output | ||||
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|
The release notes for each release are provided in the release-notes.md
file that accompanies the data files.
A table with brief descriptions for each data file is provided in the data-files-description.md
file included in the download.
Processed data files are all files derived from samples (e.g., tumors, cell lines) that are processed upstream of this repository and are not the product of any analysis code in the AlexsLemonade/OpenPBTA-analysis
or PediatricOpenTargets/OpenPedCan-analysis
repository.
Somatic calls that are retained if they are supported by at least 2 callers OR marked as HotSpotAllele
because they overlap SNV/INDELs considered as Cancer Hotspots OR are TERT promoter SNVs. Please find additional information here
snv-consensus-plus-hotspots.maf.tsv.gz
Somatic Copy Number Variant (CNV) data are provided in a modified SEG format for each of the applied software packages and denoted with the cnv
prefix.
Somatic copy number data is only generated for whole genome sequencing (WGS) samples.
cnv-cnvkit.seg.gz
is the the CNVkit SEG file. This file contains an additional columncopy.num
to denote copy number of each segment, derived from the CNS file output of the algorithm described here.cnv-controlfreec.tsv.gz
is the ControlFreeC TSV file. It is a merge of*_CNVs
files produced from the algorithm, and columns are described here.
The copy number annotated in the CNVkit SEG file is annotated with respect to ploidy 2, however, the status annotated in the ControlFreeC TSV file is annotated with respect to inferred ploidy from the algorithm, which is recorded in the histologies.tsv
file.
Gene expression estimates from the applied software packages are provided as a feature (e.g., gene or transcript) by sample matrix. Gene expression are available in multiple forms in the following files:
gene-counts-rsem-expected_count.rds
gene-expression-rsem-tpm.rds
See the data description file for more information about the individual gene expression files.
If your analysis requires de-duplicated gene symbols as row names, please use the collapsed matrices provided as part of the data download (see below).
RNA splice events rmats file generated from the established pipeline is provided as:
splice-events-rmats.tsv.gz
The filtered and prioritized fusion and downstream files are a product of the analyses/fusion_filtering
analysis module.
fusion-putative-oncogenic.tsv
contains the filtered and prioritized fusions.
Binary matrices for the presence of tumor-specific fusions across all RNA biospecimens are the product of fusion-summary
.
fusion_summary_embryonal_foi.tsv
contains a binary matrix that denotes the presence or absence of a recurrent embryonal tumor fusions of interest per individual RNA-seq specimen.fusion_summary_ependymoma_foi.tsv
contains a binary matrix that denotes the presence or absence of a recurrent ependymal tumor fusions of interest per individual RNA-seq specimen.fusion_summary_ewings_foi.tsv
contains a binary matrix that denotes the presence or absence of a recurrent Ewing's sarcoma tumor fusions of interest per individual RNA-seq specimen.fusion_summary_lgat_foi.tsv
contains a binary matrix that denotes the presence or absence of a recurrent LGAT tumor fusions of interest per individual RNA-seq specimen.
Structural Variants data produced by the MANTA
package is
provided as:
sv-manta.tsv.gz
Whole cell proteomic and phosphorylation proteomic data from project HOPE
and CPTAC
are provided as:
File name | Data type | Data source | Data description |
---|---|---|---|
cptac-protein-imputed-phospho-expression-log2-ratio.tsv.gz |
Processed data | CPTAC pediatric brain tumor phospho-proteomics expression | Imputed phospho-protein expression, log2 abundance |
cptac-protein-imputed-prot-expression-abundance.tsv.gz |
Processed data | CPTAC pediatric brain tumor protein expression | Imputed whole cell protein expression, total abundance |
cptac-protein-imputed-prot-expression-log2-ratio.tsv.gz |
Processed data | CPTAC pediatric brain tumor protein expression | Imputed whole cell protein expression, log2 abundance |
gbm-protein-imputed-phospho-expression-abundance.tsv.gz |
Processed data | CPTAC adult GBM brain tumor phospho-proteomics expression | Imputed phospho-protein expression, total abundance |
gbm-protein-imputed-prot-expression-abundance.tsv.gz |
Processed data | CPTAC adult GBM brain tumor protein expression | Imputed whole cell expression, total abundance |
hope-protein-imputed-phospho-expression-abundance.tsv.gz |
Processed data | Adult and Young Adolescent (AYA) brain tumor phospho-proteomics expression (Project HOPE) | Imputed phospho-protein expression, total abundance |
hope-protein-imputed-prot-expression-abundance.tsv.gz |
Processed data | Adult and Young Adolescent (AYA) brain tumor protein expression (Project HOPE) | Imputed whole cell protein expression, total abundance |
Harmonized clinical data are released as tab separated values in the following files:
histologies.tsv
histologies-base.tsv
Independent sample list are released as tab separated values in the following files.
wgswxspanel
indicates it includes all experimental strategies for DNA sequencing, rnaseqpanel
indicates it includes all experimental strategies for RNA sequencing.
eachcohort
indicates the selection is cohort-based.
