diff --git a/.github/linters/.markdown-lint.yml b/.github/linters/.markdown-lint.yml new file mode 100644 index 0000000..8edc9e5 --- /dev/null +++ b/.github/linters/.markdown-lint.yml @@ -0,0 +1,37 @@ +--- +########################### +########################### +## Markdown Linter rules ## +########################### +########################### + +# Linter rules doc: +# - https://github.com/DavidAnson/markdownlint +# +# Note: +# To comment out a single error: +# +# any violations you want +# +# + +############### +# Rules by id # +############### +MD004: false # Unordered list style +MD007: + indent: 2 # Unordered list indentation +MD013: false # Line length +MD026: + punctuation: ".,;:!。，；:" # List of not allowed +MD029: false # Ordered list item prefix +MD033: false # Allow inline HTML +MD036: false # Emphasis used instead of a heading +MD024: + allow_different_nesting: true # heading duplication is allowed for + # non-sibling headings + +################# +# Rules by tags # +################# +blank_lines: false # Error on blank lines diff --git a/.github/workflows/linter.yml b/.github/workflows/linter.yml index 4827b60..a5fa9ce 100644 --- a/.github/workflows/linter.yml +++ b/.github/workflows/linter.yml @@ -15,7 +15,7 @@ jobs: with: fetch-depth: 0 - name: Lint Code Base - uses: github/super-linter@v4.6.2 + uses: github/super-linter@v4.7.1 env: VALIDATE_ALL_CODEBASE: false DEFAULT_BRANCH: main @@ -35,5 +35,5 @@ jobs: - name: Lint - run: lintr::lint_dir(linters = lintr::with_defaults(object_name_linter = NULL, assignment_linter = NULL, line_length_linter = NULL, spaces_left_parentheses_linter = NULL, commented_code_linter = NULL, object_length_linter = NULL, cyclocomp_linter = lintr::cyclocomp_linter(complexity_limit = 25L))) + run: lintr::lint_dir(linters = lintr::with_defaults(object_name_linter = NULL, assignment_linter = NULL, line_length_linter = NULL, spaces_left_parentheses_linter = NULL, commented_code_linter = NULL, object_length_linter = NULL, cyclocomp_linter = lintr::cyclocomp_linter(complexity_limit = 35L))) shell: Rscript {0} diff --git a/OpenPedCan-analysis b/OpenPedCan-analysis index 61e2315..96132ae 160000 --- a/OpenPedCan-analysis +++ b/OpenPedCan-analysis @@ -1 +1 @@ -Subproject commit 61e23154a34e1d8b3fc1c50a67dd8f79c2067776 +Subproject commit 96132ae1e7485d9ab129380898fac5e255ccb36f diff --git a/README.md b/README.md index fe77645..4229c61 100644 --- a/README.md +++ b/README.md @@ -1,42 +1,49 @@ -# OpenPedCan-api +# OpenPedCan-api [![GitHub Super-Linter](https://github.com/PediatricOpenTargets/OpenPedCan-api/workflows/Lint%20Code%20Base/badge.svg)](https://github.com/marketplace/actions/super-linter) -`OpenPedCan-api` implements OpenPedCan (Open Pediatric Cancers) project public API (application programming interface) to transfer [OpenPedCan-analysis](https://github.com/PediatricOpenTargets/OpenPedCan-analysis) results and plots via HTTP, which is publicly available at . - -- [OpenPedCan-api](#openpedcan-api) - - [API endpoint specifications](#api-endpoint-specifications) - - [Deploy `OpenPedCan-api`](#deploy-openpedcan-api) - - [Test run `OpenPedCan-api` server locally](#test-run-openpedcan-api-server-locally) - - [`git clone` `OpenPedCan-api` repository](#git-clone-openpedcan-api-repository) - - [Run static R code analysis using R package `lintr`](#run-static-r-code-analysis-using-r-package-lintr) - - [(Optional) Build data model files](#optional-build-data-model-files) - - [Build `OpenPedCan-api` docker image](#build-openpedcan-api-docker-image) - - [Run `OpenPedCan-api` docker image](#run-openpedcan-api-docker-image) - - [Test `OpenPedCan-api` server using `curl`](#test-openpedcan-api-server-using-curl) - - [API system design](#api-system-design) - - [Data model layer](#data-model-layer) - - [Analysis logic layer](#analysis-logic-layer) - - [API layer](#api-layer) - - [HTTP server layer](#http-server-layer) - - [Testing layer](#testing-layer) - - [Deployment layer](#deployment-layer) - - [API Development road map](#api-development-road-map) - -## API endpoint specifications - - specifies the following API endpoint attributes. +`OpenPedCan-api` implements OpenPedCan (Open Pediatric Cancers) project public API (application programming interface) to transfer [OpenPedCan-analysis](https://github.com/PediatricOpenTargets/OpenPedCan-analysis) results and plots via HTTP, which is publicly available at . + +- [1. API endpoint specifications](#1-api-endpoint-specifications) +- [2. Deploy `OpenPedCan-api`](#2-deploy-openpedcan-api) +- [3. Test run `OpenPedCan-api` server locally](#3-test-run-openpedcan-api-server-locally) + - [3.1. `git clone` `OpenPedCan-api` repository](#31-git-clone-openpedcan-api-repository) + - [3.2. Run static R code analysis using R package `lintr`](#32-run-static-r-code-analysis-using-r-package-lintr) + - [3.3. (Optional) Build data model files](#33-optional-build-data-model-files) + - [3.4. Build `OpenPedCan-api` docker image](#34-build-openpedcan-api-docker-image) + - [3.5. Run `OpenPedCan-api` docker image](#35-run-openpedcan-api-docker-image) + - [3.6. Test `OpenPedCan-api` server using `curl`](#36-test-openpedcan-api-server-using-curl) +- [4. API system design](#4-api-system-design) + - [4.1. Data model layer](#41-data-model-layer) + - [4.2. Analysis logic layer](#42-analysis-logic-layer) + - [4.3. API layer](#43-api-layer) + - [4.4. HTTP server layer](#44-http-server-layer) + - [4.5. Testing layer](#45-testing-layer) + - [4.6. Deployment layer](#46-deployment-layer) +- [5. API Development roadmap](#5-api-development-roadmap) + +## 1. API endpoint specifications + + specifies the following API endpoint attributes. - HTTP request method - Path - Parameters - Response media type -## Deploy `OpenPedCan-api` +## 2. Deploy `OpenPedCan-api` -Following is a comment by @blackdenc at . +According to comments and messages by @blackdenc : -> As far as building in Jenkins, we build the container and tag it, then push it to ECR and give that tag to the ECS task definition at runtime. +`OpenPedCan-api` is deployed with the following steps: + +- Build and tag `OpenPedCan-api` docker image using `Dockerfile`. +- Push the built image to Amazon Elastic Container Registry (ECR). +- Pass the ECR docker image tag to Amazon Elastic Container Service (ECS) Fargate (?) task definition at runtime. + + is the QA server that will only deploy the `main` branch of the repository. + + is the DEV server that will deploy any new branch of the repository, and the QA environment will remain un-changed until a new commit is merged to main. `Dockerfile` builds the `OpenPedCan-api` docker image to be run on Amazon ECS. @@ -45,7 +52,7 @@ To deploy without using docker: - `Rscript --vanilla main.R` needs to be run with the same working directory as the last `WORKDIR` path in `Dockerfile` prior to the docker instruction `ENTRYPOINT ["Rscript", "--vanilla", "main.R"]`. - Build or download `db` files according to the commands in `Dockerfile`. -## Test run `OpenPedCan-api` server locally +## 3. Test run `OpenPedCan-api` server locally Test run `OpenPedCan-api` server with the following steps: @@ -72,7 +79,7 @@ R package jsonlite 1.7.2 R package lintr 2.0.1 ``` -### `git clone` `OpenPedCan-api` repository +### 3.1. `git clone` `OpenPedCan-api` repository ```bash # Change URL if a fork repo needs to be used @@ -86,7 +93,7 @@ git checkout -t origin/the-branch-that-needs-to-be-tested # git checkout COMMIT_HASH_ID ``` -### Run static R code analysis using R package `lintr` +### 3.2. Run static R code analysis using R package `lintr` ```bash ./tests/run_r_lintr.sh @@ -94,7 +101,7 @@ git checkout -t origin/the-branch-that-needs-to-be-tested If there is any syntax error, comment in the GitHub pull request with the full error messages. -### (Optional) Build data model files +### 3.3. (Optional) Build data model files Use the following bash command to build data model files locally to the `db` directory. This step takes > 25GB memory. @@ -108,7 +115,7 @@ Use the following bash command to build data model files locally to the `db` dir - Copy data model files from `open-ped-can-api-build-db` docker image to host `db` directory. - Check `sha256sum` for data model files. -### Build `OpenPedCan-api` docker image +### 3.4. Build `OpenPedCan-api` docker image Use the following bash commands to Build `OpenPedCan-api` docker image. @@ -126,7 +133,7 @@ Use the following bash commands to Build `OpenPedCan-api` docker image. Note for developers: For `docker build` with docker cache and remote pre-built data model files, pass `--build-arg CACHE_DATE=$(date +%s)` to the `docker build` command to use the latest remote data model files on each build. -### Run `OpenPedCan-api` docker image +### 3.5. Run `OpenPedCan-api` docker image ```bash docker run --rm -p 8082:80 open-ped-can-api @@ -134,7 +141,7 @@ docker run --rm -p 8082:80 open-ped-can-api Note for developers: To run extra R `stopifnot(...)` assertions, pass `-e DEBUG=1` to `docker run` command. -### Test `OpenPedCan-api` server using `curl` +### 3.6. Test `OpenPedCan-api` server using `curl` Test the running server with the following command. @@ -142,14 +149,14 @@ Test the running server with the following command. ./tests/curl_test_endpoints.sh ``` -`tests/curl_test_endpoints.sh` sends multiple HTTP requests to `localhost:8082` by default, with the following steps. The port number of `localhost` can be changed by passing the `bash` environment variable `API_PORT` with a different value, but there has to be a `OpenPedCan-api` server listening on the port. +`tests/curl_test_endpoints.sh` sends multiple HTTP requests to `localhost:8082` by default, with the following steps. The port number of `localhost` can be changed by passing the `bash` environment variable `LOCAL_API_HOST_PORT` with a different value, but there has to be a `OpenPedCan-api` server listening on the port. The API HTTP server host can be changed to or , by passing environment variable `API_HOST=qa` or `API_HOST=dev` respectively. - Send an HTTP request using `curl`. - Output the HTTP response body to `tests/http_response_output_files/png` or `tests/http_response_output_files/json`. - Print HTTP response status code, content type, and run time. - If response body content type is JSON, convert the JSON file to TSV file in `tests/results`. -## API system design +## 4. API system design The `OpenPedCan-api` server system has the following layers: @@ -164,7 +171,7 @@ For more details about implementations, see [Test run `OpenPedCan-api` server lo The root directory of this repository should