local/report/create/app/src/app/app.component.ts b/modules/local/report/create/app/src/app/app.component.ts new file mode 100644 index 0000000..87cca17 --- /dev/null +++ b/modules/local/report/create/app/src/app/app.component.ts @@ -0,0 +1,13 @@ +import { Component } from '@angular/core'; +import { RouterOutlet } from '@angular/router'; + +@Component({ + selector: 'app-root', + standalone: true, + imports: [RouterOutlet], + templateUrl: './app.component.html', + styleUrl: './app.component.scss' +}) +export class AppComponent { + title = 'app'; +} diff --git a/modules/local/report/create/app/src/app/app.config.ts b/modules/local/report/create/app/src/app/app.config.ts new file mode 100644 index 0000000..6c6ef60 --- /dev/null +++ b/modules/local/report/create/app/src/app/app.config.ts @@ -0,0 +1,8 @@ +import { ApplicationConfig } from '@angular/core'; +import { provideRouter } from '@angular/router'; + +import { routes } from './app.routes'; + +export const appConfig: ApplicationConfig = { + providers: [provideRouter(routes)] +}; diff --git a/modules/local/report/create/app/src/app/app.routes.ts b/modules/local/report/create/app/src/app/app.routes.ts new file mode 100644 index 0000000..dc39edb --- /dev/null +++ b/modules/local/report/create/app/src/app/app.routes.ts @@ -0,0 +1,3 @@ +import { Routes } from '@angular/router'; + +export const routes: Routes = []; diff --git a/modules/local/report/create/app/src/assets/.gitkeep b/modules/local/report/create/app/src/assets/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git 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b/modules/local/report/create/app/src/index.html new file mode 100644 index 0000000..f8ef6ac --- /dev/null +++ b/modules/local/report/create/app/src/index.html @@ -0,0 +1,13 @@ + + + + + App + + + + + + + + diff --git a/modules/local/report/create/app/src/main.ts b/modules/local/report/create/app/src/main.ts new file mode 100644 index 0000000..35b00f3 --- /dev/null +++ b/modules/local/report/create/app/src/main.ts @@ -0,0 +1,6 @@ +import { bootstrapApplication } from '@angular/platform-browser'; +import { appConfig } from './app/app.config'; +import { AppComponent } from './app/app.component'; + +bootstrapApplication(AppComponent, appConfig) + .catch((err) => console.error(err)); diff --git a/modules/local/report/create/app/src/styles.scss b/modules/local/report/create/app/src/styles.scss new file mode 100644 index 0000000..90d4ee0 --- /dev/null +++ b/modules/local/report/create/app/src/styles.scss @@ -0,0 +1 @@ +/* You can add global styles to this file, and also import other style files */ diff --git a/modules/local/report/create/app/tsconfig.app.json b/modules/local/report/create/app/tsconfig.app.json new file mode 100644 index 0000000..374cc9d --- /dev/null +++ b/modules/local/report/create/app/tsconfig.app.json @@ -0,0 +1,14 @@ +/* To learn more about this file see: https://angular.io/config/tsconfig. */ +{ + "extends": "./tsconfig.json", + "compilerOptions": { + "outDir": "./out-tsc/app", + "types": [] + }, + "files": [ + "src/main.ts" + ], + "include": [ + "src/**/*.d.ts" + ] +} diff --git a/modules/local/report/create/app/tsconfig.json b/modules/local/report/create/app/tsconfig.json new file mode 100644 index 0000000..eb49734 --- /dev/null +++ b/modules/local/report/create/app/tsconfig.json @@ -0,0 +1,32 @@ +/* To learn more about this file see: https://angular.io/config/tsconfig. */ +{ + "compileOnSave": false, + "compilerOptions": { + "outDir": "./dist/out-tsc", + "strict": true, + "noImplicitOverride": true, + "noPropertyAccessFromIndexSignature": true, + "noImplicitReturns": true, + "noFallthroughCasesInSwitch": true, + "skipLibCheck": true, + "esModuleInterop": true, + "sourceMap": true, + "declaration": false, + "experimentalDecorators": true, + "moduleResolution": "node", + "importHelpers": true, + "target": "ES2022", + "module": "ES2022", + "useDefineForClassFields": false, + "lib": [ + "ES2022", + "dom" + ] + }, + "angularCompilerOptions": { + "enableI18nLegacyMessageIdFormat": false, + "strictInjectionParameters": true, + "strictInputAccessModifiers": true, + "strictTemplates": true + } +} diff --git a/modules/local/report/create/app/tsconfig.spec.json b/modules/local/report/create/app/tsconfig.spec.json new file mode 100644 index 0000000..be7e9da --- /dev/null +++ b/modules/local/report/create/app/tsconfig.spec.json @@ -0,0 +1,14 @@ +/* To learn more about this file see: https://angular.io/config/tsconfig. */ +{ + "extends": "./tsconfig.json", + "compilerOptions": { + "outDir": "./out-tsc/spec", + "types": [ + "jasmine" + ] + }, + "include": [ + "src/**/*.spec.ts", + "src/**/*.d.ts" + ] +} diff --git a/modules/local/report/create/main.nf b/modules/local/report/create/main.nf new file mode 100644 index 0000000..846d906 --- /dev/null +++ b/modules/local/report/create/main.nf @@ -0,0 +1,12 @@ +process { + tag "$meta.id" + label "process_low" + + conda "conda-forge::nodejs" + container "docker.io/node:20.9.0-bookworm" + + script: + """ + + """ +} \ No newline at end of file From 4379b6fd32adf7cb71336b8946f16f5aa849b81e Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 23 Mar 2024 09:43:16 +0100 Subject: [PATCH 047/206] Implement dummy report creation --- conf/modules.config | 8 ++++++++ modules/local/report/create/app/src/index.html | 2 +- modules/local/report/create/main.nf | 14 +++++++++++--- subworkflows/local/report.nf | 6 ++++++ workflows/tfactivity.nf | 3 +++ 5 files changed, 29 insertions(+), 4 deletions(-) create mode 100644 subworkflows/local/report.nf diff --git a/conf/modules.config b/conf/modules.config index 3297b7f..7d1e5dc 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -76,6 +76,14 @@ process { ] } + withName: ".*:REPORT:CREATE" { + publishDir = [ + path: { "${params.outdir}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + withName: CUSTOM_DUMPSOFTWAREVERSIONS { publishDir = [ path: { "${params.outdir}/pipeline_info" }, diff --git a/modules/local/report/create/app/src/index.html b/modules/local/report/create/app/src/index.html index f8ef6ac..22ac9ce 100644 --- a/modules/local/report/create/app/src/index.html +++ b/modules/local/report/create/app/src/index.html @@ -3,7 +3,7 @@ App - + diff --git a/modules/local/report/create/main.nf b/modules/local/report/create/main.nf index 846d906..15a8ba4 100644 --- a/modules/local/report/create/main.nf +++ b/modules/local/report/create/main.nf @@ -1,12 +1,20 @@ -process { - tag "$meta.id" +process CREATE { label "process_low" conda "conda-forge::nodejs" container "docker.io/node:20.9.0-bookworm" + cache false + + output: + path("report") + script: """ - + cp -r $moduleDir/app ./app + cd app + npm install && npm run build + sed -i 's/type="module"//g' dist/app/browser/index.html + cp -r dist/app ../report """ } \ No newline at end of file diff --git a/subworkflows/local/report.nf b/subworkflows/local/report.nf new file mode 100644 index 0000000..b4bd90a --- /dev/null +++ b/subworkflows/local/report.nf @@ -0,0 +1,6 @@ +include { CREATE } from '../../modules/local/report/create/main' + +workflow REPORT { + main: + CREATE() +} \ No newline at end of file diff --git a/workflows/tfactivity.nf b/workflows/tfactivity.nf index 2f3f0fd..399fb8e 100644 --- a/workflows/tfactivity.nf +++ b/workflows/tfactivity.nf @@ -15,6 +15,7 @@ include { COUNTS } from '../subworkflows/local/counts' include { PEAKS } from '../subworkflows/local/peaks' include { DYNAMITE } from '../subworkflows/local/dynamite' include { RANKING } from '../subworkflows/local/ranking' +include { REPORT } from '../subworkflows/local/report' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -115,6 +116,8 @@ workflow TFACTIVITY { DYNAMITE.out.versions ) + REPORT() + // // Collate and save software versions // From 8b368d589a27a423be8a01f939e8beb5e7cf4447 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 23 Mar 2024 09:49:04 +0100 Subject: [PATCH 048/206] Remove dummy code --- .../create/app/src/app/app.component.html | 335 +----------------- 1 file changed, 1 insertion(+), 334 deletions(-) diff --git a/modules/local/report/create/app/src/app/app.component.html b/modules/local/report/create/app/src/app/app.component.html index 36093e1..2ccc280 100644 --- a/modules/local/report/create/app/src/app/app.component.html +++ b/modules/local/report/create/app/src/app/app.component.html @@ -1,336 +1,3 @@ - - - - - - - - - - - -
-
-
- -

Hello, {{ title }}

-

Congratulations! Your app is running. 🎉

-
- -
-
- @for (item of [ - { title: 'Explore the Docs', link: 'https://angular.dev' }, - { title: 'Learn with Tutorials', link: 'https://angular.dev/tutorials' }, - { title: 'CLI Docs', link: 'https://angular.dev/tools/cli' }, - { title: 'Angular Language Service', link: 'https://angular.dev/tools/language-service' }, - { title: 'Angular DevTools', link: 'https://angular.dev/tools/devtools' }, - ]; track item.title) { - - {{ item.title }} - - - - - } -
- -
-
-
- - - - - - - - - +

Hello, world!