Additionally, .prefer.wxs
(or .prefer.wgs
) indicates WXS (or WGS) samples were preferentially select when both WGS and WXS are available for a particular participant.
independent-specimens.methyl.primary-plus.tsv
independent-specimens.methyl.primary.tsv
independent-specimens.methyl.relapse.tsv
independent-specimens.rnaseq.primary-plus-pre-release.tsv
independent-specimens.rnaseq.primary-pre-release.tsv
independent-specimens.rnaseq.primary.eachcohort.tsv
independent-specimens.rnaseq.primary.tsv
independent-specimens.rnaseq.relapse-pre-release.tsv
independent-specimens.rnaseq.relapse.eachcohort.tsv
independent-specimens.rnaseq.relapse.tsv
independent-specimens.rnaseqpanel.primary-plus.eachcohort.tsv
independent-specimens.rnaseqpanel.primary-plus.pre-release.tsv
independent-specimens.rnaseqpanel.primary-plus.tsv
independent-specimens.rnaseqpanel.primary.eachcohort.tsv
independent-specimens.rnaseqpanel.primary.pre-release.tsv
independent-specimens.rnaseqpanel.primary.tsv
independent-specimens.rnaseqpanel.relapse.eachcohort.tsv
independent-specimens.rnaseqpanel.relapse.pre-release.tsv
independent-specimens.rnaseqpanel.relapse.tsv
independent-specimens.wgs.primary-plus.eachcohort.tsv
independent-specimens.wgs.primary-plus.tsv
independent-specimens.wgs.primary.eachcohort.tsv
independent-specimens.wgs.primary.tsv
independent-specimens.wgs.relapse.eachcohort.tsv
independent-specimens.wgs.relapse.tsv
independent-specimens.wgswxspanel.primary-plus.eachcohort.prefer.wgs.tsv
independent-specimens.wgswxspanel.primary-plus.eachcohort.prefer.wxs.tsv
independent-specimens.wgswxspanel.primary-plus.prefer.wgs.tsv
independent-specimens.wgswxspanel.primary-plus.prefer.wxs.tsv
independent-specimens.wgswxspanel.primary.eachcohort.prefer.wgs.tsv
independent-specimens.wgswxspanel.primary.eachcohort.prefer.wxs.tsv
independent-specimens.wgswxspanel.primary.eachcohort.tsv
independent-specimens.wgswxspanel.primary.prefer.wgs.tsv
independent-specimens.wgswxspanel.primary.prefer.wxs.tsv
independent-specimens.wgswxspanel.primary.tsv
independent-specimens.wgswxspanel.relapse.eachcohort.prefer.wgs.tsv
independent-specimens.wgswxspanel.relapse.eachcohort.prefer.wxs.tsv
independent-specimens.wgswxspanel.relapse.eachcohort.tsv
independent-specimens.wgswxspanel.relapse.prefer.wgs.tsv
independent-specimens.wgswxspanel.relapse.prefer.wxs.tsv
independent-specimens.wgswxspanel.relapse.tsv
Analysis files are created by a script in analyses/*
.
They can be viewed as derivatives of Processed data files.
Collapsed expression matrices are products of the analyses/collapse-rnaseq
analysis module.
In cases where more than one Ensembl gene identifier maps to the same gene symbol, the instance of the gene symbol with the maximum mean FPKM in the RSEM FPKM file is retained to produce the following files:
gene-counts-rsem-expected_count-collapsed.rds
gene-expression-rsem-tpm-collapsed.rds
rna-isoform-expression-rsem-tpm.rds
Additionally, available TCGA and GTEx gene expression files with same format are included:
tcga-gene-counts-rsem-expected_count.rds
tcga-gene-expression-rsem-tpm.rds
gtex_gene-counts-rsem-expected_count-collapsed.rds
gtex_gene-expression-rsem-tpm-collapsed.rds
Copy number consensus calls from the copy number and structural variant callers are a product of the analyses/copy_number_consensus_call
analysis module.
-
cnv-consensus.seg.gz
contains consensus segments and segment means (log R ratios) from two or more callers, as described in the analysis README - contains only WGS samples. -
cnvkit_with_status.tsv
andconsensus_seg_with_status.tsv
contain CNVkit calls for WXS or CNV consensus calls for WGS with gain/loss status, respectively
Focal copy number files map the consensus calls (genomic segments) in WGS samples to genes for downstream analysis and are a product of the analysis/focal-cn-file-preparation
.
Note: these files contain biospecimens and genes with copy number changes.
consensus_seg_annotated_cn_autosomes.tsv.gz
contains focal gene copy number alterations for all autosomes.consensus_seg_annotated_cn_x_and_y.tsv.gz
contains focal gene copy number alterations for the sex chromosomes.
Focal copy number files in WXS samples only uses results from CNVkit and no consensus calling is required. analysis/focal-cn-file-preparation
.
Note: these files contain biospecimens and genes with copy number changes.
cnvkit_annotated_cn_wxs_autosomes.tsv.gz
contains focal gene copy number alterations for all autosomes.cnvkit_annotated_cn_wxs_x_and_y.tsv.gz
contains focal gene copy number alterations for the sex chromosomes.
Additionally, autosomes file and x_and_y file for either WGS or WXS to generate the two combined files as followed:
consensus_wgs_plus_cnvkit_wxs_plus_freec_tumor_only_autosomes.tsv.gz
consensus_wgs_plus_cnvkit_wxs_plus_freec_tumor_only_x_and_y.tsv.gz
And these two files are further merged to generate:
consensus_wgs_plus_cnvkit_wxs_plus_freec_tumor_only.tsv.gz