only contain starting points of different layer and configuration files. -### Data model layer +### 4.1. Data model layer `db` directory contains files that implement the data model layer. @@ -172,15 +179,15 @@ The root directory of this repository should only contain starting points of dif `db/load_db.sh` loads local or remote pre-built data model files to the HTTP server layer. -### Analysis logic layer +### 4.2. Analysis logic layer `src` directory contains files that implement the analysis logic layer. -### API layer +### 4.3. API layer Discussions in PedOT meetings, Slack work space, GitHub issues, etc specify the API layer. -### HTTP server layer +### 4.4. HTTP server layer `main.R` runs the `OpenPedCan-api` HTTP server. The HTTP server is implemented using [libuv](http://docs.libuv.org/en/stable/design.html) and [http-parser](https://github.com/nodejs/http-parser) and called by [R package plumber](https://github.com/rstudio/plumber). @@ -192,22 +199,18 @@ The API HTTP server handles every HTTP request [sequentially](https://www.rplumb - Convert the return value of the endpoint R function to defined response content type, e.g. JSON and PNG. - Send HTTP response to the request address. -### Testing layer +### 4.5. Testing layer The `tests` directory contain all tools and code for testing the API server. `tests/http_response_output_files` contains the API server response plots and tables. `tests/results` contains results generated during test run. -### Deployment layer +### 4.6. Deployment layer Jenkinsfile and Dockerfile specify the procedures to deploy the `OpenPedCan-api` server. -## API Development road map +## 5. API Development roadmap Implementation action items: -- Implement endpoint `GET /tpm/gene-all-cancer/json`. -- Implement endpoint `GET /tpm/gene-all-cancer/plot`. -- Remove gene down-sampling procedure in `db/tpm_data_lists.R`, in order to include all genes. -- Build data model in another R process. Load the data model in the API server R process. This may reduce RAM usage. - Build data model into a Postgres database. Implement/refactor R functions to interact with the Postgres database. This will reduce RAM usage. This may reduce run time. - Add unit tests to R functions. - Send more informative response HTTP status code. Currently, all failures use status code 500. diff --git a/changelog.md b/changelog.md new file mode 100644 index 0000000..e5ec9f0 --- /dev/null +++ b/changelog.md @@ -0,0 +1,35 @@ +# OpenPedCan-api + +## v0.2.0-alpha + +### Changed + +- Updated data model using [`OpenPedCan-analysis` v9 release data](https://github.com/PediatricOpenTargets/OpenPedCan-analysis/pull/103). +- Enabled endpoint Cross-Origin Resource Sharing (CORS) by default. +- Changed `/tpm/gene-disease-gtex` boxplot title from "Disease vs. GTEx tissue bulk gene expression" to "Primary tumor vs GTEx tissue bulk gene expression". +- Changed "cohort =" to "Dataset =" in boxplot and summary table x-axis labels. +- Changed "cohort" to "Dataset" in boxplot summary table columns. +- Increased minimum number of samples required per `Disease` or `GTEx_tissue_subgroup` from 1 to 3. +- Rotated boxplot x-axis labels by 45 degrees. +- Changed `tests/curl_test_endpoints.sh` variable `API_PORT` to `LOCAL_API_HOST_PORT`. +- Updated `README.md`. + +### Added + +- Implemented HTTP GET method for `/tpm/gene-all-cancer/json` API endpoint. +- Implemented HTTP GET method for `/tpm/gene-all-cancer/plot` API endpoint. +- Added `cors` filter to enable endpoint CORS by default. +- Added `API_HOST` variable in `tests/curl_test_endpoints.sh`, in order to test DEV and QA hosts. +- Added this `changelog.md`. + +## v0.1.0-alpha + +### Added + +- HTTP GET method for `/tpm/gene-disease-gtex/json` API endpoint. +- HTTP GET method for `/tpm/gene-disease-gtex/plot` API endpoint. +- Tools for building API data model in `db` directory. +- Tools for testing local API HTTP server, in `tests` directory. +- `Dockerfile` for running API HTTP server. +- This `README.md` that specifies development procedure, system design, and development roadmap. +- Git submodule [`OpenPedCan-analysis`](https://github.com/PediatricOpenTargets/OpenPedCan-analysis). diff --git a/db/build_db.sh b/db/build_db.sh index 0f75af2..fccf1be 100755 --- a/db/build_db.sh +++ b/db/build_db.sh @@ -14,9 +14,9 @@ cd .. echo "Download OpenPedCan-analysis data release..." # The commit ID to checkout to build data model. # -# 61e23154a34e1d8b3fc1c50a67dd8f79c2067776 points to v8 release with updated +# 96132ae1e7485d9ab129380898fac5e255ccb36f points to v9 release with updated # OpenPedCan-analysis/analyses/long-format-table-utils/annotator. -OPEN_PED_CAN_ANALYSIS_COMMIT="61e23154a34e1d8b3fc1c50a67dd8f79c2067776" +OPEN_PED_CAN_ANALYSIS_COMMIT="96132ae1e7485d9ab129380898fac5e255ccb36f" # If submodule repo url changes, e.g. rename, this will update the URL according # to the one in .gitmodules. diff --git a/db/sha256sum.txt b/db/sha256sum.txt index e0a1104..ad58e1f 100644 --- a/db/sha256sum.txt +++ b/db/sha256sum.txt @@ -1 +1 @@ -173554ee34308ccd63bd4ce2d408a87d24b7dc925b539f172f150dce001700d5 tpm_data_lists.rds +f381ed881caec94a0b9a4be8fdb800fa69c3b9d2f3b4e44766ebe42117e2ba5b tpm_data_lists.rds diff --git a/src/get_gene_tpm_boxplot.R b/src/get_gene_tpm_boxplot.R index fbe6d31..f827009 100644 --- a/src/get_gene_tpm_boxplot.R +++ b/src/get_gene_tpm_boxplot.R @@ -36,9 +36,9 @@ get_gene_tpm_boxplot <- function(gene_tpm_boxplot_tbl) { stopifnot(is.factor(uniq_x_label_vec)) stopifnot(all(!is.na(uniq_x_label_vec))) - sample_type_vec <- unique(gene_tpm_boxplot_tbl$sample_type) - stopifnot(is.character(sample_type_vec)) - stopifnot(all(sample_type_vec %in% c("disease", "normal"))) + uniq_sample_type_vec <- unique(gene_tpm_boxplot_tbl$sample_type) + stopifnot(is.character(uniq_sample_type_vec)) + stopifnot(all(uniq_sample_type_vec %in% c("disease", "normal"))) efo_id_vec <- purrr::discard(unique(gene_tpm_boxplot_tbl$EFO), is.na) stopifnot(is.character(efo_id_vec)) @@ -51,15 +51,41 @@ get_gene_tpm_boxplot <- function(gene_tpm_boxplot_tbl) { if (length(gtex_subgroup_vec) > 0) { title <- paste( paste0(gene_symbol, " (", ensg_id, ")"), - "Disease vs. GTEx tissue bulk gene expression", + "Primary tumor vs GTEx tissue bulk gene expression", sep = "\n") } else { title <- paste( paste0(gene_symbol, " (", ensg_id, ")"), - "Disease tissue bulk gene expression", + "Primary tumor tissue bulk gene expression", sep = "\n") } + if (identical(length(uniq_sample_type_vec), 1L)) { + # Only one sample type. + # + # Use grey for either one. + box_fill_colors = c("disease" = "grey80", "normal" = "grey80") + } else { + # More than one saple types. + # + # Use red for diease and grey for normal. + box_fill_colors = c("disease" = "red3", "normal" = "grey80") + } + + # The x-axis labels are long and rotated 45 degrees, so they are out of the + # plot in the default margin. Increase right margin to fit all text. + plot_margin <- ggplot2::theme_get()$plot.margin + + if (!identical(length(plot_margin), 4L)) { + plot_margin <- rep(grid::unit(x = 5.5, units = "points"), 4) + } + + rightmost_x_label <- dplyr::last( + levels(gene_tpm_boxplot_tbl$x_labels), default = "") + # increase right margin by the width of the last x label * 0.71 + plot_margin[2] <- grid::unit( + x = 0.8, units = "strwidth", data = rightmost_x_label) + gene_tpm_boxplot <- ggplot2::ggplot(gene_tpm_boxplot_tbl, ggplot2::aes(x = x_labels, y = TPM, fill = sample_type)) + @@ -69,12 +95,11 @@ get_gene_tpm_boxplot <- function(gene_tpm_boxplot_tbl) { ggplot2::ylab("TPM") + ggplot2::xlab("") + ggplot2_publication_theme(base_size = 12) + - ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90, - vjust = 0.5, - hjust = 1)) + + ggplot2::theme( + axis.text.x = ggplot2::element_text(angle = -45, vjust = 1, hjust = 0), + plot.margin = plot_margin) + ggplot2::ggtitle(title) + - ggplot2::scale_fill_manual(values = c("disease" = "red3", - "normal" = "grey80")) + + ggplot2::scale_fill_manual(values = box_fill_colors) + ggplot2::guides(fill = "none") return(gene_tpm_boxplot) diff --git a/src/get_gene_tpm_boxplot_summary_tbl.R b/src/get_gene_tpm_boxplot_summary_tbl.R index 1a713e6..d23f57d 100644 --- a/src/get_gene_tpm_boxplot_summary_tbl.R +++ b/src/get_gene_tpm_boxplot_summary_tbl.R @@ -30,7 +30,7 @@ get_gene_tpm_boxplot_summary_tbl <- function(gene_tpm_boxplot_tbl) { Gene_Ensembl_ID = unique(Gene_Ensembl_ID), Gene_symbol = unique(Gene_symbol), PMTL = unique(RMTL), - cohort = unique(cohort), + Dataset = unique(cohort), Disease = unique(Disease), GTEx_tissue_subgroup = unique(GTEx_tissue_subgroup), EFO = unique(EFO), diff --git a/src/get_gene_tpm_boxplot_tbl.R b/src/get_gene_tpm_boxplot_tbl.R index d48567a..0821403 100644 --- a/src/get_gene_tpm_boxplot_tbl.R +++ b/src/get_gene_tpm_boxplot_tbl.R @@ -39,7 +39,7 @@ get_gene_tpm_boxplot_tbl <- function(gene_tpm_tbl) { gene_tpm_boxplot_tbl <- dplyr::mutate( gene_tpm_boxplot_tbl, x_labels = paste0( - box_group, " (cohort = ", cohort, ", N = ", cohort_box_group_n, ")")) + box_group, " (Dataset = ", cohort, ", N = ", cohort_box_group_n, ")")) # If is.na(EFO), sample_type is normal. If !is.na(EFO), sample_type is # disease. diff --git a/src/get_gene_tpm_tbl.R b/src/get_gene_tpm_tbl.R index 4997625..58c46bc 100644 --- a/src/get_gene_tpm_tbl.R +++ b/src/get_gene_tpm_tbl.R @@ -12,15 +12,24 @@ # - get_gene_tpm_tbl -# Get a TPM tibble of a single-gene, one or more diseasees, and zero or more -# GTEx tissue(s). +# Get a TPM tibble of a single-gene, one or more disease group(s), and zero or +# more GTEx tissue subgroup(s). # # Args: # - tpm_data_lists: tpm_data_lists loaded from the tpm_data_lists.rds output of -# db/tpm_data_lists.R. -# - ensg_id: a single character value of gene ENSG ID. -# - efo_id: a single character value of EFO ID. -# - gene_symbol: an optional single character value of gene symbol. +# db/tpm_data_lists.R. Required. +# - ensg_id: a single character value of gene ENSG ID. Required. +# - efo_id: NULL or a single character value of EFO ID. Default is NULL, which +# is to include all diseases and zero GTEx tissue, aka gene-all-cancer. If +# efo_id is not NULL, include all samples that have the EFO ID and all GTEx +# tissues, aka gene-disease-gtex. +# - gene_symbol: NULL or a single character value of gene symbol. Default is +# NULL, which is to select the first sorted gene symbol when one ENSG ID maps +# to multiple gene symbols. If gene_symbol is not NULL, the (efo_id, +# gene_symbol) tuple is selected when one ENSG ID maps to multiple gene +# symbols. +# - min_n_per_sample_group: a single numeric value of