From 033e8c1fe2bf4074f1bc78d0a038ddf2c3d24b42 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 23 Mar 2024 10:26:22 +0100 Subject: [PATCH 049/206] Prettier --- modules/local/report/create/app/angular.json | 27 +++++-------------- .../create/app/src/app/app.component.ts | 2 +- .../report/create/app/src/app/app.config.ts | 2 +- .../local/report/create/app/src/index.html | 20 +++++++------- modules/local/report/create/app/src/main.ts | 3 +-- .../local/report/create/app/tsconfig.app.json | 8 ++---- modules/local/report/create/app/tsconfig.json | 5 +--- .../report/create/app/tsconfig.spec.json | 9 ++----- 8 files changed, 24 insertions(+), 52 deletions(-) diff --git a/modules/local/report/create/app/angular.json b/modules/local/report/create/app/angular.json index 09c35f7..a6faf71 100644 --- a/modules/local/report/create/app/angular.json +++ b/modules/local/report/create/app/angular.json @@ -20,18 +20,11 @@ "outputPath": "dist/app", "index": "src/index.html", "browser": "src/main.ts", - "polyfills": [ - "zone.js" - ], + "polyfills": ["zone.js"], "tsConfig": "tsconfig.app.json", "inlineStyleLanguage": "scss", - "assets": [ - "src/favicon.ico", - "src/assets" - ], - "styles": [ - "src/styles.scss" - ], + "assets": ["src/favicon.ico", "src/assets"], + "styles": ["src/styles.scss"], "scripts": [] }, "configurations": { @@ -79,19 +72,11 @@ "test": { "builder": "@angular-devkit/build-angular:karma", "options": { - "polyfills": [ - "zone.js", - "zone.js/testing" - ], + "polyfills": ["zone.js", "zone.js/testing"], "tsConfig": "tsconfig.spec.json", "inlineStyleLanguage": "scss", - "assets": [ - "src/favicon.ico", - "src/assets" - ], - "styles": [ - "src/styles.scss" - ], + "assets": ["src/favicon.ico", "src/assets"], + "styles": ["src/styles.scss"], "scripts": [] } } diff --git a/modules/local/report/create/app/src/app/app.component.ts b/modules/local/report/create/app/src/app/app.component.ts index 87cca17..95d3f59 100644 --- a/modules/local/report/create/app/src/app/app.component.ts +++ b/modules/local/report/create/app/src/app/app.component.ts @@ -6,7 +6,7 @@ import { RouterOutlet } from '@angular/router'; standalone: true, imports: [RouterOutlet], templateUrl: './app.component.html', - styleUrl: './app.component.scss' + styleUrl: './app.component.scss', }) export class AppComponent { title = 'app'; diff --git a/modules/local/report/create/app/src/app/app.config.ts b/modules/local/report/create/app/src/app/app.config.ts index 6c6ef60..e7d665f 100644 --- a/modules/local/report/create/app/src/app/app.config.ts +++ b/modules/local/report/create/app/src/app/app.config.ts @@ -4,5 +4,5 @@ import { provideRouter } from '@angular/router'; import { routes } from './app.routes'; export const appConfig: ApplicationConfig = { - providers: [provideRouter(routes)] + providers: [provideRouter(routes)], }; diff --git a/modules/local/report/create/app/src/index.html b/modules/local/report/create/app/src/index.html index 22ac9ce..21a1731 100644 --- a/modules/local/report/create/app/src/index.html +++ b/modules/local/report/create/app/src/index.html @@ -1,13 +1,13 @@ - - - App - - - - - - - + + + App + + + + + + + diff --git a/modules/local/report/create/app/src/main.ts b/modules/local/report/create/app/src/main.ts index 35b00f3..17447a5 100644 --- a/modules/local/report/create/app/src/main.ts +++ b/modules/local/report/create/app/src/main.ts @@ -2,5 +2,4 @@ import { bootstrapApplication } from '@angular/platform-browser'; import { appConfig } from './app/app.config'; import { AppComponent } from './app/app.component'; -bootstrapApplication(AppComponent, appConfig) - .catch((err) => console.error(err)); +bootstrapApplication(AppComponent, appConfig).catch((err) => console.error(err)); diff --git a/modules/local/report/create/app/tsconfig.app.json b/modules/local/report/create/app/tsconfig.app.json index 374cc9d..84f1f99 100644 --- a/modules/local/report/create/app/tsconfig.app.json +++ b/modules/local/report/create/app/tsconfig.app.json @@ -5,10 +5,6 @@ "outDir": "./out-tsc/app", "types": [] }, - "files": [ - "src/main.ts" - ], - "include": [ - "src/**/*.d.ts" - ] + "files": ["src/main.ts"], + "include": ["src/**/*.d.ts"] } diff --git a/modules/local/report/create/app/tsconfig.json b/modules/local/report/create/app/tsconfig.json index eb49734..67d2944 100644 --- a/modules/local/report/create/app/tsconfig.json +++ b/modules/local/report/create/app/tsconfig.json @@ -18,10 +18,7 @@ "target": "ES2022", "module": "ES2022", "useDefineForClassFields": false, - "lib": [ - "ES2022", - "dom" - ] + "lib": ["ES2022", "dom"] }, "angularCompilerOptions": { "enableI18nLegacyMessageIdFormat": false, diff --git a/modules/local/report/create/app/tsconfig.spec.json b/modules/local/report/create/app/tsconfig.spec.json index be7e9da..47e3dd7 100644 --- a/modules/local/report/create/app/tsconfig.spec.json +++ b/modules/local/report/create/app/tsconfig.spec.json @@ -3,12 +3,7 @@ "extends": "./tsconfig.json", "compilerOptions": { "outDir": "./out-tsc/spec", - "types": [ - "jasmine" - ] + "types": ["jasmine"] }, - "include": [ - "src/**/*.spec.ts", - "src/**/*.d.ts" - ] + "include": ["src/**/*.spec.ts", "src/**/*.d.ts"] } From d015e6d83d2499fd391e5c10659649f524b99e49 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 23 Mar 2024 10:34:16 +0100 Subject: [PATCH 050/206] Set up angular material --- modules/local/report/create/app/angular.json | 4 +- .../local/report/create/app/package-lock.json | 859 +++++++++++++++++- modules/local/report/create/app/package.json | 3 + .../create/app/src/app/app.component.html | 3 +- .../create/app/src/app/app.component.ts | 5 +- .../report/create/app/src/app/app.config.ts | 3 +- .../local/report/create/app/src/index.html | 4 +- .../local/report/create/app/src/styles.scss | 14 +- 8 files changed, 886 insertions(+), 9 deletions(-) diff --git a/modules/local/report/create/app/angular.json b/modules/local/report/create/app/angular.json index a6faf71..ef062f3 100644 --- a/modules/local/report/create/app/angular.json +++ b/modules/local/report/create/app/angular.json @@ -24,7 +24,7 @@ "tsConfig": "tsconfig.app.json", "inlineStyleLanguage": "scss", "assets": ["src/favicon.ico", "src/assets"], - "styles": ["src/styles.scss"], + "styles": ["@angular/material/prebuilt-themes/indigo-pink.css", "src/styles.scss"], "scripts": [] }, "configurations": { @@ -76,7 +76,7 @@ "tsConfig": "tsconfig.spec.json", "inlineStyleLanguage": "scss", "assets": ["src/favicon.ico", "src/assets"], - "styles": ["src/styles.scss"], + "styles": ["@angular/material/prebuilt-themes/indigo-pink.css", "src/styles.scss"], "scripts": [] } } diff --git a/modules/local/report/create/app/package-lock.json b/modules/local/report/create/app/package-lock.json index 2f32796..bce9da7 100644 --- a/modules/local/report/create/app/package-lock.json +++ b/modules/local/report/create/app/package-lock.json @@ -9,10 +9,12 @@ "version": "0.0.0", "dependencies": { "@angular/animations": "^17.3.0", + "@angular/cdk": "~17.3.1", "@angular/common": "^17.3.0", "@angular/compiler": "^17.3.0", "@angular/core": "^17.3.0", "@angular/forms": "^17.3.0", + "@angular/material": "~17.3.1", "@angular/platform-browser": "^17.3.0", "@angular/platform-browser-dynamic": "^17.3.0", "@angular/router": "^17.3.0", @@ -31,6 +33,7 @@ "karma-coverage": "~2.2.0", "karma-jasmine": "~5.1.0", "karma-jasmine-html-reporter": "~2.1.0", + "prettier": "3.2.5", "typescript": "~5.4.2" } }, @@ -269,6 +272,22 @@ "@angular/core": "17.3.1" } }, + "node_modules/@angular/cdk": { + "version": "17.3.1", + "resolved": "https://registry.npmjs.org/@angular/cdk/-/cdk-17.3.1.tgz", + "integrity": "sha512-pHSN+KlCmdo2u9jY7Yxsry/ZK+EcjOYGzdwxXxcKragMzm7etY3BJiTl4N+qZRuV6cJlMj2PRkij8ABi/HQdEA==", + "dependencies": { + "tslib": "^2.3.0" + }, + "optionalDependencies": { + "parse5": "^7.1.2" + }, + "peerDependencies": { + "@angular/common": "^17.0.0 || ^18.0.0", + "@angular/core": "^17.0.0 || ^18.0.0", + "rxjs": "^6.5.3 || ^7.4.0" + } + }, "node_modules/@angular/cli": { "version": "17.3.1", "resolved": "https://registry.npmjs.org/@angular/cli/-/cli-17.3.1.tgz", @@ -442,6 +461,70 @@ "rxjs": "^6.5.3 || ^7.4.0" } }, + "node_modules/@angular/material": { + "version": "17.3.1", + "resolved": "https://registry.npmjs.org/@angular/material/-/material-17.3.1.tgz", + "integrity": "sha512-Md1OnO0/sQvK5GkTQyE4v1DAaMswXt1TnjjY07KG7cICTrUN8lc0a2P9dMjlSFXIhxC7PTlNH6plSZ1uspbU8Q==", + "dependencies": { + "@material/animation": "15.0.0-canary.7f224ddd4.0", + "@material/auto-init": "15.0.0-canary.7f224ddd4.0", + "@material/banner": "15.0.0-canary.7f224ddd4.0", + "@material/base": "15.0.0-canary.7f224ddd4.0", + "@material/button": "15.0.0-canary.7f224ddd4.0", + "@material/card": "15.0.0-canary.7f224ddd4.0", + "@material/checkbox": "15.0.0-canary.7f224ddd4.0", + "@material/chips": "15.0.0-canary.7f224ddd4.0", + "@material/circular-progress": "15.0.0-canary.7f224ddd4.0", + 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-9471,6 +10306,21 @@ "integrity": "sha512-1NNCs6uurfkVbeXG4S8JFT9t19m45ICnif8zWLd5oPSZ50QnwMfK+H3jv408d4jw/7Bttv5axS5IiHoLaVNHeQ==", "dev": true }, + "node_modules/prettier": { + "version": "3.2.5", + "resolved": "https://registry.npmjs.org/prettier/-/prettier-3.2.5.tgz", + "integrity": "sha512-3/GWa9aOC0YeD7LUfvOG2NiDyhOWRvt1k+rcKhOuYnMY24iiCphgneUfJDyFXd6rZCAnuLBv6UeAULtrhT/F4A==", + "dev": true, + "bin": { + "prettier": "bin/prettier.cjs" + }, + "engines": { + "node": ">=14" + }, + "funding": { + "url": "https://github.com/prettier/prettier?sponsor=1" + } + }, "node_modules/proc-log": { "version": "3.0.0", "resolved": "https://registry.npmjs.org/proc-log/-/proc-log-3.0.0.tgz", @@ -10055,6 +10905,11 @@ "integrity": "sha512-YZo3K82SD7Riyi0E1EQPojLz7kpepnSQI9IyPbHHg1XXXevb5dJI7tpyN2ADxGcQbHG7vcyRHk0cbwqcQriUtg==", "dev": true }, + "node_modules/safevalues": { + "version": "0.3.4", + "resolved": "https://registry.npmjs.org/safevalues/-/safevalues-0.3.4.tgz", + "integrity": "sha512-LRneZZRXNgjzwG4bDQdOTSbze3fHm1EAKN/8bePxnlEZiBmkYEDggaHbuvHI9/hoqHbGfsEA7tWS9GhYHZBBsw==" + }, "node_modules/sass": { "version": "1.71.1", "resolved": "https://registry.npmjs.org/sass/-/sass-1.71.1.tgz", diff --git a/modules/local/report/create/app/package.json b/modules/local/report/create/app/package.json index d42cc66..b880f5a 100644 --- a/modules/local/report/create/app/package.json +++ b/modules/local/report/create/app/package.json @@ -11,10 +11,12 @@ "private": true, "dependencies": { "@angular/animations": "^17.3.0", + "@angular/cdk": "~17.3.1", "@angular/common": "^17.3.0", "@angular/compiler": "^17.3.0", "@angular/core": "^17.3.0", "@angular/forms": "^17.3.0", + "@angular/material": "~17.3.1", "@angular/platform-browser": "^17.3.0", "@angular/platform-browser-dynamic": "^17.3.0", "@angular/router": "^17.3.0", @@ -33,6 +35,7 @@ "karma-coverage": "~2.2.0", "karma-jasmine": "~5.1.0", "karma-jasmine-html-reporter": "~2.1.0", + "prettier": "3.2.5", "typescript": "~5.4.2" } } diff --git a/modules/local/report/create/app/src/app/app.component.html b/modules/local/report/create/app/src/app/app.component.html index 2ccc280..a21442c 100644 --- a/modules/local/report/create/app/src/app/app.component.html +++ b/modules/local/report/create/app/src/app/app.component.html @@ -1,3 +1,4 @@ -