the minimum number of +# samples per Disease or GTEx_tissue_subgroup. Default is 1. # # Returns a tibble with the following columns: # - Kids_First_Biospecimen_ID: a single Kids_First_Biospecimen_ID @@ -50,14 +59,30 @@ # may not match PedOT. # - Identify the gene symbol that match PedOT. # - Completely drop gene_symbol, as it is also shown on PedOT. -get_gene_tpm_tbl <- function(tpm_data_lists, ensg_id, efo_id, - gene_symbol = NULL) { +get_gene_tpm_tbl <- function(tpm_data_lists, ensg_id, efo_id = NULL, + gene_symbol = NULL, min_n_per_sample_group = 1L) { + # Adapted from https://stackoverflow.com/a/38539734/4638182 + stopifnot(inherits(tpm_data_lists, "list")) + stopifnot(is.character(ensg_id)) - stopifnot(is.character(efo_id)) stopifnot(identical(length(ensg_id), 1L)) - stopifnot(identical(length(efo_id), 1L)) stopifnot(!is.na(ensg_id)) - stopifnot(!is.na(efo_id)) + + if (!is.null(efo_id)) { + stopifnot(is.character(efo_id)) + stopifnot(identical(length(efo_id), 1L)) + stopifnot(!is.na(efo_id)) + } + + if (!is.null(gene_symbol)) { + stopifnot(is.character(gene_symbol)) + stopifnot(identical(length(gene_symbol), 1L)) + stopifnot(!is.na(gene_symbol)) + } + + stopifnot(is.numeric(min_n_per_sample_group)) + stopifnot(identical(length(min_n_per_sample_group), 1L)) + stopifnot(!is.na(min_n_per_sample_group)) all_cohorts_str_id <- "all_cohorts" @@ -111,33 +136,118 @@ get_gene_tpm_tbl <- function(tpm_data_lists, ensg_id, efo_id, stopifnot(identical(nrow(ensg_tpm_df), 1L)) } - if (!identical(xname, "gtex")) { - efo_selected_sids <- dplyr::filter( - xl$histology_df, EFO == efo_id)$Kids_First_Biospecimen_ID - - min_n_samples <- 1 - if (length(efo_selected_sids) < min_n_samples) { - stop(paste( - efo_id, "has", length(efo_selected_sids), "samples, which", - "is less than the minimum", min_n_samples, "requirements.")) + # The annotation columns of ensg_tpm_df, all other columns must be samples + # TPM values. + ensg_tpm_df_ann_cols <- c("Gene_symbol", "RMTL", "Gene_Ensembl_ID") + + # Subset samples + if (identical(xname, "gtex")) { + if (is.null(efo_id)) { + # all-diseases table and plot + # + # - keep zero gtex subgroups + selected_sids <- character() + } else { + # disease vs gtex table and plot + # + # - keep all gtex subgroups that have >= min_n_per_sample_group samples + selected_sids <- dplyr::filter( + dplyr::add_count( + xl$histology_df, GTEx_tissue_subgroup, + name = "gtex_subgroup_n"), + gtex_subgroup_n >= min_n_per_sample_group)$Kids_First_Biospecimen_ID } + } else { + disease_n_histology_df <- dplyr::filter( + dplyr::add_count(xl$histology_df, Disease, name = "disease_n"), + disease_n >= min_n_per_sample_group) + + if (is.null(efo_id)) { + # all-diseases table and plot + # + # - keep all cancer groups that have >= min_n_per_sample_group samples + selected_sids <- disease_n_histology_df$Kids_First_Biospecimen_ID + } else { + # disease vs gtex table and plot + # + # - keep all cancer groups that are mapped to input efo_id and have >= + # min_n_per_sample_group samples + selected_sids <- dplyr::filter( + disease_n_histology_df, EFO == efo_id)$Kids_First_Biospecimen_ID + } + } + + ensg_tpm_df <- ensg_tpm_df[, c(ensg_tpm_df_ann_cols, selected_sids)] + + if (DEBUG) { + # Assert all sample columns are numeric. + purrr::walk( + dplyr::select(ensg_tpm_df, !dplyr::all_of(ensg_tpm_df_ann_cols)), + function(xcol) { + stopifnot(is.numeric(xcol)) + } + ) + } + + # initial ensg_long_tpm_tbl column names + init_ensg_long_tpm_tbl_cols <- c(ensg_tpm_df_ann_cols, + "Kids_First_Biospecimen_ID", "TPM") - efo_selected_columns <- c("Gene_Ensembl_ID", "Gene_symbol", "RMTL", - efo_selected_sids) - ensg_tpm_df <- ensg_tpm_df[, efo_selected_columns] + if (identical(sort(colnames(ensg_tpm_df)), sort(ensg_tpm_df_ann_cols))) { + # no sample selected + # + # For gtex, use empty tibble. + # + # For disease, raise error. + if (identical(xname, "gtex")) { + # Create empty tibble. + ensg_long_tpm_tbl <- purrr::map_dfc( + init_ensg_long_tpm_tbl_cols, + function(xcol) { + empty_tbl <- tibble::tibble() + if (identical(xcol, "TPM")) { + empty_tbl[, xcol] <- numeric() + } else { + empty_tbl[, xcol] <- character() + } + return(empty_tbl) + } + ) + } else { + if (is.null(efo_id)) { + stop(paste("No Disease has >=", min_n_per_sample_group, "samples.")) + } else { + stop(paste( + efo_id, "has no Disease with >=", min_n_per_sample_group, + "samples.")) + } + } + } else { + # >= 1 sample selected + + # Each row of ensg_long_tpm_tbl is Gene_Ensembl_ID, Gene_symbol, + # Kids_First_Biospecimen_ID (prev colname), TPM. + ensg_long_tpm_tbl <- tidyr::pivot_longer( + ensg_tpm_df, !dplyr::all_of(ensg_tpm_df_ann_cols), + names_to = "Kids_First_Biospecimen_ID", values_to = "TPM") } - # Each row is Gene_symbol, Kids_First_Biospecimen_ID (prev colname), tpm - ensg_long_tpm_tbl <- tidyr::pivot_longer( - ensg_tpm_df, !dplyr::all_of(c("Gene_Ensembl_ID", "Gene_symbol", "RMTL")), - names_to = "Kids_First_Biospecimen_ID", values_to = "TPM") + # Ensure constent column names of ensg_long_tpm_tbl. + ensg_long_tpm_tbl <- dplyr::select( + ensg_long_tpm_tbl, dplyr::all_of(init_ensg_long_tpm_tbl_cols)) if (DEBUG) { stopifnot(identical( - sum(is.na(dplyr::select(ensg_long_tpm_tbl, -RMTL))), 0L)) + colnames(ensg_long_tpm_tbl), init_ensg_long_tpm_tbl_cols)) stopifnot(identical( - sort(unique(ensg_long_tpm_tbl$Gene_symbol)), - sort(unique(ensg_tpm_df$Gene_symbol)))) + sum(is.na(dplyr::select(ensg_long_tpm_tbl, -RMTL))), 0L)) + + if (nrow(ensg_long_tpm_tbl) > 0) { + stopifnot(identical( + sort(unique(ensg_long_tpm_tbl$Gene_symbol)), + sort(unique(ensg_tpm_df$Gene_symbol)))) + } + stopifnot(identical( sort(unique( c("Gene_Ensembl_ID", "Gene_symbol", "RMTL", @@ -161,6 +271,11 @@ get_gene_tpm_tbl <- function(tpm_data_lists, ensg_id, efo_id, stopifnot(identical(sum(is.na(ensg_long_tpm_tbl$cohort)), 0L)) stopifnot(!all_cohorts_str_id %in% ensg_long_tpm_tbl$cohort) if (identical(xname, "gtex")) { + if (is.null(efo_id)) { + # gene-all-cancer + stopifnot(identical(nrow(ensg_long_tpm_tbl), 0L)) + } + stopifnot(identical( sum(is.na(ensg_long_tpm_tbl$GTEx_tissue_subgroup)), 0L)) @@ -168,7 +283,11 @@ get_gene_tpm_tbl <- function(tpm_data_lists, ensg_id, efo_id, stopifnot(identical(sum(!is.na(ensg_long_tpm_tbl$Disease)), 0L)) } else { - stopifnot(identical(unique(ensg_long_tpm_tbl$EFO), efo_id)) + if (!is.null(efo_id)) { + # gene-disease-gtex + stopifnot(identical(unique(ensg_long_tpm_tbl$EFO), efo_id)) + } + stopifnot(identical(sum(is.na(ensg_long_tpm_tbl$EFO)), 0L)) stopifnot(identical( diff --git a/src/plumber.R b/src/plumber.R index a70a0bc..b4f115a 100644 --- a/src/plumber.R +++ b/src/plumber.R @@ -23,7 +23,7 @@ #* Pediatric Open Targets project. -#* @apiVersion 0.1 +#* @apiVersion v0.2.0-alpha #* @apiContact list(name = "API Support", url = #* "https://github.com/PediatricOpenTargets/OpenPedCan-api/issues") @@ -32,7 +32,8 @@ # Plumber API definitions ------------------------------------------------------ -#* Logger adapted from https://www.rplumber.io/articles/routing-and-input.html#forward-to-another-handler +#* Logger adapted from +#* https://www.rplumber.io/articles/routing-and-input.html#forward-to-another-handler #* #* Log some information about the incoming request #* @filter logger @@ -50,16 +51,31 @@ function(req, res) { plumber::forward() } +#* Cross-Origin Resource Sharing (CORS) workaround. +#* +#* Copied from +#* https://www.rplumber.io/articles/security.html#cross-origin-resource-sharing-cors +#* +#* Enable Cross-Origin Resource Sharing (CORS) by default for all endpoints. To +#* disable for certain endpoints, add preempt annotation to exclude this filter. +#* +#* @filter cors +cors <- function(res) { + res$setHeader("Access-Control-Allow-Origin", "*") + plumber::forward() +} + #* Get a single-gene single-disease all-GTEx-tissue-subgroups TPM summary table #* #* @tag "Bulk tissue gene expression" -#* @param ensemblId:str a single character value of gene ENSG ID. -#* @param efoId:str a single character value of EFO ID. +#* @param ensemblId:str one gene ENSG ID. +#* @param efoId:str one EFO ID. #* @serializer json #* @get /tpm/gene-disease-gtex/json function(ensemblId, efoId) { gene_tpm_tbl <- get_gene_tpm_tbl( - tpm_data_lists = tpm_data_lists, ensg_id = ensemblId, efo_id = efoId) + tpm_data_lists = tpm_data_lists, ensg_id = ensemblId, efo_id = efoId, + min_n_per_sample_group = 3) gene_tpm_tbl <- add_gene_tpm_box_group(gene_tpm_tbl) @@ -74,13 +90,14 @@ function(ensemblId, efoId) { #* Get a single-gene single-disease all-GTEx-tissue-subgroups TPM boxplot #* #* @tag "Bulk tissue gene expression" -#* @param ensemblId:str a single character value of gene ENSG ID. -#* @param efoId:str a single character value of EFO ID. +#* @param ensemblId:str one gene ENSG ID. +#* @param efoId:str one EFO ID. #* @serializer png list(res = 300, width = 3900, height = 2700) #* @get /tpm/gene-disease-gtex/plot function(ensemblId, efoId) { gene_tpm_tbl <- get_gene_tpm_tbl( - tpm_data_lists = tpm_data_lists, ensg_id = ensemblId, efo_id = efoId) + tpm_data_lists = tpm_data_lists, ensg_id = ensemblId, efo_id = efoId, + min_n_per_sample_group = 3) gene_tpm_tbl <- add_gene_tpm_box_group(gene_tpm_tbl) @@ -91,27 +108,43 @@ function(ensemblId, efoId) { print(res_plot) } -#* [Not implemented] Get a single-gene all-diseases TPM summary table +#* Get a single-gene all-diseases TPM summary table #* #* @tag "Bulk tissue gene expression" -#* @param ensemblId:str a single character value of gene ENSG ID. +#* @param ensemblId:str one gene ENSG ID. #* @serializer json #* @get /tpm/gene-all-cancer/json function(ensemblId) { - res_tbl <- tibble::tibble(ensemblId = ensemblId) - return(res_tbl) + gene_tpm_tbl <- get_gene_tpm_tbl( + tpm_data_lists = tpm_data_lists, ensg_id = ensemblId, + min_n_per_sample_group = 3) + + gene_tpm_tbl <- add_gene_tpm_box_group(gene_tpm_tbl) + + gene_tpm_boxplot_tbl <- get_gene_tpm_boxplot_tbl(gene_tpm_tbl) + + gene_tpm_boxplot_summary_tbl <- get_gene_tpm_boxplot_summary_tbl( + gene_tpm_boxplot_tbl) + + return(gene_tpm_boxplot_summary_tbl) } -#* [Not implemented] Get a single-gene all-diseases TPM boxplot +#* Get a single-gene all-diseases TPM boxplot #* #* @tag "Bulk tissue gene expression" -#* @param ensemblId:str a single character value of gene ENSG ID. +#* @param ensemblId:str one gene ENSG ID. #* @serializer png list(res = 300, width = 3900, height = 2700) #* @get /tpm/gene-all-cancer/plot function(ensemblId) { - res_plot <- ggplot2::ggplot(mtcars, ggplot2::aes(mpg, wt)) + - ggplot2::geom_point() + - ggplot2::ggtitle(ensemblId) + gene_tpm_tbl <- get_gene_tpm_tbl( + tpm_data_lists = tpm_data_lists, ensg_id = ensemblId, + min_n_per_sample_group = 3) + + gene_tpm_tbl <- add_gene_tpm_box_group(gene_tpm_tbl) + + gene_tpm_boxplot_tbl <- get_gene_tpm_boxplot_tbl(gene_tpm_tbl) + + res_plot <- get_gene_tpm_boxplot(gene_tpm_boxplot_tbl) print(res_plot) } @@ -119,7 +152,7 @@ function(ensemblId) { # Testing endpoints ------------------------------------------------------------ -# Placeholder until the actual code is written. +# Placeholder for simple testing # Source https://github.com/rstudio/plumber/ @@ -131,25 +164,3 @@ function(ensemblId) { function(msg="") { list(msg = paste0("The message is: '", msg, "'")) } - - -#* Plot a histogram -#* -#* @tag "API testing" -#* @serializer png -#* @get /plot -function() { - rand <- rnorm(100) - hist(rand) -} - - -#* Return the sum of two numbers -#* -#* @tag "API testing" -#* @param a The first number to add -#* @param b The second number to add -#* @post /sum -function(a, b) { - as.numeric(a) + as.numeric(b) -} diff --git a/tests/curl_test_endpoints.sh b/tests/curl_test_endpoints.sh index b9292c8..f71fd4c 100755 --- a/tests/curl_test_endpoints.sh +++ b/tests/curl_test_endpoints.sh @@ -9,24 +9,38 @@ set -o pipefail # Adapted from https://stackoverflow.com/a/3355423/4638182 cd "$(dirname "$0")" || exit -# Set API_PORT to 8082 if not set. +# Set LOCAL_API_HOST_PORT to 8082 if not set. # # Adapted from # # - https://google.github.io/styleguide/shellguide.html # - https://stackoverflow.com/a/13864829/4638182 -if [[ -z "${API_PORT+x}" ]]; then - API_PORT=8082 +if [[ -z "${LOCAL_API_HOST_PORT+x}" ]]; then + LOCAL_API_HOST_PORT="8082" +fi + +if [[ -z "${API_HOST+x}" ]]; then + API_HOST="local" fi # Adapted from https://stackoverflow.com/a/17030976/4638182 printf "%0.s\n" {1..20} -base_url="http://localhost:${API_PORT}" +if [[ "${API_HOST}" == "local" ]]; then + base_url="http://localhost:${LOCAL_API_HOST_PORT}" +elif [[ "${API_HOST}" == "qa" ]]; then + base_url="https://openpedcan-api-qa.d3b.io" +elif [[ "${API_HOST}" == "dev" ]]; then + base_url="https://openpedcan-api-dev.d3b.io" +else + echo "Invalid API_HOST=${API_HOST}. Please choose from local, qa, and dev and rerun." 1>&2 + exit 1 +fi + http_request_method="GET" for ensg_id in "ENSG00000213420" "ENSG00000157764" "ENSG00000273032"; do - for efo_id in "EFO_0000621" "EFO_0005543" "EFO_0007206"; do + for efo_id in "EFO_0000621" "Orphanet_178" "MONDO_0016718" "MONDO_0016680" "MONDO_0016685"; do query_url="${base_url}/tpm/gene-disease-gtex/json?ensemblId=${ensg_id}&efoId=${efo_id}" output_dir="http_response_output_files/json" output_fn="test-tpm-gene-disease-gtex-${ensg_id}-${efo_id}.json" diff --git a/tests/http_response_output_files/json/test-tpm-gene-all-cancer-ENSG00000157764.json b/tests/http_response_output_files/json/test-tpm-gene-all-cancer-ENSG00000157764.json index 8b33f4f..e3156ec 100644 --- a/tests/http_response_output_files/json/test-tpm-gene-all-cancer-ENSG00000157764.json +++ b/tests/http_response_output_files/json/test-tpm-gene-all-cancer-ENSG00000157764.json @@ -1 +1 @@ -[{"ensemblId":"ENSG00000157764"}] \ No newline at end of file +[{"x_labels":"Acute Lymphoblastic Leukemia (Dataset = TARGET, N = 458)","Gene_Ensembl_ID":"ENSG00000157764","Gene_symbol":"BRAF","PMTL":"Relevant Molecular Target (RMTL version 1.0)","Dataset":"TARGET","Disease":"Acute Lymphoblastic Leukemia","GTEx_tissue_subgroup":"","EFO":"EFO_0000220","MONDO":"MONDO_0004967","GTEx_tissue_subgroup_UBERON":"","TPM_mean":14.04,"TPM_sd":14.67,"TPM_min":0.9,"TPM_25th_percentile":4.23,"TPM_median":7.8,"TPM_75th_percentile":18.7,"TPM_max":100.26},{"x_labels":"Acute Myeloid Leukemia (Dataset = TARGET, N = 141)","Gene_Ensembl_ID":"ENSG00000157764","Gene_symbol":"BRAF","PMTL":"Relevant Molecular Target (RMTL version 1.0)","Dataset":"TARGET","Disease":"Acute Myeloid Leukemia","GTEx_tissue_subgroup":"","EFO":"EFO_0000222","MONDO":"MONDO_0018874","GTEx_tissue_subgroup_UBERON":"","TPM_mean":10.96,"TPM_sd":8.21,"TPM_min":2.02,"TPM_25th_percentile":5.27,"TPM_median":8.3,"TPM_75th_percentile":14.33,"TPM_max":48.07},{"x_labels":"Adamantinomatous Craniopharyngioma (Dataset = PBTA, N = 17)","Gene_Ensembl_ID":"ENSG00000157764","Gene_symbol":"BRAF","PMTL":"Relevant Molecular Target (RMTL version 1.0)","Dataset":"PBTA","Disease":"Adamantinomatous Craniopharyngioma","GTEx_tissue_subgroup":"","EFO":"EFO_1000069","MONDO":"MONDO_0002787","GTEx_tissue_subgroup_UBERON":"","TPM_mean":9.54,"TPM_sd":3.77,"TPM_min":3.42,"TPM_25th_percentile":6.45,"TPM_median":8.82,"TPM_75th_percentile":13.55,"TPM_max":16.64},{"x_labels":"Adenoma (Dataset = PBTA, N = 3)","Gene_Ensembl_ID":"ENSG00000157764","Gene_symbol":"BRAF","PMTL":"Relevant Molecular Target (RMTL version 1.0)","Dataset":"PBTA","Disease":"Adenoma","GTEx_tissue_subgroup":"","EFO":"EFO_0000232","MONDO":"MONDO_0002454","GTEx_tissue_subgroup_UBERON":"","TPM_mean":8.38,"TPM_sd":3.72,"TPM_min":4.53,"TPM_25th_percentile":6.6,"TPM_median":8.66,"TPM_75th_percentile":10.31,"TPM_max":11.96},{"x_labels":"Atypical Teratoid Rhabdoid Tumor (Dataset = PBTA, N = 24)","Gene_Ensembl_ID":"ENSG00000157764","Gene_symbol":"BRAF","PMTL":"Relevant Molecular Target (RMTL version 1.0)","Dataset":"PBTA","Disease":"Atypical Teratoid Rhabdoid Tumor","GTEx_tissue_subgroup":"","EFO":"EFO_1002008","MONDO":"MONDO_0020560","GTEx_tissue_subgroup_UBERON":"","TPM_mean":6.91,"TPM_sd":2.82,"TPM_min":2.19,"TPM_25th_percentile":5.32,"TPM_median":6.73,"TPM_75th_percentile":8.12,"TPM_max":15.37},{"x_labels":"Chordoma (Dataset = PBTA, N = 3)","Gene_Ensembl_ID":"ENSG00000157764","Gene_symbol":"BRAF","PMTL":"Relevant Molecular Target (RMTL version 1.0)","Dataset":"PBTA","Disease":"Chordoma","GTEx_tissue_subgroup":"","EFO":"Orphanet_178","MONDO":"MONDO_0008978","GTEx_tissue_subgroup_UBERON":"","TPM_mean":3.45,"TPM_sd":0.51,"TPM_min":2.95,"TPM_25th_percentile":3.18,"TPM_median":3.42,"TPM_75th_percentile":3.7,"TPM_max":3.97},{"x_labels":"Choroid plexus carcinoma (Dataset = PBTA, N = 4)","Gene_Ensembl_ID":"ENSG00000157764","Gene_symbol":"BRAF","PMTL":"Relevant Molecular Target (RMTL version 1.0)","Dataset":"PBTA","Disease":"Choroid plexus carcinoma","GTEx_tissue_subgroup":"","EFO":"MONDO_0016718","MONDO":"MONDO_0016718","GTEx_tissue_subgroup_UBERON":"","TPM_mean":5.78,"TPM_sd":2.77,"TPM_min":3.39,"TPM_25th_percentile":4.07,"TPM_median":5.04,"TPM_75th_percentile":6.76,"TPM_max":9.66},{"x_labels":"Choroid plexus papilloma (Dataset = PBTA, N = 15)","Gene_Ensembl_ID":"ENSG00000157764","Gene_symbol":"BRAF","PMTL":"Relevant Molecular Target (RMTL version 1.0)","Dataset":"PBTA","Disease":"Choroid plexus papilloma","GTEx_tissue_subgroup":"","EFO":"EFO_1000177","MONDO":"MONDO_0009837","GTEx_tissue_subgroup_UBERON":"","TPM_mean":7.89,"TPM_sd":2.54,"TPM_min":2.99,"TPM_25th_percentile":6.7,"TPM_median":8.46,"TPM_75th_percentile":9.16,"TPM_max":12.03},{"x_labels":"Clear cell sarcoma of the kidney (Dataset = TARGET, N = 13)","Gene_Ensembl_ID":"ENSG00000157764","Gene_symbol":"BRAF","PMTL":"Relevant Molecular Target (RMTL version 1.0)","Dataset":"TARGET","Disease":"Clear cell sarcoma of the kidney","GTEx_tissue_subgroup":"","EFO":"EFO_0000350","MONDO":"MONDO_0005006","GTEx_tissue_subgroup_UBERON":"","TPM_mean":5.82,"TPM_sd":0.67,"TPM_min":4.71,"TPM_25th_percentile":5.34,"TPM_median":6.05,"TPM_75th_percentile":6.28,"TPM_max":6.8},{"x_labels":"CNS Embryonal tumor (Dataset = PBTA, N = 9)","Gene_Ensembl_ID":"ENSG00000157764","Gene_symbol":"BRAF","PMTL":"Relevant Molecular Target (RMTL version 1.0)","Dataset":"PBTA","Disease":"CNS Embryonal tumor","GTEx_tissue_subgroup":"","EFO":"EFO_0005784","MONDO":"MONDO_0018843","GTEx_tissue_subgroup_UBERON":"","TPM_mean":10.09,"TPM_sd":5.74,"TPM_min":3.63,"TPM_25th_percentile":5.98,"TPM_median":8.35,"TPM_75th_percentile":11.29,"TPM_max":19.56},{"x_labels":"Craniopharyngioma (Dataset = PBTA, N = 11)","Gene_Ensembl_ID":"ENSG00000157764","Gene_symbol":"BRAF","PMTL":"Relevant Molecular Target (RMTL version 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a/tests/http_response_output_files/json/test-tpm-gene-disease-gtex-ENSG00000157764-EFO_0005543.json +++ /dev/null @@ -1 +0,0 @@ -[{"x_labels":"High-grade glioma/astrocytoma (cohort = PBTA, N = 51)","Gene_Ensembl_ID":"ENSG00000157764","Gene_symbol":"BRAF","PMTL":"Relevant Molecular Target (RMTL version 1.0)","cohort":"PBTA","Disease":"High-grade glioma/astrocytoma","GTEx_tissue_subgroup":"","EFO":"EFO_0005543","MONDO":"MONDO_0100342","GTEx_tissue_subgroup_UBERON":"","TPM_mean":8.24,"TPM_sd":3.4,"TPM_min":1.02,"TPM_25th_percentile":5.94,"TPM_median":8.04,"TPM_75th_percentile":10,"TPM_max":19.39},{"x_labels":"Low-grade glioma/astrocytoma (cohort = PBTA, N = 237)","Gene_Ensembl_ID":"ENSG00000157764","Gene_symbol":"BRAF","PMTL":"Relevant Molecular Target (RMTL version 1.0)","cohort":"PBTA","Disease":"Low-grade 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a/tests/http_response_output_files/json/test-tpm-gene-disease-gtex-ENSG00000157764-EFO_0007206.json +++ /dev/null @@ -1 +0,0 @@ -[{"x_labels":"Choroid plexus carcinoma (cohort = PBTA, N = 4)","Gene_Ensembl_ID":"ENSG00000157764","Gene_symbol":"BRAF","PMTL":"Relevant Molecular Target (RMTL version 1.0)","cohort":"PBTA","Disease":"Choroid plexus carcinoma","GTEx_tissue_subgroup":"","EFO":"EFO_0007206","MONDO":"MONDO_0016718","GTEx_tissue_subgroup_UBERON":"","TPM_mean":5.78,"TPM_sd":"2.77","TPM_min":3.39,"TPM_25th_percentile":4.07,"TPM_median":5.04,"TPM_75th_percentile":6.76,"TPM_max":9.66},{"x_labels":"Choroid plexus cyst (cohort = PBTA, N = 1)","Gene_Ensembl_ID":"ENSG00000157764","Gene_symbol":"BRAF","PMTL":"Relevant Molecular Target (RMTL version 1.0)","cohort":"PBTA","Disease":"Choroid plexus 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a/tests/http_response_output_files/json/test-tpm-gene-disease-gtex-ENSG00000213420-EFO_0000621.json +++ b/tests/http_response_output_files/json/test-tpm-gene-disease-gtex-ENSG00000213420-EFO_0000621.json @@ -1 +1 @@ -[{"x_labels":"Neuroblastoma (cohort = all_cohorts, N = 347)","Gene_Ensembl_ID":"ENSG00000213420","Gene_symbol":"GPC2","PMTL":"Relevant Molecular Target (RMTL version 1.0)","cohort":"all_cohorts","Disease":"Neuroblastoma","GTEx_tissue_subgroup":"","EFO":"EFO_0000621","MONDO":"MONDO_0005072","GTEx_tissue_subgroup_UBERON":"","TPM_mean":50.05,"TPM_sd":45.34,"TPM_min":0.52,"TPM_25th_percentile":21.65,"TPM_median":37,"TPM_75th_percentile":63.88,"TPM_max":332.67},{"x_labels":"Neuroblastoma (cohort = GMKF, N = 209)","Gene_Ensembl_ID":"ENSG00000213420","Gene_symbol":"GPC2","PMTL":"Relevant Molecular Target (RMTL version 