Hello, world!

+

Hello world!

+ diff --git a/modules/local/report/create/app/src/app/app.component.ts b/modules/local/report/create/app/src/app/app.component.ts index 95d3f59..04a3bf1 100644 --- a/modules/local/report/create/app/src/app/app.component.ts +++ b/modules/local/report/create/app/src/app/app.component.ts @@ -1,10 +1,13 @@ import { Component } from '@angular/core'; import { RouterOutlet } from '@angular/router'; +import { MatButton } from '@angular/material/button'; +import { MatDivider } from '@angular/material/divider'; +import { MatIcon } from '@angular/material/icon'; @Component({ selector: 'app-root', standalone: true, - imports: [RouterOutlet], + imports: [RouterOutlet, MatButton, MatDivider, MatIcon], templateUrl: './app.component.html', styleUrl: './app.component.scss', }) diff --git a/modules/local/report/create/app/src/app/app.config.ts b/modules/local/report/create/app/src/app/app.config.ts index e7d665f..bcd5df3 100644 --- a/modules/local/report/create/app/src/app/app.config.ts +++ b/modules/local/report/create/app/src/app/app.config.ts @@ -2,7 +2,8 @@ import { ApplicationConfig } from '@angular/core'; import { provideRouter } from '@angular/router'; import { routes } from './app.routes'; +import { provideAnimationsAsync } from '@angular/platform-browser/animations/async'; export const appConfig: ApplicationConfig = { - providers: [provideRouter(routes)], + providers: [provideRouter(routes), provideAnimationsAsync()], }; diff --git a/modules/local/report/create/app/src/index.html b/modules/local/report/create/app/src/index.html index 21a1731..e34ef65 100644 --- a/modules/local/report/create/app/src/index.html +++ b/modules/local/report/create/app/src/index.html @@ -6,8 +6,10 @@ + + - + diff --git a/modules/local/report/create/app/src/styles.scss b/modules/local/report/create/app/src/styles.scss index 90d4ee0..8fc4604 100644 --- a/modules/local/report/create/app/src/styles.scss +++ b/modules/local/report/create/app/src/styles.scss @@ -1 +1,13 @@ -/* You can add global styles to this file, and also import other style files */ +@use "@angular/material" as mat; + +$my-palette: mat.$indigo-palette; + +html, +body { + height: 100%; +} + +body { + margin: 0; + font-family: Roboto, "Helvetica Neue", sans-serif; +} From 0a2810ff32057d978692e6619d46d3ec2fb4b51f Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 23 Mar 2024 12:23:15 +0100 Subject: [PATCH 051/206] Switch to jinja --- modules/local/report/create/app/.editorconfig | 16 - modules/local/report/create/app/.gitignore | 42 - .../report/create/app/.vscode/extensions.json | 4 - .../report/create/app/.vscode/launch.json | 20 - .../report/create/app/.vscode/tasks.json | 42 - modules/local/report/create/app/README.md | 27 - .../app/app.component.scss => __init__.py} | 0 modules/local/report/create/app/angular.json | 86 - .../local/report/create/app/package-lock.json | 13225 ---------------- modules/local/report/create/app/package.json | 41 - .../create/app/src/app/app.component.html | 4 - .../create/app/src/app/app.component.spec.ts | 29 - .../create/app/src/app/app.component.ts | 16 - .../report/create/app/src/app/app.config.ts | 9 - .../report/create/app/src/app/app.routes.ts | 3 - .../local/report/create/app/src/favicon.ico | Bin 15086 -> 0 bytes .../local/report/create/app/src/index.html | 15 - modules/local/report/create/app/src/main.ts | 5 - .../local/report/create/app/src/styles.scss | 13 - .../assets/.gitkeep => templates/__init__.py} | 0 .../report/create/app/templates/index.html | 16 + .../local/report/create/app/tsconfig.app.json | 10 - modules/local/report/create/app/tsconfig.json | 29 - .../report/create/app/tsconfig.spec.json | 9 - modules/local/report/create/main.nf | 16 +- .../local/report/create/templates/build.py | 31 + 26 files changed, 52 insertions(+), 13656 deletions(-) delete mode 100644 modules/local/report/create/app/.editorconfig delete mode 100644 modules/local/report/create/app/.gitignore delete mode 100644 modules/local/report/create/app/.vscode/extensions.json delete mode 100644 modules/local/report/create/app/.vscode/launch.json delete mode 100644 modules/local/report/create/app/.vscode/tasks.json delete mode 100644 modules/local/report/create/app/README.md rename modules/local/report/create/app/{src/app/app.component.scss => __init__.py} (100%) delete mode 100644 modules/local/report/create/app/angular.json delete mode 100644 modules/local/report/create/app/package-lock.json delete mode 100644 modules/local/report/create/app/package.json delete mode 100644 modules/local/report/create/app/src/app/app.component.html delete mode 100644 modules/local/report/create/app/src/app/app.component.spec.ts delete mode 100644 modules/local/report/create/app/src/app/app.component.ts delete mode 100644 modules/local/report/create/app/src/app/app.config.ts delete mode 100644 modules/local/report/create/app/src/app/app.routes.ts delete mode 100644 modules/local/report/create/app/src/favicon.ico delete mode 100644 modules/local/report/create/app/src/index.html delete mode 100644 modules/local/report/create/app/src/main.ts delete mode 100644 modules/local/report/create/app/src/styles.scss rename modules/local/report/create/app/{src/assets/.gitkeep => templates/__init__.py} (100%) create mode 100644 modules/local/report/create/app/templates/index.html delete mode 100644 modules/local/report/create/app/tsconfig.app.json delete mode 100644 modules/local/report/create/app/tsconfig.json delete mode 100644 modules/local/report/create/app/tsconfig.spec.json create mode 100644 modules/local/report/create/templates/build.py diff --git a/modules/local/report/create/app/.editorconfig b/modules/local/report/create/app/.editorconfig deleted file mode 100644 index 59d9a3a..0000000 --- a/modules/local/report/create/app/.editorconfig +++ /dev/null @@ -1,16 +0,0 @@ -# Editor configuration, see https://editorconfig.org -root = true - -[*] -charset = utf-8 -indent_style = space -indent_size = 2 -insert_final_newline = true -trim_trailing_whitespace = true - -[*.ts] -quote_type = single - -[*.md] -max_line_length = off -trim_trailing_whitespace = false diff --git a/modules/local/report/create/app/.gitignore b/modules/local/report/create/app/.gitignore deleted file mode 100644 index 0711527..0000000 --- a/modules/local/report/create/app/.gitignore +++ /dev/null @@ -1,42 +0,0 @@ -# See http://help.github.com/ignore-files/ for more about ignoring files. - -# Compiled output -/dist -/tmp -/out-tsc -/bazel-out - -# Node -/node_modules -npm-debug.log -yarn-error.log - -# IDEs and editors -.idea/ -.project -.classpath -.c9/ -*.launch -.settings/ -*.sublime-workspace - -# Visual Studio Code -.vscode/* -!.vscode/settings.json -!.vscode/tasks.json -!.vscode/launch.json -!.vscode/extensions.json -.history/* - -# Miscellaneous -/.angular/cache -.sass-cache/ -/connect.lock -/coverage -/libpeerconnection.log -testem.log -/typings - -# System files -.DS_Store -Thumbs.db diff --git a/modules/local/report/create/app/.vscode/extensions.json b/modules/local/report/create/app/.vscode/extensions.json deleted file mode 100644 index 77b3745..0000000 --- a/modules/local/report/create/app/.vscode/extensions.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - // For more information, visit: https://go.microsoft.com/fwlink/?linkid=827846 - "recommendations": ["angular.ng-template"] -} diff --git a/modules/local/report/create/app/.vscode/launch.json b/modules/local/report/create/app/.vscode/launch.json deleted file mode 100644 index 925af83..0000000 --- a/modules/local/report/create/app/.vscode/launch.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387 - "version": "0.2.0", - "configurations": [ - { - "name": "ng serve", - "type": "chrome", - "request": "launch", - "preLaunchTask": "npm: start", - "url": "http://localhost:4200/" - }, - { - "name": "ng test", - "type": "chrome", - "request": "launch", - "preLaunchTask": "npm: test", - "url": "http://localhost:9876/debug.html" - } - ] -} diff --git a/modules/local/report/create/app/.vscode/tasks.json b/modules/local/report/create/app/.vscode/tasks.json deleted file mode 100644 index a298b5b..0000000 --- a/modules/local/report/create/app/.vscode/tasks.json +++ /dev/null @@ -1,42 +0,0 @@ -{ - // For more information, visit: https://go.microsoft.com/fwlink/?LinkId=733558 - "version": "2.0.0", - "tasks": [ - { - "type": "npm", - "script": "start", - "isBackground": true, - "problemMatcher": { - "owner": "typescript", - "pattern": "$tsc", - "background": { - "activeOnStart": true, - "beginsPattern": { - "regexp": "(.*?)" - }, - "endsPattern": { - "regexp": "bundle generation complete" - } - } - } - }, - { - "type": "npm", - "script": "test", - "isBackground": true, - "problemMatcher": { - "owner": "typescript", - "pattern": "$tsc", - "background": { - "activeOnStart": true, - "beginsPattern": { - "regexp": "(.*?)" - }, - "endsPattern": { - "regexp": "bundle generation complete" - } - } - } - } - ] -} diff --git a/modules/local/report/create/app/README.md b/modules/local/report/create/app/README.md deleted file mode 100644 index 209eaef..0000000 --- a/modules/local/report/create/app/README.md +++ /dev/null @@ -1,27 +0,0 @@ -# App - -This project was generated with [Angular CLI](https://github.com/angular/angular-cli) version 17.3.1. - -## Development server - -Run `ng serve` for a dev server. Navigate to `http://localhost:4200/`. The application will automatically reload if you change any of the source files. - -## Code scaffolding - -Run `ng generate component component-name` to generate a new component. You can also use `ng generate directive|pipe|service|class|guard|interface|enum|module`. - -## Build - -Run `ng build` to build the project. The build artifacts will be stored in the `dist/` directory. - -## Running unit tests - -Run `ng test` to execute the unit tests via [Karma](https://karma-runner.github.io). - -## Running end-to-end tests - -Run `ng e2e` to execute the end-to-end tests via a platform of your choice. To use this command, you need to first add a package that implements end-to-end testing capabilities. - -## Further help - -To get more help on the Angular CLI use `ng help` or go check out the [Angular CLI Overview and Command Reference](https://angular.io/cli) page. diff --git a/modules/local/report/create/app/src/app/app.component.scss b/modules/local/report/create/app/__init__.py similarity index 100% rename from modules/local/report/create/app/src/app/app.component.scss rename to modules/local/report/create/app/__init__.py diff --git a/modules/local/report/create/app/angular.json b/modules/local/report/create/app/angular.json deleted file mode 100644 index ef062f3..0000000 --- a/modules/local/report/create/app/angular.json +++ /dev/null @@ -1,86 +0,0 @@ -{ - "$schema": "./node_modules/@angular/cli/lib/config/schema.json", - "version": 1, - "newProjectRoot": "projects", - "projects": { - "app": { - "projectType": "application", - "schematics": { - "@schematics/angular:component": { - "style": "scss" - } - }, - "root": "", - "sourceRoot": "src", - "prefix": "app", - "architect": { - "build": { - "builder": "@angular-devkit/build-angular:application", - "options": { - "outputPath": "dist/app", - "index": "src/index.html", - "browser": "src/main.ts", - "polyfills": ["zone.js"], - "tsConfig": "tsconfig.app.json", - "inlineStyleLanguage": "scss", - "assets": ["src/favicon.ico", "src/assets"], - "styles": ["@angular/material/prebuilt-themes/indigo-pink.css", "src/styles.scss"], - "scripts": [] - }, - "configurations": { - "production": { - "budgets": [ - { - "type": "initial", - "maximumWarning": "500kb", - "maximumError": "1mb" - }, - { - "type": "anyComponentStyle", - "maximumWarning": "2kb", - "maximumError": "4kb" - } - ], - "outputHashing": "all" - }, - "development": { - "optimization": false, - "extractLicenses": false, - "sourceMap": true - } - }, - "defaultConfiguration": "production" - }, - "serve": { - "builder": "@angular-devkit/build-angular:dev-server", - "configurations": { - "production": { - "buildTarget": "app:build:production" - }, - "development": { - "buildTarget": "app:build:development" - } - }, - "defaultConfiguration": "development" - }, - "extract-i18n": { - "builder": "@angular-devkit/build-angular:extract-i18n", - "options": { - "buildTarget": "app:build" - } - }, - "test": { - "builder": "@angular-devkit/build-angular:karma", - "options": { - "polyfills": ["zone.js", "zone.js/testing"], - "tsConfig": "tsconfig.spec.json", - "inlineStyleLanguage": "scss", - "assets": ["src/favicon.ico", "src/assets"], - "styles": ["@angular/material/prebuilt-themes/indigo-pink.css", "src/styles.scss"], - "scripts": [] - } - } - } - } - } -} diff --git a/modules/local/report/create/app/package-lock.json b/modules/local/report/create/app/package-lock.json deleted file mode 100644 index bce9da7..0000000 --- a/modules/local/report/create/app/package-lock.json +++ /dev/null @@ -1,13225 +0,0 @@ -{ - "name": "app", - "version": "0.0.0", - "lockfileVersion": 3, - "requires": true, - "packages": { - "": { - "name": "app", - "version": "0.0.0", - "dependencies": { - "@angular/animations": "^17.3.0", - "@angular/cdk": "~17.3.1", - "@angular/common": "^17.3.0", - "@angular/compiler": "^17.3.0", - "@angular/core": "^17.3.0", - "@angular/forms": "^17.3.0", - "@angular/material": "~17.3.1", - "@angular/platform-browser": "^17.3.0", - "@angular/platform-browser-dynamic": "^17.3.0", - "@angular/router": "^17.3.0", - "rxjs": "~7.8.0", - "tslib": "^2.3.0", - "zone.js": "~0.14.3" - }, - "devDependencies": { - "@angular-devkit/build-angular": "^17.3.1", - "@angular/cli": "^17.3.1", - "@angular/compiler-cli": "^17.3.0", - "@types/jasmine": "~5.1.0", - "jasmine-core": "~5.1.0", - "karma": "~6.4.0", - "karma-chrome-launcher": "~3.2.0", - "karma-coverage": "~2.2.0", - "karma-jasmine": "~5.1.0", - "karma-jasmine-html-reporter": "~2.1.0", - "prettier": "3.2.5", - "typescript": "~5.4.2" - } - }, - "node_modules/@ampproject/remapping": { - "version": "2.3.0", - "resolved": "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.3.0.tgz", - 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"@angular/cli": "^17.3.1", - "@angular/compiler-cli": "^17.3.0", - "@types/jasmine": "~5.1.0", - "jasmine-core": "~5.1.0", - "karma": "~6.4.0", - "karma-chrome-launcher": "~3.2.0", - "karma-coverage": "~2.2.0", - "karma-jasmine": "~5.1.0", - "karma-jasmine-html-reporter": "~2.1.0", - "prettier": "3.2.5", - "typescript": "~5.4.2" - } -} diff --git a/modules/local/report/create/app/src/app/app.component.html b/modules/local/report/create/app/src/app/app.component.html deleted file mode 100644 index a21442c..0000000 --- a/modules/local/report/create/app/src/app/app.component.html +++ /dev/null @@ -1,4 +0,0 @@ -