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a/tests/http_response_output_files/json/test-tpm-gene-disease-gtex-ENSG00000273032-EFO_0005543.json +++ /dev/null @@ -1 +0,0 @@ -[{"x_labels":"High-grade glioma/astrocytoma (cohort = PBTA, N = 51)","Gene_Ensembl_ID":"ENSG00000273032","Gene_symbol":"DGCR5","PMTL":"","cohort":"PBTA","Disease":"High-grade glioma/astrocytoma","GTEx_tissue_subgroup":"","EFO":"EFO_0005543","MONDO":"MONDO_0100342","GTEx_tissue_subgroup_UBERON":"","TPM_mean":1.45,"TPM_sd":2.63,"TPM_min":0.01,"TPM_25th_percentile":0.24,"TPM_median":0.7,"TPM_75th_percentile":1.81,"TPM_max":17.8},{"x_labels":"Low-grade glioma/astrocytoma (cohort = PBTA, N = 237)","Gene_Ensembl_ID":"ENSG00000273032","Gene_symbol":"DGCR5","PMTL":"","cohort":"PBTA","Disease":"Low-grade 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a/tests/http_response_output_files/json/test-tpm-gene-disease-gtex-ENSG00000273032-EFO_0007206.json +++ /dev/null @@ -1 +0,0 @@ -[{"x_labels":"Choroid plexus carcinoma (cohort = PBTA, N = 4)","Gene_Ensembl_ID":"ENSG00000273032","Gene_symbol":"DGCR5","PMTL":"","cohort":"PBTA","Disease":"Choroid plexus carcinoma","GTEx_tissue_subgroup":"","EFO":"EFO_0007206","MONDO":"MONDO_0016718","GTEx_tissue_subgroup_UBERON":"","TPM_mean":0.55,"TPM_sd":"0.17","TPM_min":0.37,"TPM_25th_percentile":0.44,"TPM_median":0.52,"TPM_75th_percentile":0.64,"TPM_max":0.77},{"x_labels":"Choroid plexus cyst (cohort = PBTA, N = 1)","Gene_Ensembl_ID":"ENSG00000273032","Gene_symbol":"DGCR5","PMTL":"","cohort":"PBTA","Disease":"Choroid plexus cyst","GTEx_tissue_subgroup":"","EFO":"EFO_0007206","MONDO":"","GTEx_tissue_subgroup_UBERON":"","TPM_mean":0.25,"TPM_sd":"","TPM_min":0.25,"TPM_25th_percentile":0.25,"TPM_median":0.25,"TPM_75th_percentile":0.25,"TPM_max":0.25},{"x_labels":"Adipose - Subcutaneous (cohort = GTEx, N = 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GTEx_tissue_subgroup_UBERON TPM_mean TPM_sd TPM_min TPM_25th_percentile TPM_median TPM_75th_percentile TPM_max +Acute Lymphoblastic Leukemia (Dataset = TARGET, N = 458) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) TARGET Acute Lymphoblastic Leukemia EFO_0000220 MONDO_0004967 14.04 14.67 0.9 4.23 7.8 18.7 100.26 +Acute Myeloid Leukemia (Dataset = TARGET, N = 141) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) TARGET Acute Myeloid Leukemia EFO_0000222 MONDO_0018874 10.96 8.21 2.02 5.27 8.3 14.33 48.07 +Adamantinomatous Craniopharyngioma (Dataset = PBTA, N = 17) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Adamantinomatous Craniopharyngioma EFO_1000069 MONDO_0002787 9.54 3.77 3.42 6.45 8.82 13.55 16.64 +Adenoma (Dataset = PBTA, N = 3) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Adenoma EFO_0000232 MONDO_0002454 8.38 3.72 4.53 6.6 8.66 10.31 11.96 +Atypical Teratoid Rhabdoid Tumor (Dataset = PBTA, N = 24) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Atypical Teratoid Rhabdoid Tumor EFO_1002008 MONDO_0020560 6.91 2.82 2.19 5.32 6.73 8.12 15.37 +Chordoma (Dataset = PBTA, N = 3) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Chordoma Orphanet_178 MONDO_0008978 3.45 0.51 2.95 3.18 3.42 3.7 3.97 +Choroid plexus carcinoma (Dataset = PBTA, N = 4) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Choroid plexus carcinoma MONDO_0016718 MONDO_0016718 5.78 2.77 3.39 4.07 5.04 6.76 9.66 +Choroid plexus papilloma (Dataset = PBTA, N = 15) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Choroid plexus papilloma EFO_1000177 MONDO_0009837 7.89 2.54 2.99 6.7 8.46 9.16 12.03 +Clear cell sarcoma of the kidney (Dataset = TARGET, N = 13) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) TARGET Clear cell sarcoma of the kidney EFO_0000350 MONDO_0005006 5.82 0.67 4.71 5.34 6.05 6.28 6.8 +CNS Embryonal tumor (Dataset = PBTA, N = 9) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA CNS Embryonal tumor EFO_0005784 MONDO_0018843 10.09 5.74 3.63 5.98 8.35 11.29 19.56 +Craniopharyngioma (Dataset = PBTA, N = 11) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Craniopharyngioma EFO_1000209 MONDO_0002787 3.77 2.07 1.4 2.17 3.44 5.01 7.97 +Diffuse intrinsic pontine glioma (Dataset = PBTA, N = 4) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Diffuse intrinsic pontine glioma EFO_1000026 MONDO_0006033 13.31 10.45 7.03 7.92 8.64 14.02 28.94 +Diffuse midline glioma (Dataset = PBTA, N = 47) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Diffuse midline glioma MONDO_0003869 MONDO_0006033 9.39 7.05 0.7 5.6 8.98 11.04 43.53 +Dysembryoplastic neuroepithelial tumor (Dataset = PBTA, N = 19) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Dysembryoplastic neuroepithelial tumor EFO_0005551 MONDO_0005505 9.48 4.53 2.9 6.86 8.95 10.27 23.68 +Embryonal tumor with multilayer rosettes (Dataset = PBTA, N = 4) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Embryonal tumor with multilayer rosettes MONDO_0016715 MONDO_0016715 11.57 0.84 10.62 11.05 11.56 12.08 12.55 +Ependymoma (Dataset = PBTA, N = 69) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Ependymoma EFO_1000028 MONDO_0016698 5.77 2.11 0.29 4.34 5.4 7.45 10.88 +Ewing sarcoma (Dataset = PBTA, N = 7) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Ewing sarcoma EFO_0000174 MONDO_0012817 8.41 2.29 4.22 7.52 8.61 10.05 10.89 +Germinoma (Dataset = PBTA, N = 4) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Germinoma EFO_0000514 MONDO_0005040 8.89 7.23 2.25 4.05 7.39 12.23 18.55 +Glial-neuronal tumor NOS (Dataset = PBTA, N = 5) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Glial-neuronal tumor NOS MONDO_0016729 MONDO_0016729 9.81 2.32 6.94 8.8 8.97 11.76 12.59 +High-grade glioma/astrocytoma (Dataset = PBTA, N = 51) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA High-grade glioma/astrocytoma MONDO_0016680 MONDO_0100342 8.24 3.4 1.02 5.94 8.04 10 19.39 +Langerhans Cell histiocytosis (Dataset = PBTA, N = 4) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Langerhans Cell histiocytosis EFO_1000318 MONDO_0009519 2.95 0.71 1.94 2.8 3.12 3.27 3.62 +Low-grade glioma/astrocytoma (Dataset = PBTA, N = 237) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Low-grade glioma/astrocytoma MONDO_0016685 MONDO_0016685 7.9 3.34 1.63 5.72 7.55 9.61 26.49 +Malignant peripheral nerve sheath tumor (Dataset = PBTA, N = 3) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Malignant peripheral nerve sheath tumor EFO_0000760 MONDO_0018078 4.08 1.4 2.52 3.5 4.47 4.86 5.24 +Medulloblastoma (Dataset = PBTA, N = 105) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Medulloblastoma EFO_0002939 MONDO_0007959 12.17 5.45 3.38 8.24 11.41 15.36 32.68 +Meningioma (Dataset = PBTA, N = 14) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Meningioma Orphanet_2495 MONDO_0016642 5.72 2.02 2.4 4.43 5.36 6.64 10.17 +Metastatic secondary tumors (Dataset = PBTA, N = 3) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Metastatic secondary tumors EFO_0009812 MONDO_0024883 4.61 1.16 3.31 4.16 5.02 5.26 5.51 +Neuroblastoma (Dataset = all_cohorts, N = 347) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) all_cohorts Neuroblastoma EFO_0000621 MONDO_0005072 25.31 13.28 3.32 15.16 22 34.62 69.06 +Neuroblastoma (Dataset = GMKF, N = 209) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GMKF Neuroblastoma EFO_0000621 MONDO_0005072 32.19 12.7 8.32 21.83 31.12 41.14 69.06 +Neuroblastoma (Dataset = TARGET, N = 149) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) TARGET Neuroblastoma EFO_0000621 MONDO_0005072 15.93 6.69 3.32 11.27 15.1 20.03 37.21 +Neurofibroma/Plexiform (Dataset = PBTA, N = 10) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Neurofibroma/Plexiform EFO_0000658 MONDO_0003304 3.55 1.81 1.81 2.2 2.91 4.67 7.45 +Osteosarcoma (Dataset = TARGET, N = 87) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) TARGET Osteosarcoma EFO_0000637 MONDO_0009807 7.39 3.6 1.45 4.97 6.6 9.52 17.72 +Pineoblastoma (Dataset = PBTA, N = 4) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Pineoblastoma EFO_1000475 MONDO_0016722 6.64 2.21 5.2 5.55 5.72 6.8 9.94 +Rhabdoid tumor (Dataset = TARGET, N = 64) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) TARGET Rhabdoid tumor EFO_0005701 MONDO_0002728 6.87 3.43 0 4.19 6.46 9.12 21.61 +Sarcoma (Dataset = PBTA, N = 3) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Sarcoma EFO_0000691 MONDO_0005089 6.83 1.33 5.34 6.31 7.28 7.58 7.88 +Schwannoma (Dataset = PBTA, N = 14) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Schwannoma EFO_0000693 MONDO_0002546 6.68 2.89 3.22 4.09 5.98 8.8 12.49 +Teratoma (Dataset = PBTA, N = 4) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Teratoma MONDO_0002601 MONDO_0002601 8.67 6.46 2.46 3.57 8.3 13.4 15.64 +Wilms tumor (Dataset = TARGET, N = 124) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) TARGET Wilms tumor MONDO_0019004 MONDO_0006058 14.16 6.69 3.1 9.25 13.38 17.36 38.96 diff --git a/tests/results/test-tpm-gene-all-cancer-ENSG00000213420.tsv b/tests/results/test-tpm-gene-all-cancer-ENSG00000213420.tsv index f24344d..33ce251 100644 --- a/tests/results/test-tpm-gene-all-cancer-ENSG00000213420.tsv +++ b/tests/results/test-tpm-gene-all-cancer-ENSG00000213420.tsv @@ -1,2 +1,38 @@ -ensemblId -ENSG00000213420 +x_labels Gene_Ensembl_ID Gene_symbol PMTL Dataset Disease GTEx_tissue_subgroup EFO MONDO GTEx_tissue_subgroup_UBERON TPM_mean TPM_sd TPM_min TPM_25th_percentile TPM_median TPM_75th_percentile TPM_max +Acute Lymphoblastic Leukemia (Dataset = TARGET, N = 458) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) TARGET Acute Lymphoblastic Leukemia EFO_0000220 MONDO_0004967 7.81 12.99 0.08 1.91 3.5 7.4 117.72 +Acute Myeloid Leukemia (Dataset = TARGET, N = 141) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) TARGET Acute Myeloid Leukemia EFO_0000222 MONDO_0018874 0.5 0.83 0 0.1 0.22 0.48 5.21 +Adamantinomatous Craniopharyngioma (Dataset = PBTA, N = 17) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Adamantinomatous Craniopharyngioma EFO_1000069 MONDO_0002787 1.42 0.59 0.5 0.99 1.44 1.91 2.27 +Adenoma (Dataset = PBTA, N = 3) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Adenoma EFO_0000232 MONDO_0002454 0.3 0.26 0.12 0.16 0.19 0.4 0.6 +Atypical Teratoid Rhabdoid Tumor (Dataset = PBTA, N = 24) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Atypical Teratoid Rhabdoid Tumor EFO_1002008 MONDO_0020560 3.96 4.18 0.15 0.91 1.8 6.41 14.53 +Chordoma (Dataset = PBTA, N = 3) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Chordoma Orphanet_178 MONDO_0008978 0.54 0.12 0.4 0.49 0.58 0.61 0.64 +Choroid plexus carcinoma (Dataset = PBTA, N = 4) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Choroid plexus carcinoma MONDO_0016718 MONDO_0016718 12.53 11.31 2.74 3.27 10.87 20.14 25.64 +Choroid plexus papilloma (Dataset = PBTA, N = 15) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Choroid plexus papilloma EFO_1000177 MONDO_0009837 0.32 0.19 0.05 0.16 0.28 0.45 0.68 +Clear cell sarcoma of the kidney (Dataset = TARGET, N = 13) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) TARGET Clear cell sarcoma of the kidney EFO_0000350 MONDO_0005006 1.63 0.96 0.59 1.08 1.38 1.77 4.5 +CNS Embryonal tumor (Dataset = PBTA, N = 9) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA CNS Embryonal tumor EFO_0005784 MONDO_0018843 36.28 37.13 2.25 14.75 23.04 50.91 118.9 +Craniopharyngioma (Dataset = PBTA, N = 11) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Craniopharyngioma EFO_1000209 MONDO_0002787 0.47 0.25 0.14 0.26 0.42 0.68 0.9 +Diffuse intrinsic pontine glioma (Dataset = PBTA, N = 4) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Diffuse intrinsic pontine glioma EFO_1000026 MONDO_0006033 3.83 1.82 2.16 2.72 3.41 4.51 6.35 +Diffuse midline glioma (Dataset = PBTA, N = 47) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Diffuse midline glioma MONDO_0003869 MONDO_0006033 9.73 10.24 0.98 2.99 6.28 12.61 59.85 +Dysembryoplastic neuroepithelial tumor (Dataset = PBTA, N = 19) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Dysembryoplastic neuroepithelial tumor EFO_0005551 MONDO_0005505 3.95 3.2 0.47 0.84 3.99 6.93 9.24 +Embryonal tumor with multilayer rosettes (Dataset = PBTA, N = 4) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Embryonal tumor with multilayer rosettes MONDO_0016715 MONDO_0016715 46.28 20.46 20.58 35.02 48.96 60.23 66.64 +Ependymoma (Dataset = PBTA, N = 69) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Ependymoma EFO_1000028 MONDO_0016698 1.16 1.42 0.02 0.43 0.73 1.11 7.9 +Ewing sarcoma (Dataset = PBTA, N = 7) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Ewing sarcoma EFO_0000174 MONDO_0012817 6 6.36 0.75 1.52 2.87 8.61 18.13 +Germinoma (Dataset = PBTA, N = 4) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Germinoma EFO_0000514 MONDO_0005040 6.31 4.95 1.96 3.96 4.93 7.28 13.43 +Glial-neuronal tumor NOS (Dataset = PBTA, N = 5) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Glial-neuronal tumor NOS MONDO_0016729 MONDO_0016729 2.55 1.69 1.02 1.07 2.25 3.42 5 +High-grade glioma/astrocytoma (Dataset = PBTA, N = 51) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA High-grade glioma/astrocytoma MONDO_0016680 MONDO_0100342 11.23 14 0.15 2.74 5.66 14.88 59.91 +Langerhans Cell histiocytosis (Dataset = PBTA, N = 4) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Langerhans Cell histiocytosis EFO_1000318 MONDO_0009519 0.47 0.25 0.28 0.31 0.39 0.55 0.83 +Low-grade glioma/astrocytoma (Dataset = PBTA, N = 237) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Low-grade glioma/astrocytoma MONDO_0016685 MONDO_0016685 2.88 2.14 0.17 1.27 2.48 4.11 12.52 +Malignant peripheral nerve sheath tumor (Dataset = PBTA, N = 3) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Malignant peripheral nerve sheath tumor EFO_0000760 MONDO_0018078 0.42 0.09 0.33 0.38 0.43 0.47 0.51 +Medulloblastoma (Dataset = PBTA, N = 105) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Medulloblastoma EFO_0002939 MONDO_0007959 27.55 17.65 3.21 15.51 24.29 32.75 87.11 +Meningioma (Dataset = PBTA, N = 14) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Meningioma Orphanet_2495 MONDO_0016642 0.68 0.5 0.16 0.39 0.58 0.78 2.03 +Metastatic secondary tumors (Dataset = PBTA, N = 3) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Metastatic secondary tumors EFO_0009812 MONDO_0024883 12 19.27 0.33 0.88 1.43 17.84 34.24 +Neuroblastoma (Dataset = all_cohorts, N = 347) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) all_cohorts Neuroblastoma EFO_0000621 MONDO_0005072 50.05 45.34 0.52 21.65 37 63.88 332.67 +Neuroblastoma (Dataset = GMKF, N = 209) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GMKF Neuroblastoma EFO_0000621 MONDO_0005072 27.83 15.74 0.52 17.23 26.63 38.92 73.07 +Neuroblastoma (Dataset = TARGET, N = 149) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) TARGET Neuroblastoma EFO_0000621 MONDO_0005072 81.2 53.17 1.2 43.22 72.03 112.68 332.67 +Neurofibroma/Plexiform (Dataset = PBTA, N = 10) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Neurofibroma/Plexiform EFO_0000658 MONDO_0003304 0.38 0.2 0.08 0.24 0.3 0.54 0.68 +Osteosarcoma (Dataset = TARGET, N = 87) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) TARGET Osteosarcoma EFO_0000637 MONDO_0009807 4.18 5.59 0.28 1.41 3.17 4.8 47.24 +Pineoblastoma (Dataset = PBTA, N = 4) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Pineoblastoma EFO_1000475 MONDO_0016722 12.37 14.77 2.15 4.52 6.54 14.38 34.25 +Rhabdoid tumor (Dataset = TARGET, N = 64) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) TARGET Rhabdoid tumor EFO_0005701 MONDO_0002728 4.94 16.77 0.06 0.49 1.07 3.24 131.03 +Sarcoma (Dataset = PBTA, N = 3) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Sarcoma EFO_0000691 MONDO_0005089 2.29 2.65 0.17 0.8 1.44 3.35 5.27 +Schwannoma (Dataset = PBTA, N = 14) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Schwannoma EFO_0000693 MONDO_0002546 0.62 0.2 0.3 0.48 0.6 0.75 0.98 +Teratoma (Dataset = PBTA, N = 4) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Teratoma MONDO_0002601 MONDO_0002601 3.31 3.44 0.6 0.92 2.28 4.66 8.1 +Wilms tumor (Dataset = TARGET, N = 124) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) TARGET Wilms tumor MONDO_0019004 MONDO_0006058 6.44 3.57 0.2 3.48 6.14 8.78 17.93 diff --git a/tests/results/test-tpm-gene-all-cancer-ENSG00000273032.tsv b/tests/results/test-tpm-gene-all-cancer-ENSG00000273032.tsv index 140148e..7c8d812 100644 --- a/tests/results/test-tpm-gene-all-cancer-ENSG00000273032.tsv +++ b/tests/results/test-tpm-gene-all-cancer-ENSG00000273032.tsv @@ -1,2 +1,38 @@ -ensemblId -ENSG00000273032 +x_labels Gene_Ensembl_ID Gene_symbol PMTL Dataset Disease GTEx_tissue_subgroup EFO MONDO GTEx_tissue_subgroup_UBERON TPM_mean TPM_sd TPM_min TPM_25th_percentile TPM_median TPM_75th_percentile TPM_max +Acute Lymphoblastic Leukemia (Dataset = TARGET, N = 458) ENSG00000273032 DGCR5 TARGET Acute Lymphoblastic Leukemia EFO_0000220 MONDO_0004967 0.02 0.08 0 0 0 0.01 1.18 +Acute Myeloid Leukemia (Dataset = TARGET, N = 141) ENSG00000273032 DGCR5 TARGET Acute Myeloid Leukemia EFO_0000222 MONDO_0018874 0.01 0.03 0 0 0 0 0.17 +Adamantinomatous Craniopharyngioma (Dataset = PBTA, N = 17) ENSG00000273032 DGCR5 PBTA Adamantinomatous Craniopharyngioma EFO_1000069 MONDO_0002787 0.65 0.4 0.09 0.41 0.63 0.81 1.89 +Adenoma (Dataset = PBTA, N = 3) ENSG00000273032 DGCR5 PBTA Adenoma EFO_0000232 MONDO_0002454 0.98 1.1 0.27 0.34 0.41 1.33 2.25 +Atypical Teratoid Rhabdoid Tumor (Dataset = PBTA, N = 24) ENSG00000273032 DGCR5 PBTA Atypical Teratoid Rhabdoid Tumor EFO_1002008 MONDO_0020560 1.87 5.08 0.03 0.47 0.64 0.98 25.47 +Chordoma (Dataset = PBTA, N = 3) ENSG00000273032 DGCR5 PBTA Chordoma Orphanet_178 MONDO_0008978 0.02 0.01 0.01 0.01 0.02 0.02 0.02 +Choroid plexus carcinoma (Dataset = PBTA, N = 4) ENSG00000273032 DGCR5 PBTA Choroid plexus carcinoma MONDO_0016718 MONDO_0016718 0.55 0.17 0.37 0.44 0.52 0.64 0.77 +Choroid plexus papilloma (Dataset = PBTA, N = 15) ENSG00000273032 DGCR5 PBTA Choroid plexus papilloma EFO_1000177 MONDO_0009837 1.19 0.58 0.37 0.83 1.2 1.48 2.61 +Clear cell sarcoma of the kidney (Dataset = TARGET, N = 13) ENSG00000273032 DGCR5 TARGET Clear cell sarcoma of the kidney EFO_0000350 MONDO_0005006 0.01 0.03 0 0 0 0.01 0.12 +CNS Embryonal tumor (Dataset = PBTA, N = 9) ENSG00000273032 DGCR5 PBTA CNS Embryonal tumor EFO_0005784 MONDO_0018843 1.38 1.49 0 0.37 1.15 1.79 4.71 +Craniopharyngioma (Dataset = PBTA, N = 11) ENSG00000273032 DGCR5 PBTA Craniopharyngioma EFO_1000209 MONDO_0002787 0.38 0.5 0.08 0.12 0.18 0.36 1.74 +Diffuse intrinsic pontine glioma (Dataset = PBTA, N = 4) ENSG00000273032 DGCR5 PBTA Diffuse intrinsic pontine glioma EFO_1000026 MONDO_0006033 2.38 2.78 0.1 0.6 1.55 3.33 6.31 +Diffuse midline glioma (Dataset = PBTA, N = 47) ENSG00000273032 DGCR5 PBTA Diffuse midline glioma MONDO_0003869 MONDO_0006033 2 1.49 0.15 0.61 1.86 3.08 6.22 +Dysembryoplastic neuroepithelial tumor (Dataset = PBTA, N = 19) ENSG00000273032 DGCR5 PBTA Dysembryoplastic neuroepithelial tumor EFO_0005551 MONDO_0005505 2.73 2.92 0.14 0.7 1 3.77 10.11 +Embryonal tumor with multilayer rosettes (Dataset = PBTA, N = 4) ENSG00000273032 DGCR5 PBTA Embryonal tumor with multilayer rosettes MONDO_0016715 MONDO_0016715 1.58 0.77 0.56 1.35 1.66 1.89 2.43 +Ependymoma (Dataset = PBTA, N = 69) ENSG00000273032 DGCR5 PBTA Ependymoma EFO_1000028 MONDO_0016698 0.96 0.98 0 0.39 0.69 1.26 7.16 +Ewing sarcoma (Dataset = PBTA, N = 7) ENSG00000273032 DGCR5 PBTA Ewing sarcoma EFO_0000174 MONDO_0012817 0.59 0.78 0 0.06 0.38 0.71 2.18 +Germinoma (Dataset = PBTA, N = 4) ENSG00000273032 DGCR5 PBTA Germinoma EFO_0000514 MONDO_0005040 0.3 0.39 0.05 0.06 0.14 0.38 0.88 +Glial-neuronal tumor NOS (Dataset = PBTA, N = 5) ENSG00000273032 DGCR5 PBTA Glial-neuronal tumor NOS MONDO_0016729 MONDO_0016729 1.2 1.07 0.14 0.39 0.83 2.06 2.58 +High-grade glioma/astrocytoma (Dataset = PBTA, N = 51) ENSG00000273032 DGCR5 PBTA High-grade glioma/astrocytoma MONDO_0016680 MONDO_0100342 1.45 2.63 0.01 0.24 0.7 1.81 17.8 +Langerhans Cell histiocytosis (Dataset = PBTA, N = 4) ENSG00000273032 DGCR5 PBTA Langerhans Cell histiocytosis EFO_1000318 MONDO_0009519 0.03 0.01 0.01 0.02 0.03 0.03 0.04 +Low-grade glioma/astrocytoma (Dataset = PBTA, N = 237) ENSG00000273032 DGCR5 PBTA Low-grade glioma/astrocytoma MONDO_0016685 MONDO_0016685 1.15 1.58 0 0.25 0.6 1.24 10.82 +Malignant peripheral nerve sheath tumor (Dataset = PBTA, N = 3) ENSG00000273032 DGCR5 PBTA Malignant peripheral nerve sheath tumor EFO_0000760 MONDO_0018078 0.08 0.11 0.02 0.02 0.02 0.11 0.21 +Medulloblastoma (Dataset = PBTA, N = 105) ENSG00000273032 DGCR5 PBTA Medulloblastoma EFO_0002939 MONDO_0007959 2.13 1.55 0.15 0.85 1.73 3.1 8.45 +Meningioma (Dataset = PBTA, N = 14) ENSG00000273032 DGCR5 PBTA Meningioma Orphanet_2495 MONDO_0016642 1.15 0.89 0.24 0.36 0.94 1.87 2.75 +Metastatic secondary tumors (Dataset = PBTA, N = 3) ENSG00000273032 DGCR5 PBTA Metastatic secondary tumors EFO_0009812 MONDO_0024883 1 0.99 0.11 0.46 0.81 1.44 2.07 +Neuroblastoma (Dataset = all_cohorts, N = 347) ENSG00000273032 DGCR5 all_cohorts Neuroblastoma EFO_0000621 MONDO_0005072 2.92 2.35 0 1.28 2.34 3.95 15.96 +Neuroblastoma (Dataset = GMKF, N = 209) ENSG00000273032 DGCR5 GMKF Neuroblastoma