Hello world!

- - - diff --git a/modules/local/report/create/app/src/app/app.component.spec.ts b/modules/local/report/create/app/src/app/app.component.spec.ts deleted file mode 100644 index 44771e7..0000000 --- a/modules/local/report/create/app/src/app/app.component.spec.ts +++ /dev/null @@ -1,29 +0,0 @@ -import { TestBed } from '@angular/core/testing'; -import { AppComponent } from './app.component'; - -describe('AppComponent', () => { - beforeEach(async () => { - await TestBed.configureTestingModule({ - imports: [AppComponent], - }).compileComponents(); - }); - - it('should create the app', () => { - const fixture = TestBed.createComponent(AppComponent); - const app = fixture.componentInstance; - expect(app).toBeTruthy(); - }); - - it(`should have the 'app' title`, () => { - const fixture = TestBed.createComponent(AppComponent); - const app = fixture.componentInstance; - expect(app.title).toEqual('app'); - }); - - it('should render title', () => { - const fixture = TestBed.createComponent(AppComponent); - fixture.detectChanges(); - const compiled = fixture.nativeElement as HTMLElement; - expect(compiled.querySelector('h1')?.textContent).toContain('Hello, app'); - }); -}); diff --git a/modules/local/report/create/app/src/app/app.component.ts b/modules/local/report/create/app/src/app/app.component.ts deleted file mode 100644 index 04a3bf1..0000000 --- a/modules/local/report/create/app/src/app/app.component.ts +++ /dev/null @@ -1,16 +0,0 @@ -import { Component } from '@angular/core'; -import { RouterOutlet } from '@angular/router'; -import { MatButton } from '@angular/material/button'; -import { MatDivider } from '@angular/material/divider'; -import { MatIcon } from '@angular/material/icon'; - -@Component({ - selector: 'app-root', - standalone: true, - imports: [RouterOutlet, MatButton, MatDivider, MatIcon], - templateUrl: './app.component.html', - styleUrl: './app.component.scss', -}) -export class AppComponent { - title = 'app'; -} diff --git a/modules/local/report/create/app/src/app/app.config.ts b/modules/local/report/create/app/src/app/app.config.ts deleted file mode 100644 index bcd5df3..0000000 --- a/modules/local/report/create/app/src/app/app.config.ts +++ /dev/null @@ -1,9 +0,0 @@ -import { ApplicationConfig } from '@angular/core'; -import { provideRouter } from '@angular/router'; - -import { routes } from './app.routes'; -import { provideAnimationsAsync } from '@angular/platform-browser/animations/async'; - -export const appConfig: ApplicationConfig = { - providers: [provideRouter(routes), provideAnimationsAsync()], -}; diff --git a/modules/local/report/create/app/src/app/app.routes.ts b/modules/local/report/create/app/src/app/app.routes.ts deleted file mode 100644 index dc39edb..0000000 --- a/modules/local/report/create/app/src/app/app.routes.ts +++ /dev/null @@ -1,3 +0,0 @@ -import { Routes } from '@angular/router'; - -export const routes: Routes = []; diff --git a/modules/local/report/create/app/src/favicon.ico b/modules/local/report/create/app/src/favicon.ico deleted file mode 100644 index 57614f9c967596fad0a3989bec2b1deff33034f6..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 15086 zcmd^G33O9Omi+`8$@{|M-I6TH3wzF-p5CV8o}7f~KxR60LK+ApEFB<$bcciv%@SmA zV{n>g85YMFFeU*Uvl=i4v)C*qgnb;$GQ=3XTe9{Y%c`mO%su)noNCCQ*@t1WXn|B(hQ7i~ zrUK8|pUkD6#lNo!bt$6)jR!&C?`P5G(`e((P($RaLeq+o0Vd~f11;qB05kdbAOm?r zXv~GYr_sibQO9NGTCdT;+G(!{4Xs@4fPak8#L8PjgJwcs-Mm#nR_Z0s&u?nDX5^~@ z+A6?}g0|=4e_LoE69pPFO`yCD@BCjgKpzMH0O4Xs{Ahc?K3HC5;l=f zg>}alhBXX&);z$E-wai+9TTRtBX-bWYY@cl$@YN#gMd~tM_5lj6W%8ah4;uZ;jP@Q zVbuel1rPA?2@x9Y+u?e`l{Z4ngfG5q5BLH5QsEu4GVpt{KIp1?U)=3+KQ;%7ec8l* zdV=zZgN5>O3G(3L2fqj3;oBbZZw$Ij@`Juz@?+yy#OPw)>#wsTewVgTK9BGt5AbZ&?K&B3GVF&yu?@(Xj3fR3n+ZP0%+wo)D9_xp>Z$`A4 zfV>}NWjO#3lqumR0`gvnffd9Ka}JJMuHS&|55-*mCD#8e^anA<+sFZVaJe7{=p*oX zE_Uv?1>e~ga=seYzh{9P+n5<+7&9}&(kwqSaz;1aD|YM3HBiy<))4~QJSIryyqp| z8nGc(8>3(_nEI4n)n7j(&d4idW1tVLjZ7QbNLXg;LB ziHsS5pXHEjGJZb59KcvS~wv;uZR-+4qEqow`;JCfB*+b^UL^3!?;-^F%yt=VjU|v z39SSqKcRu_NVvz!zJzL0CceJaS6%!(eMshPv_0U5G`~!a#I$qI5Ic(>IONej@aH=f z)($TAT#1I{iCS4f{D2+ApS=$3E7}5=+y(rA9mM#;Cky%b*Gi0KfFA`ofKTzu`AV-9 znW|y@19rrZ*!N2AvDi<_ZeR3O2R{#dh1#3-d%$k${Rx42h+i&GZo5!C^dSL34*AKp z27mTd>k>?V&X;Nl%GZ(>0s`1UN~Hfyj>KPjtnc|)xM@{H_B9rNr~LuH`Gr5_am&Ep zTjZA8hljNj5H1Ipm-uD9rC}U{-vR!eay5&6x6FkfupdpT*84MVwGpdd(}ib)zZ3Ky z7C$pnjc82(W_y_F{PhYj?o!@3__UUvpX)v69aBSzYj3 zdi}YQkKs^SyXyFG2LTRz9{(w}y~!`{EuAaUr6G1M{*%c+kP1olW9z23dSH!G4_HSK zzae-DF$OGR{ofP*!$a(r^5Go>I3SObVI6FLY)N@o<*gl0&kLo-OT{Tl*7nCz>Iq=? 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{{text}}

+ + + + \ No newline at end of file diff --git a/modules/local/report/create/app/tsconfig.app.json b/modules/local/report/create/app/tsconfig.app.json deleted file mode 100644 index 84f1f99..0000000 --- a/modules/local/report/create/app/tsconfig.app.json +++ /dev/null @@ -1,10 +0,0 @@ -/* To learn more about this file see: https://angular.io/config/tsconfig. */ -{ - "extends": "./tsconfig.json", - "compilerOptions": { - "outDir": "./out-tsc/app", - "types": [] - }, - "files": ["src/main.ts"], - "include": ["src/**/*.d.ts"] -} diff --git a/modules/local/report/create/app/tsconfig.json b/modules/local/report/create/app/tsconfig.json deleted file mode 100644 index 67d2944..0000000 --- a/modules/local/report/create/app/tsconfig.json +++ /dev/null @@ -1,29 +0,0 @@ -/* To learn more about this file see: https://angular.io/config/tsconfig. */ -{ - "compileOnSave": false, - "compilerOptions": { - "outDir": "./dist/out-tsc", - "strict": true, - "noImplicitOverride": true, - "noPropertyAccessFromIndexSignature": true, - "noImplicitReturns": true, - "noFallthroughCasesInSwitch": true, - "skipLibCheck": true, - "esModuleInterop": true, - "sourceMap": true, - "declaration": false, - "experimentalDecorators": true, - "moduleResolution": "node", - "importHelpers": true, - "target": "ES2022", - "module": "ES2022", - "useDefineForClassFields": false, - "lib": ["ES2022", "dom"] - }, - "angularCompilerOptions": { - "enableI18nLegacyMessageIdFormat": false, - "strictInjectionParameters": true, - "strictInputAccessModifiers": true, - "strictTemplates": true - } -} diff --git a/modules/local/report/create/app/tsconfig.spec.json b/modules/local/report/create/app/tsconfig.spec.json deleted file mode 100644 index 47e3dd7..0000000 --- a/modules/local/report/create/app/tsconfig.spec.json +++ /dev/null @@ -1,9 +0,0 @@ -/* To learn more about this file see: https://angular.io/config/tsconfig. */ -{ - "extends": "./tsconfig.json", - "compilerOptions": { - "outDir": "./out-tsc/spec", - "types": ["jasmine"] - }, - "include": ["src/**/*.spec.ts", "src/**/*.d.ts"] -} diff --git a/modules/local/report/create/main.nf b/modules/local/report/create/main.nf index 15a8ba4..f414d02 100644 --- a/modules/local/report/create/main.nf +++ b/modules/local/report/create/main.nf @@ -1,20 +1,14 @@ process CREATE { label "process_low" - conda "conda-forge::nodejs" - container "docker.io/node:20.9.0-bookworm" - - cache false + conda "bioconda::mulled-v2-ab48c38c3be93a696d7773767d9287b4a0d3bf19==e3c8a1ac0a27058d7922e8b6d02f303c30d93e3a-0" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-ab48c38c3be93a696d7773767d9287b4a0d3bf19:e3c8a1ac0a27058d7922e8b6d02f303c30d93e3a-0': + 'biocontainers/mulled-v2-ab48c38c3be93a696d7773767d9287b4a0d3bf19:e3c8a1ac0a27058d7922e8b6d02f303c30d93e3a-0' }" output: path("report") script: - """ - cp -r $moduleDir/app ./app - cd app - npm install && npm run build - sed -i 's/type="module"//g' dist/app/browser/index.html - cp -r dist/app ../report - """ + template "build.py" } \ No newline at end of file diff --git a/modules/local/report/create/templates/build.py b/modules/local/report/create/templates/build.py new file mode 100644 index 0000000..fe5116a --- /dev/null +++ b/modules/local/report/create/templates/build.py @@ -0,0 +1,31 @@ +#!/usr/bin/env python3 + +from jinja2 import Environment, PackageLoader, select_autoescape +import os +import shutil + +module_app = os.path.abspath("$moduleDir/app") +app_dir = "app" +out_dir = "report" + +# Copy app_dir to current directory +shutil.copytree(module_app, os.path.join(os.getcwd(), app_dir), dirs_exist_ok=True) + +print(os.listdir(".")) + +print("Hello from build.py") +print("ModuleDir: $moduleDir") +print("AppDir: " + app_dir) + +env = Environment( + loader=PackageLoader(app_dir), + autoescape=select_autoescape() +) + +text = "Hello, World!" + +template = env.get_template("index.html") + +os.makedirs(out_dir, exist_ok=True) +with open(os.path.join(out_dir, "index.html"), "w") as f: + f.write(template.render(text=text)) From 54e66eaddd096cfc20e37f378bd8de7cc2e0c582 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sun, 24 Mar 2024 10:10:26 +0100 Subject: [PATCH 052/206] Add basic tf, tg and snp pages --- .../report/create/app/templates/base.html | 22 +++++++++++++++++++ .../report/create/app/templates/index.html | 16 -------------- .../report/create/app/templates/macros.html | 13 +++++++++++ .../report/create/app/templates/snp.html | 20 +++++++++++++++++ .../report/create/app/templates/styles.css | 3 +++ .../local/report/create/app/templates/tf.html | 20 +++++++++++++++++ .../local/report/create/app/templates/tg.html | 20 +++++++++++++++++ modules/local/report/create/main.nf | 2 ++ .../local/report/create/templates/build.py | 12 ++++++++-- 9 files changed, 110 insertions(+), 18 deletions(-) create mode 100644 modules/local/report/create/app/templates/base.html delete mode 100644 modules/local/report/create/app/templates/index.html create mode 100644 modules/local/report/create/app/templates/macros.html create mode 100644 modules/local/report/create/app/templates/snp.html create mode 100644 modules/local/report/create/app/templates/styles.css create mode 100644 modules/local/report/create/app/templates/tf.html create mode 100644 modules/local/report/create/app/templates/tg.html diff --git a/modules/local/report/create/app/templates/base.html b/modules/local/report/create/app/templates/base.html new file mode 100644 index 0000000..b0f5c4e --- /dev/null +++ b/modules/local/report/create/app/templates/base.html @@ -0,0 +1,22 @@ + + + + + Report + + + + + + + +
+

Report

+ +
+ {% block tabs %}{% endblock %} + {% block content %}{% endblock %} + + + \ No newline at end of file diff --git a/modules/local/report/create/app/templates/index.html b/modules/local/report/create/app/templates/index.html deleted file mode 100644 index e210609..0000000 --- a/modules/local/report/create/app/templates/index.html +++ /dev/null @@ -1,16 +0,0 @@ - - - - - Report - - - - - - -

{{text}}

- - - - \ No newline at end of file diff --git a/modules/local/report/create/app/templates/macros.html b/modules/local/report/create/app/templates/macros.html new file mode 100644 index 0000000..5d6a341 --- /dev/null +++ b/modules/local/report/create/app/templates/macros.html @@ -0,0 +1,13 @@ +{% macro tabs(active="tf") %} + +{% endmacro %} \ No newline at end of file diff --git a/modules/local/report/create/app/templates/snp.html b/modules/local/report/create/app/templates/snp.html new file mode 100644 index 0000000..c0652ad --- /dev/null +++ b/modules/local/report/create/app/templates/snp.html @@ -0,0 +1,20 @@ + +{% extends "base.html" %} + +{% block tabs %} +{% from 'macros.html' import tabs %} +{{ tabs(active="snp") }} +{% endblock %} + +{% block content %} +
+ + +
+

Hello

+
+
+{% endblock %} \ No newline at end of file diff --git a/modules/local/report/create/app/templates/styles.css b/modules/local/report/create/app/templates/styles.css new file mode 100644 index 0000000..549608f --- /dev/null +++ b/modules/local/report/create/app/templates/styles.css @@ -0,0 +1,3 @@ +img { + object-fit: contain; +} \ No newline at end of file diff --git a/modules/local/report/create/app/templates/tf.html b/modules/local/report/create/app/templates/tf.html new file mode 100644 index 0000000..572cf91 --- /dev/null +++ b/modules/local/report/create/app/templates/tf.html @@ -0,0 +1,20 @@ + +{% extends "base.html" %} + +{% block tabs %} +{% from 'macros.html' import tabs %} +{{ tabs(active="tf") }} +{% endblock %} + +{% block content %} +
+ + +
+

Hello

+
+
+{% endblock %} \ No newline at end of file diff --git a/modules/local/report/create/app/templates/tg.html b/modules/local/report/create/app/templates/tg.html new file mode 100644 index 0000000..c612625 --- /dev/null +++ b/modules/local/report/create/app/templates/tg.html @@ -0,0 +1,20 @@ + +{% extends "base.html" %} + +{% block tabs %} +{% from 'macros.html' import tabs %} +{{ tabs(active="tg") }} +{% endblock %} + +{% block content %} +
+ + +
+

Hello

+
+
+{% endblock %} \ No newline at end of file diff --git a/modules/local/report/create/main.nf b/modules/local/report/create/main.nf index f414d02..189969b 100644 --- a/modules/local/report/create/main.nf +++ b/modules/local/report/create/main.nf @@ -6,6 +6,8 @@ process CREATE { 'https://depot.galaxyproject.org/singularity/mulled-v2-ab48c38c3be93a696d7773767d9287b4a0d3bf19:e3c8a1ac0a27058d7922e8b6d02f303c30d93e3a-0': 'biocontainers/mulled-v2-ab48c38c3be93a696d7773767d9287b4a0d3bf19:e3c8a1ac0a27058d7922e8b6d02f303c30d93e3a-0' }" + cache false + output: path("report") diff --git a/modules/local/report/create/templates/build.py b/modules/local/report/create/templates/build.py index fe5116a..384e7f1 100644 --- a/modules/local/report/create/templates/build.py +++ b/modules/local/report/create/templates/build.py @@ -24,8 +24,16 @@ text = "Hello, World!" -template = env.get_template("index.html") +tf = env.get_template("tf.html") +tg = env.get_template("tg.html") +snp = env.get_template("snp.html") os.makedirs(out_dir, exist_ok=True) with open(os.path.join(out_dir, "index.html"), "w") as f: - f.write(template.render(text=text)) + f.write(tf.render()) + +with open(os.path.join(out_dir, "target_genes.html"), "w") as f: + f.write(tg.render()) + +with open(os.path.join(out_dir, "snps.html"), "w") as f: + f.write(snp.render()) From 7a0615c8292f984acb4bbfbd66174b684ace4504 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sun, 24 Mar 2024 11:09:30 +0100 Subject: [PATCH 053/206] Implement dummy ranking --- .../report/create/app/templates/styles.css | 10 ++++++ .../local/report/create/app/templates/tf.html | 35 ++++++++++++++----- .../local/report/create/templates/build.py | 25 ++++++++++++- 3 files changed, 60 insertions(+), 10 deletions(-) diff --git a/modules/local/report/create/app/templates/styles.css b/modules/local/report/create/app/templates/styles.css index 549608f..34697aa 100644 --- a/modules/local/report/create/app/templates/styles.css +++ b/modules/local/report/create/app/templates/styles.css @@ -1,3 +1,13 @@ img { object-fit: contain; +} + +.ranking-container { + display: flex; + flex-wrap: wrap; + justify-content: center; +} + +.card { + margin: 5px } \ No newline at end of file diff --git a/modules/local/report/create/app/templates/tf.html b/modules/local/report/create/app/templates/tf.html index 572cf91..8cd788c 100644 --- a/modules/local/report/create/app/templates/tf.html +++ b/modules/local/report/create/app/templates/tf.html @@ -1,4 +1,3 @@ - {% extends "base.html" %} {% block tabs %} @@ -7,14 +6,32 @@ {% endblock %} {% block content %} -
- - -
-

Hello

+ +
+ {% for tf, ranks in ranking.items() %} +
+
+ + +
+

Hello

+
+
+ {% endfor %}
{% endblock %} \ No newline at end of file diff --git a/modules/local/report/create/templates/build.py b/modules/local/report/create/templates/build.py index 384e7f1..d44ce69 100644 --- a/modules/local/report/create/templates/build.py +++ b/modules/local/report/create/templates/build.py @@ -27,13 +27,36 @@ tf = env.get_template("tf.html") tg = env.get_template("tg.html") snp = env.get_template("snp.html") +styles = env.get_template("styles.css") + +ranking = { + "TF1": { + "A": 1, + "B": 2, + }, + "TF2": { + "A": 2, + "B": 1, + }, + "TF3": { + "A": 3, + } +} + +assay_sizes = { + "A": 3, + "B": 3, +} os.makedirs(out_dir, exist_ok=True) with open(os.path.join(out_dir, "index.html"), "w") as f: - f.write(tf.render()) + f.write(tf.render(ranking=ranking, assay_sizes=assay_sizes)) with open(os.path.join(out_dir, "target_genes.html"), "w") as f: f.write(tg.render()) with open(os.path.join(out_dir, "snps.html"), "w") as f: f.write(snp.render()) + +with open(os.path.join(out_dir, "styles.css"), "w") as f: + f.write(styles.render()) \ No newline at end of file From 965c006f97e8d25ab8137504f8bace8e084b55c3 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sun, 24 Mar 2024 12:41:10 +0100 Subject: [PATCH 054/206] Add params to file to report --- .../local/report/create/app/templates/styles.css | 4 ++++ modules/local/report/create/app/templates/tf.html | 1 + modules/local/report/create/main.nf | 6 ++++++ modules/local/report/create/templates/build.py | 14 ++++++-------- subworkflows/local/report.nf | 2 +- 5 files changed, 18 insertions(+), 9 deletions(-) diff --git a/modules/local/report/create/app/templates/styles.css b/modules/local/report/create/app/templates/styles.css index 34697aa..e24a925 100644 --- a/modules/local/report/create/app/templates/styles.css +++ b/modules/local/report/create/app/templates/styles.css @@ -10,4 +10,8 @@ img { .card { margin: 5px +} + +button { + margin: 2px; } \ No newline at end of file diff --git a/modules/local/report/create/app/templates/tf.html b/modules/local/report/create/app/templates/tf.html index 8cd788c..02d51f8 100644 --- a/modules/local/report/create/app/templates/tf.html +++ b/modules/local/report/create/app/templates/tf.html @@ -26,6 +26,7 @@ {{ assay }} {% endfor %} +

Hello

diff --git a/modules/local/report/create/main.nf b/modules/local/report/create/main.nf index 189969b..8be75d3 100644 --- a/modules/local/report/create/main.nf +++ b/modules/local/report/create/main.nf @@ -1,3 +1,5 @@ +import groovy.json.JsonOutput + process CREATE { label "process_low" @@ -8,9 +10,13 @@ process CREATE { cache false + input: + val(params) + output: path("report") script: + params_string = JsonOutput.toJson(params) template "build.py" } \ No newline at end of file diff --git a/modules/local/report/create/templates/build.py b/modules/local/report/create/templates/build.py index d44ce69..672a1d9 100644 --- a/modules/local/report/create/templates/build.py +++ b/modules/local/report/create/templates/build.py @@ -3,6 +3,7 @@ from jinja2 import Environment, PackageLoader, select_autoescape import os import shutil +import json module_app = os.path.abspath("$moduleDir/app") app_dir = "app" @@ -11,19 +12,13 @@ # Copy app_dir to current directory shutil.copytree(module_app, os.path.join(os.getcwd(), app_dir), dirs_exist_ok=True) -print(os.listdir(".")) - -print("Hello from build.py") -print("ModuleDir: $moduleDir") -print("AppDir: " + app_dir) +params = json.loads(r'$params_string') env = Environment( loader=PackageLoader(app_dir), autoescape=select_autoescape() ) -text = "Hello, World!" - tf = env.get_template("tf.html") tg = env.get_template("tg.html") snp = env.get_template("snp.html") @@ -59,4 +54,7 @@ f.write(snp.render()) with open(os.path.join(out_dir, "styles.css"), "w") as f: - f.write(styles.render()) \ No newline at end of file + f.write(styles.render()) + +with open(os.path.join(out_dir, "params.json"), "w") as f: + json.dump(params, f, indent=4) \ No newline at end of file diff --git a/subworkflows/local/report.nf b/subworkflows/local/report.nf index b4bd90a..4c20261 100644 --- a/subworkflows/local/report.nf +++ b/subworkflows/local/report.nf @@ -2,5 +2,5 @@ include { CREATE } from '../../modules/local/report/create/main' workflow REPORT { main: - CREATE() + CREATE(params) } \ No newline at end of file From 5e965ad01238c20537e692ba1dd054eec1c575ba Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sun, 24 Mar 2024 13:25:31 +0100 Subject: [PATCH 055/206] Improve ranking aggregation --- bin/combine_rankings.py | 5 +++++ modules/local/ranking/combine_rankings.nf | 4 ++-- modules/local/report/create/main.nf | 1 + subworkflows/local/ranking.nf | 18 +++++++++++------- subworkflows/local/report.nf | 8 +++++++- workflows/tfactivity.nf | 4 +++- 6 files changed, 29 insertions(+), 11 deletions(-) diff --git a/bin/combine_rankings.py b/bin/combine_rankings.py index 04ef996..5f1e127 100755 --- a/bin/combine_rankings.py +++ b/bin/combine_rankings.py @@ -13,6 +13,11 @@ df = pd.concat([df[['dcg']] for df in dfs]) df = df.groupby(df.index).sum() + +# Todo: Check if we should use number of comparisons per assay as weights +# In this case, the next line should be commented out +df["dcg"] = df["dcg"] / len(dfs) + df.sort_values(by=['dcg'], ascending=False, inplace=True) df['rank'] = range(1, len(df.index) + 1) diff --git a/modules/local/ranking/combine_rankings.nf b/modules/local/ranking/combine_rankings.nf index 4dfd3f4..0fefeec 100644 --- a/modules/local/ranking/combine_rankings.nf +++ b/modules/local/ranking/combine_rankings.nf @@ -11,13 +11,13 @@ process COMBINE_RANKINGS { tuple val(meta), path(rankings) output: - tuple val(meta), path("combined.ranking.tsv"), emit: ranking + tuple val(meta), path("${meta.id}.ranking.tsv"), emit: ranking path "versions.yml" , emit: versions script: """ - combine_rankings.py --input ${rankings} --output combined.ranking.tsv + combine_rankings.py --input ${rankings} --output ${meta.id}.ranking.tsv cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/local/report/create/main.nf b/modules/local/report/create/main.nf index 8be75d3..84e8e6c 100644 --- a/modules/local/report/create/main.nf +++ b/modules/local/report/create/main.nf @@ -11,6 +11,7 @@ process CREATE { cache false input: + tuple val(meta), path(assay_ranking) val(params) output: diff --git a/subworkflows/local/ranking.nf b/subworkflows/local/ranking.nf index c632cfb..3f647ea 100644 --- a/subworkflows/local/ranking.nf +++ b/subworkflows/local/ranking.nf @@ -1,6 +1,7 @@ -include { TF_TG_SCORE } from '../../modules/local/ranking/tf_tg_score' -include { RANKING as CREATE_RANKING } from '../../modules/local/ranking/ranking' -include { COMBINE_RANKINGS } from '../../modules/local/ranking/combine_rankings' +include { TF_TG_SCORE } from '../../modules/local/ranking/tf_tg_score' +include { RANKING as CREATE_RANKING } from '../../modules/local/ranking/ranking' +include { COMBINE_RANKINGS as COMBINE_PER_ASSAY } from '../../modules/local/ranking/combine_rankings' +include { COMBINE_RANKINGS as COMBINE_ASSAYS } from '../../modules/local/ranking/combine_rankings' workflow RANKING { @@ -27,20 +28,23 @@ workflow RANKING { TF_TG_SCORE(ch_combined) CREATE_RANKING(TF_TG_SCORE.out.score, alpha) - COMBINE_RANKINGS(CREATE_RANKING.out.ranking .map{ meta, ranking -> ranking } + COMBINE_PER_ASSAY(CREATE_RANKING.out.ranking.map{ meta, ranking -> [[id: meta.assay], ranking]} + .groupTuple()) + COMBINE_ASSAYS(COMBINE_PER_ASSAY.out.ranking.map{ meta, ranking -> ranking } .collect() .map{ rankings -> [[id: "all"], rankings]} ) ch_versions = ch_versions.mix(TF_TG_SCORE.out.versions, CREATE_RANKING.out.versions, - COMBINE_RANKINGS.out.versions + COMBINE_PER_ASSAY.out.versions, + COMBINE_ASSAYS.out.versions ) emit: - assay_specific = CREATE_RANKING.out.ranking - combined = COMBINE_RANKINGS.out.ranking + assay_specific = COMBINE_PER_ASSAY.out.ranking + combined = COMBINE_ASSAYS.out.ranking versions = ch_versions // channel: [ versions.yml ] diff --git a/subworkflows/local/report.nf b/subworkflows/local/report.nf index 4c20261..5dc5986 100644 --- a/subworkflows/local/report.nf +++ b/subworkflows/local/report.nf @@ -1,6 +1,12 @@ include { CREATE } from '../../modules/local/report/create/main' workflow REPORT { + take: + ch_assay_rankings + main: - CREATE(params) + CREATE(ch_assay_rankings.map{meta, ranking -> ranking} + .collect() + .map{rankings -> [[id: "ranking"], rankings]}, + params) } \ No newline at end of file diff --git a/workflows/tfactivity.nf b/workflows/tfactivity.nf index 399fb8e..002ecdd 100644 --- a/workflows/tfactivity.nf +++ b/workflows/tfactivity.nf @@ -116,7 +116,9 @@ workflow TFACTIVITY { DYNAMITE.out.versions ) - REPORT() + REPORT( + RANKING.out.assay_specific + ) // // Collate and save software versions From bde7da3af5edd58b60e9aba4d976d60b025fe488 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sun, 24 Mar 2024 14:03:40 +0100 Subject: [PATCH 056/206] Use real TFs in ranking --- .../local/report/create/app/templates/tf.html | 10 +++---- .../local/report/create/templates/build.py | 30 +++++++++---------- 2 files changed, 19 insertions(+), 21 deletions(-) diff --git a/modules/local/report/create/app/templates/tf.html b/modules/local/report/create/app/templates/tf.html index 02d51f8..a12ac1d 100644 --- a/modules/local/report/create/app/templates/tf.html +++ b/modules/local/report/create/app/templates/tf.html @@ -8,19 +8,19 @@ {% block content %}
- {% for tf, ranks in ranking.items() %} + {% for tf, dcgs in ranking.items() %}

Hello

From 67feadf1905a13ac0523b08b55bc224c84e5cc90 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sun, 24 Mar 2024 14:29:09 +0100 Subject: [PATCH 058/206] Make assays clickable --- modules/local/report/create/app/templates/styles.css | 4 ++++ modules/local/report/create/app/templates/tf.html | 4 ++-- modules/local/report/create/templates/build.py | 5 ++++- 3 files changed, 10 insertions(+), 3 deletions(-) diff --git a/modules/local/report/create/app/templates/styles.css b/modules/local/report/create/app/templates/styles.css index 745e131..3f7942c 100644 --- a/modules/local/report/create/app/templates/styles.css +++ b/modules/local/report/create/app/templates/styles.css @@ -35,4 +35,8 @@ button { max-width: 100%; display: flex; justify-content: center; +} + +.clickable { + cursor: pointer; } \ No newline at end of file diff --git a/modules/local/report/create/app/templates/tf.html b/modules/local/report/create/app/templates/tf.html index e28cf60..86b5b2f 100644 --- a/modules/local/report/create/app/templates/tf.html +++ b/modules/local/report/create/app/templates/tf.html @@ -10,14 +10,14 @@
{% for assay in assays %} - {{ assay }} + {{ assay }} {% endfor %}
{% for tf, dcgs in ranking.items() %}
-
-{% endblock %} \ No newline at end of file +{% endblock %} + +{% block scripts %} + +{% endblock %} From 89e562dc75943bc08d0ab169911c162ca044f0bc Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sun, 24 Mar 2024 15:17:22 +0100 Subject: [PATCH 060/206] Implement dynamic ranking --- .../report/create/app/templates/styles.css | 4 ++ .../local/report/create/app/templates/tf.html | 58 +++++++++++++++++-- 2 files changed, 57 insertions(+), 5 deletions(-) diff --git a/modules/local/report/create/app/templates/styles.css b/modules/local/report/create/app/templates/styles.css index 3f7942c..9f95721 100644 --- a/modules/local/report/create/app/templates/styles.css +++ b/modules/local/report/create/app/templates/styles.css @@ -39,4 +39,8 @@ button { .clickable { cursor: pointer; +} + +.forbidden { + cursor: not-allowed; } \ No newline at end of file diff --git a/modules/local/report/create/app/templates/tf.html b/modules/local/report/create/app/templates/tf.html index 7b94e2a..9e024c3 100644 --- a/modules/local/report/create/app/templates/tf.html +++ b/modules/local/report/create/app/templates/tf.html @@ -14,13 +14,13 @@ {% endfor %}
{% for tf, dcgs in ranking.items() %} -
+
+
+
+ +

Hello, {{ title }}

+

Congratulations! Your app is running. 🎉

+
+ +
+
+ @for (item of [ + { title: 'Explore the Docs', link: 'https://angular.dev' }, + { title: 'Learn with Tutorials', link: 'https://angular.dev/tutorials' }, + { title: 'CLI Docs', link: 'https://angular.dev/tools/cli' }, + { title: 'Angular Language Service', link: 'https://angular.dev/tools/language-service' }, + { title: 'Angular DevTools', link: 'https://angular.dev/tools/devtools' }, + ]; track item.title) { + + {{ item.title }} + + + + + } +
+ +
+
+