EFO_0000621 MONDO_0005072 2.81 2.26 0 1.13 2.28 4.02 14.69 +Neuroblastoma (Dataset = TARGET, N = 149) ENSG00000273032 DGCR5 TARGET Neuroblastoma EFO_0000621 MONDO_0005072 3.11 2.44 0.04 1.67 2.49 3.86 15.96 +Neurofibroma/Plexiform (Dataset = PBTA, N = 10) ENSG00000273032 DGCR5 PBTA Neurofibroma/Plexiform EFO_0000658 MONDO_0003304 0.12 0.09 0.04 0.04 0.09 0.19 0.28 +Osteosarcoma (Dataset = TARGET, N = 87) ENSG00000273032 DGCR5 TARGET Osteosarcoma EFO_0000637 MONDO_0009807 0.29 0.45 0 0.01 0.07 0.44 2.36 +Pineoblastoma (Dataset = PBTA, N = 4) ENSG00000273032 DGCR5 PBTA Pineoblastoma EFO_1000475 MONDO_0016722 1.39 1.27 0.01 0.65 1.27 2.01 3 +Rhabdoid tumor (Dataset = TARGET, N = 64) ENSG00000273032 DGCR5 TARGET Rhabdoid tumor EFO_0005701 MONDO_0002728 0.78 1.03 0.01 0.16 0.44 0.97 5.97 +Sarcoma (Dataset = PBTA, N = 3) ENSG00000273032 DGCR5 PBTA Sarcoma EFO_0000691 MONDO_0005089 0.01 0.02 0 0 0 0.02 0.04 +Schwannoma (Dataset = PBTA, N = 14) ENSG00000273032 DGCR5 PBTA Schwannoma EFO_0000693 MONDO_0002546 0.54 0.95 0.02 0.07 0.11 0.38 2.98 +Teratoma (Dataset = PBTA, N = 4) ENSG00000273032 DGCR5 PBTA Teratoma MONDO_0002601 MONDO_0002601 0.82 0.88 0.23 0.36 0.46 0.92 2.13 +Wilms tumor (Dataset = TARGET, N = 124) ENSG00000273032 DGCR5 TARGET Wilms tumor MONDO_0019004 MONDO_0006058 0.16 0.38 0 0.02 0.06 0.15 3.64 diff --git a/tests/results/test-tpm-gene-disease-gtex-ENSG00000157764-EFO_0000621.tsv b/tests/results/test-tpm-gene-disease-gtex-ENSG00000157764-EFO_0000621.tsv index ad69f54..3578a86 100644 --- a/tests/results/test-tpm-gene-disease-gtex-ENSG00000157764-EFO_0000621.tsv +++ b/tests/results/test-tpm-gene-disease-gtex-ENSG00000157764-EFO_0000621.tsv @@ -1,57 +1,57 @@ -x_labels Gene_Ensembl_ID Gene_symbol PMTL cohort Disease GTEx_tissue_subgroup EFO MONDO GTEx_tissue_subgroup_UBERON TPM_mean TPM_sd TPM_min TPM_25th_percentile TPM_median TPM_75th_percentile TPM_max -Neuroblastoma (cohort = all_cohorts, N = 347) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) all_cohorts Neuroblastoma EFO_0000621 MONDO_0005072 25.31 13.28 3.32 15.16 22 34.62 69.06 -Neuroblastoma (cohort = GMKF, N = 209) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GMKF Neuroblastoma EFO_0000621 MONDO_0005072 32.19 12.7 8.32 21.83 31.12 41.14 69.06 -Neuroblastoma (cohort = TARGET, N = 149) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) TARGET Neuroblastoma EFO_0000621 MONDO_0005072 15.93 6.69 3.32 11.27 15.1 20.03 37.21 -Adipose - Subcutaneous (cohort = GTEx, N = 663) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Subcutaneous UBERON_0002190 12.82 2.87 4.28 10.93 12.52 14.49 31.91 -Adipose - Visceral (Omentum) (cohort = GTEx, N = 541) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Visceral (Omentum) UBERON_0010414 10.51 3.39 2.39 7.84 10.25 12.89 24.23 -Adrenal Gland (cohort = GTEx, N = 258) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Adrenal Gland UBERON_0002369 6.08 1.32 2.22 5.31 6.03 6.91 10.85 -Artery - Aorta (cohort = GTEx, N = 432) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Aorta UBERON_0001496 13.14 2.72 5.41 11.31 12.96 14.79 24.63 -Artery - Coronary (cohort = GTEx, N = 240) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Coronary UBERON_0001621 12.43 3.46 4.44 9.96 11.8 14.15 23.58 -Artery - Tibial (cohort = GTEx, N = 663) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Tibial UBERON_0007610 16.02 3.65 3.67 13.7 15.83 17.99 32.95 -Bladder (cohort = GTEx, N = 21) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Bladder UBERON_0001255 15.52 6.04 6.36 11.79 12.95 20.06 29.41 -Blood (cohort = GTEx, N = 755) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Blood UBERON_0013756 6.38 3.8 0.36 3.73 5.53 7.93 30.85 -Brain - Amygdala (cohort = GTEx, N = 152) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Amygdala UBERON_0001876 5.09 2.49 0.77 3.26 4.67 6.85 12.19 -Brain - Anterior cingulate cortex (BA24) (cohort = GTEx, N = 176) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Anterior cingulate cortex (BA24) UBERON_0009835 7.78 4.2 1.53 4.62 7.13 9.88 24.3 -Brain - Caudate (basal ganglia) (cohort = GTEx, N = 246) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Caudate (basal ganglia) UBERON_0001873 6.87 3.73 0.77 3.89 6.64 9.37 22.01 -Brain - Cerebellum (cohort = GTEx, N = 456) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cerebellum UBERON_0002037 23.77 8.18 4.58 18.59 23.31 28.61 59.09 -Brain - Cortex (cohort = GTEx, N = 255) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cortex UBERON_0001870 8.42 3.06 1.78 6.34 8.39 10.38 20.64 -Brain - Frontal Cortex (BA9) (cohort = GTEx, N = 209) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Frontal Cortex (BA9) UBERON_0009834 11.8 5.24 1.68 7.94 11.98 15.12 32.8 -Brain - Hippocampus (cohort = GTEx, N = 197) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hippocampus UBERON_0001954 5.63 2.99 0.99 3.4 5.13 7.28 17.57 -Brain - Hypothalamus (cohort = GTEx, N = 202) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hypothalamus UBERON_0001898 7.08 3.92 0.84 4.22 6.48 9.27 24.09 -Brain - Nucleus accumbens (basal ganglia) (cohort = GTEx, N = 246) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Nucleus accumbens (basal ganglia) UBERON_0001882 7.97 4.44 0.77 4.76 7.81 10.75 22.12 -Brain - Putamen (basal ganglia) (cohort = GTEx, N = 205) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Putamen (basal ganglia) UBERON_0001874 5.57 3.36 0.77 3.04 5.08 7.41 21.08 -Brain - Spinal cord (cervical c-1) (cohort = GTEx, N = 159) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Spinal cord (cervical c-1) UBERON_0006469 5.98 2.58 1.09 4.28 5.81 7.48 14.2 -Brain - Substantia nigra (cohort = GTEx, N = 139) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Substantia nigra UBERON_0002038 4.69 2.36 1.07 2.9 4.31 6.11 12.65 -Breast - Mammary Tissue (cohort = GTEx, N = 459) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Breast - Mammary Tissue UBERON_0008367 13.52 4.74 4.38 9.63 12.91 16.74 28.59 -Cells - Cultured fibroblasts (cohort = GTEx, N = 504) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cells - Cultured fibroblasts 11.05 2.77 4.75 9.36 10.52 11.93 23.14 -Cells - EBV-transformed lymphocytes (cohort = GTEx, N = 174) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cells - EBV-transformed lymphocytes 16.82 5.02 6.68 13.51 16.31 19.28 40.77 -Cervix - Ectocervix (cohort = GTEx, N = 9) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Ectocervix UBERON_0012249 14.89 4.3 8.52 12.25 14.82 16.37 23.71 -Cervix - Endocervix (cohort = GTEx, N = 10) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Endocervix UBERON_0000458 16.39 2.95 12.68 14.5 15.54 18.15 21.4 -Colon - Sigmoid (cohort = GTEx, N = 373) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Sigmoid UBERON_0001159 12.52 2.95 2.89 10.76 12.66 14.22 23.28 -Colon - Transverse (cohort = GTEx, N = 406) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Transverse UBERON_0001157 8.88 3.67 3.13 5.87 7.91 11.19 21.44 -Esophagus - Gastroesophageal Junction (cohort = GTEx, N = 375) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Gastroesophageal Junction UBERON_0004550 12.04 3.04 4.02 10 11.75 13.82 24.94 -Esophagus - Mucosa (cohort = GTEx, N = 555) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Mucosa UBERON_0006920 7.66 1.85 2.77 6.44 7.44 8.71 18.73 -Esophagus - Muscularis (cohort = GTEx, N = 515) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Muscularis UBERON_0004648 12.05 2.77 4.53 10.2 11.93 13.83 23.34 -Fallopian Tube (cohort = GTEx, N = 9) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Fallopian Tube UBERON_0003889 14.97 3.73 8.41 12.7 16.7 16.96 19.98 -Heart - Atrial Appendage (cohort = GTEx, N = 429) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Atrial Appendage UBERON_0006631 5.31 1.75 1.05 4.12 5.05 6.36 11.83 -Heart - Left Ventricle (cohort = GTEx, N = 432) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Left Ventricle UBERON_0006566 3.35 1.66 0.52 2.43 3.31 4.13 14.39 -Kidney - Cortex (cohort = GTEx, N = 85) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Cortex UBERON_0001225 6.67 4.04 2.38 4.05 5.39 7.58 23 -Kidney - Medulla (cohort = GTEx, N = 4) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Medulla UBERON_0001293 8.9 3.06 5.3 6.99 9.12 11.04 12.07 -Liver (cohort = GTEx, N = 226) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Liver UBERON_0001114 3.63 0.95 1.15 2.97 3.53 4.22 7.74 -Lung (cohort = GTEx, N = 578) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Lung UBERON_0008952 16.39 4.91 6.11 12.79 15.59 18.8 37.04 -Minor Salivary Gland (cohort = GTEx, N = 162) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Minor Salivary Gland UBERON_0006330 8.57 2.06 3.73 7.14 8.49 9.87 14.97 -Muscle - Skeletal (cohort = GTEx, N = 803) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Muscle - Skeletal UBERON_0011907 4.85 1.84 1 3.56 4.56 5.74 14.81 -Nerve - Tibial (cohort = GTEx, N = 619) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Nerve - Tibial UBERON_0001323 16.83 3.21 8.21 14.73 16.65 18.47 46.67 -Ovary (cohort = GTEx, N = 180) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Ovary UBERON_0000992 17.3 3.94 8.23 14.5 16.94 19.15 32.61 -Pancreas (cohort = GTEx, N = 328) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Pancreas UBERON_0001150 4.44 1.49 1.83 3.43 4.19 5.08 15.2 -Pituitary (cohort = GTEx, N = 283) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Pituitary UBERON_0000007 15.06 3.21 6.49 13.16 14.88 16.56 27.8 -Prostate (cohort = GTEx, N = 245) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Prostate UBERON_0002367 13.59 3.43 5.21 10.97 13.49 15.78 26.64 -Skin - Not Sun Exposed (Suprapubic) (cohort = GTEx, N = 604) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Not Sun Exposed (Suprapubic) UBERON_0036149 13.63 3.14 5.81 11.49 13.68 15.46 28.18 -Skin - Sun Exposed (Lower leg) (cohort = GTEx, N = 701) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Sun Exposed (Lower leg) UBERON_0004264 14.29 3.23 5.23 12.1 14.05 16.32 25.49 -Small Intestine - Terminal Ileum (cohort = GTEx, N = 187) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Small Intestine - Terminal Ileum UBERON_0001211 9.85 4.2 3.46 6.53 8.97 11.98 25.59 -Spleen (cohort = GTEx, N = 241) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Spleen UBERON_0002106 10.3 3.13 3.4 8.18 9.55 11.69 20.61 -Stomach (cohort = GTEx, N = 359) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Stomach UBERON_0000945 8.41 3.06 3.57 6.25 7.64 10.02 21.83 -Testis (cohort = GTEx, N = 361) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Testis UBERON_0000473 20.57 3.47 13.28 17.95 20.28 22.95 30.33 -Thyroid (cohort = GTEx, N = 653) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Thyroid UBERON_0002046 18.4 4.17 4.99 15.65 17.94 20.71 37.77 -Uterus (cohort = GTEx, N = 142) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Uterus UBERON_0000995 17.86 4.4 10.39 14.66 17.04 21 37.98 -Vagina (cohort = GTEx, N = 156) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Vagina UBERON_0000996 13.63 3.72 6.02 10.65 13.57 16.66 22.92 +x_labels Gene_Ensembl_ID Gene_symbol PMTL Dataset Disease GTEx_tissue_subgroup EFO MONDO GTEx_tissue_subgroup_UBERON TPM_mean TPM_sd TPM_min TPM_25th_percentile TPM_median TPM_75th_percentile TPM_max +Neuroblastoma (Dataset = all_cohorts, N = 347) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) all_cohorts Neuroblastoma EFO_0000621 MONDO_0005072 25.31 13.28 3.32 15.16 22 34.62 69.06 +Neuroblastoma (Dataset = GMKF, N = 209) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GMKF Neuroblastoma EFO_0000621 MONDO_0005072 32.19 12.7 8.32 21.83 31.12 41.14 69.06 +Neuroblastoma (Dataset = TARGET, N = 149) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) TARGET Neuroblastoma EFO_0000621 MONDO_0005072 15.93 6.69 3.32 11.27 15.1 20.03 37.21 +Adipose - Subcutaneous (Dataset = GTEx, N = 663) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Subcutaneous UBERON_0002190 12.82 2.87 4.28 10.93 12.52 14.49 31.91 +Adipose - Visceral (Omentum) (Dataset = GTEx, N = 541) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Visceral (Omentum) UBERON_0010414 10.51 3.39 2.39 7.84 10.25 12.89 24.23 +Adrenal Gland (Dataset = GTEx, N = 258) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Adrenal Gland UBERON_0002369 6.08 1.32 2.22 5.31 6.03 6.91 10.85 +Artery - Aorta (Dataset = GTEx, N = 432) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Aorta UBERON_0001496 13.14 2.72 5.41 11.31 12.96 14.79 24.63 +Artery - Coronary (Dataset = GTEx, N = 240) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Coronary UBERON_0001621 12.43 3.46 4.44 9.96 11.8 14.15 23.58 +Artery - Tibial (Dataset = GTEx, N = 663) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Tibial UBERON_0007610 16.02 3.65 3.67 13.7 15.83 17.99 32.95 +Bladder (Dataset = GTEx, N = 21) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Bladder UBERON_0001255 15.52 6.04 6.36 11.79 12.95 20.06 29.41 +Blood (Dataset = GTEx, N = 755) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Blood UBERON_0013756 6.38 3.8 0.36 3.73 5.53 7.93 30.85 +Brain - Amygdala (Dataset = GTEx, N = 152) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Amygdala UBERON_0001876 5.09 2.49 0.77 3.26 4.67 6.85 12.19 +Brain - Anterior cingulate cortex (BA24) (Dataset = GTEx, N = 176) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Anterior cingulate cortex (BA24) UBERON_0009835 7.78 4.2 1.53 4.62 7.13 9.88 24.3 +Brain - Caudate (basal ganglia) (Dataset = GTEx, N = 246) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Caudate (basal ganglia) UBERON_0001873 6.87 3.73 0.77 3.89 6.64 9.37 22.01 +Brain - Cerebellum (Dataset = GTEx, N = 456) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cerebellum UBERON_0002037 23.77 8.18 4.58 18.59 23.31 28.61 59.09 +Brain - Cortex (Dataset = GTEx, N = 255) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cortex UBERON_0001870 8.42 3.06 1.78 6.34 8.39 10.38 20.64 +Brain - Frontal Cortex (BA9) (Dataset = GTEx, N = 209) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Frontal Cortex (BA9) UBERON_0009834 11.8 5.24 1.68 7.94 11.98 15.12 32.8 +Brain - Hippocampus (Dataset = GTEx, N = 197) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hippocampus UBERON_0001954 5.63 2.99 0.99 3.4 5.13 7.28 17.57 +Brain - Hypothalamus (Dataset = GTEx, N = 202) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hypothalamus UBERON_0001898 7.08 3.92 0.84 4.22 6.48 9.27 24.09 +Brain - Nucleus accumbens (basal ganglia) (Dataset = GTEx, N = 246) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Nucleus accumbens (basal ganglia) UBERON_0001882 7.97 4.44 0.77 4.76 7.81 10.75 22.12 +Brain - Putamen (basal ganglia) (Dataset = GTEx, N = 205) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Putamen (basal ganglia) UBERON_0001874 5.57 3.36 0.77 3.04 5.08 7.41 21.08 +Brain - Spinal cord (cervical c-1) (Dataset = GTEx, N = 159) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Spinal cord (cervical c-1) UBERON_0006469 5.98 2.58 1.09 4.28 5.81 7.48 14.2 +Brain - Substantia nigra (Dataset = GTEx, N = 139) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Substantia nigra UBERON_0002038 4.69 2.36 1.07 2.9 4.31 6.11 12.65 +Breast - Mammary Tissue (Dataset = GTEx, N = 459) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Breast - Mammary Tissue UBERON_0008367 13.52 4.74 4.38 9.63 12.91 16.74 28.59 +Cells - Cultured fibroblasts (Dataset = GTEx, N = 504) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cells - Cultured fibroblasts 11.05 2.77 4.75 9.36 10.52 11.93 23.14 +Cells - EBV-transformed lymphocytes (Dataset = GTEx, N = 174) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cells - EBV-transformed lymphocytes 16.82 5.02 6.68 13.51 16.31 19.28 40.77 +Cervix - Ectocervix (Dataset = GTEx, N = 9) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Ectocervix UBERON_0012249 14.89 4.3 8.52 12.25 14.82 16.37 23.71 +Cervix - Endocervix (Dataset = GTEx, N = 10) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Endocervix UBERON_0000458 16.39 2.95 12.68 14.5 15.54 18.15 21.4 +Colon - Sigmoid (Dataset = GTEx, N = 373) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Sigmoid UBERON_0001159 12.52 2.95 2.89 10.76 12.66 14.22 23.28 +Colon - Transverse (Dataset = GTEx, N = 406) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Transverse UBERON_0001157 8.88 3.67 3.13 5.87 7.91 11.19 21.44 +Esophagus - Gastroesophageal Junction (Dataset = GTEx, N = 375) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Gastroesophageal Junction UBERON_0004550 12.04 3.04 4.02 10 11.75 13.82 24.94 +Esophagus - Mucosa (Dataset = GTEx, N = 555) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Mucosa UBERON_0006920 7.66 1.85 2.77 6.44 7.44 8.71 18.73 +Esophagus - Muscularis (Dataset = GTEx, N = 515) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Muscularis UBERON_0004648 12.05 2.77 4.53 10.2 11.93 13.83 23.34 +Fallopian Tube (Dataset = GTEx, N = 9) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Fallopian Tube UBERON_0003889 14.97 3.73 8.41 12.7 16.7 16.96 19.98 +Heart - Atrial Appendage (Dataset = GTEx, N = 429) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Atrial Appendage UBERON_0006631 5.31 1.75 1.05 4.12 5.05 6.36 11.83 +Heart - Left Ventricle (Dataset = GTEx, N = 432) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Left Ventricle UBERON_0006566 3.35 1.66 0.52 2.43 3.31 4.13 14.39 +Kidney - Cortex (Dataset = GTEx, N = 85) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Cortex UBERON_0001225 6.67 4.04 2.38 4.05 5.39 7.58 23 +Kidney - Medulla (Dataset = GTEx, N = 4) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Medulla UBERON_0001293 8.9 3.06 5.3 6.99 9.12 11.04 12.07 +Liver (Dataset = GTEx, N = 226) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Liver UBERON_0001114 3.63 0.95 1.15 2.97 3.53 4.22 7.74 +Lung (Dataset = GTEx, N = 578) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Lung UBERON_0008952 16.39 4.91 6.11 12.79 15.59 18.8 37.04 +Minor Salivary Gland (Dataset = GTEx, N = 162) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Minor Salivary Gland UBERON_0006330 8.57 2.06 3.73 7.14 8.49 9.87 14.97 +Muscle - Skeletal (Dataset = GTEx, N = 803) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Muscle - Skeletal UBERON_0011907 4.85 1.84 1 3.56 4.56 5.74 14.81 +Nerve - Tibial (Dataset = GTEx, N = 619) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Nerve - Tibial UBERON_0001323 16.83 3.21 8.21 14.73 16.65 18.47 46.67 +Ovary (Dataset = GTEx, N = 180) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Ovary UBERON_0000992 17.3 3.94 8.23 14.5 16.94 19.15 32.61 +Pancreas (Dataset = GTEx, N = 328) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Pancreas UBERON_0001150 4.44 1.49 1.83 3.43 4.19 5.08 15.2 +Pituitary (Dataset = GTEx, N = 283) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Pituitary UBERON_0000007 15.06 3.21 6.49 13.16 14.88 16.56 27.8 +Prostate (Dataset = GTEx, N = 245) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Prostate UBERON_0002367 13.59 3.43 5.21 10.97 13.49 15.78 26.64 +Skin - Not Sun Exposed (Suprapubic) (Dataset = GTEx, N = 604) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Not Sun Exposed (Suprapubic) UBERON_0036149 13.63 3.14 5.81 11.49 13.68 15.46 28.18 +Skin - Sun Exposed (Lower leg) (Dataset = GTEx, N = 701) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Sun Exposed (Lower leg) UBERON_0004264 14.29 3.23 5.23 12.1 14.05 16.32 25.49 +Small Intestine - Terminal Ileum (Dataset = GTEx, N = 187) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Small Intestine - Terminal Ileum UBERON_0001211 9.85 4.2 3.46 6.53 8.97 11.98 25.59 +Spleen (Dataset = GTEx, N = 241) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Spleen UBERON_0002106 10.3 3.13 3.4 8.18 9.55 11.69 20.61 +Stomach (Dataset = GTEx, N = 359) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Stomach UBERON_0000945 8.41 3.06 3.57 6.25 7.64 10.02 21.83 +Testis (Dataset = GTEx, N = 361) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Testis UBERON_0000473 20.57 3.47 13.28 17.95 20.28 22.95 30.33 +Thyroid (Dataset = GTEx, N = 653) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Thyroid UBERON_0002046 18.4 4.17 4.99 15.65 17.94 20.71 37.77 +Uterus (Dataset = GTEx, N = 142) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Uterus UBERON_0000995 17.86 4.4 10.39 14.66 17.04 21 37.98 +Vagina (Dataset = GTEx, N = 156) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Vagina UBERON_0000996 13.63 3.72 6.02 10.65 13.57 16.66 22.92 diff --git a/tests/results/test-tpm-gene-disease-gtex-ENSG00000157764-EFO_0005543.tsv b/tests/results/test-tpm-gene-disease-gtex-ENSG00000157764-EFO_0005543.tsv deleted file mode 100644 index 63c8a95..0000000 --- a/tests/results/test-tpm-gene-disease-gtex-ENSG00000157764-EFO_0005543.tsv +++ /dev/null @@ -1,56 +0,0 @@ -x_labels Gene_Ensembl_ID Gene_symbol PMTL cohort Disease GTEx_tissue_subgroup EFO MONDO GTEx_tissue_subgroup_UBERON TPM_mean TPM_sd TPM_min TPM_25th_percentile TPM_median TPM_75th_percentile TPM_max -High-grade glioma/astrocytoma (cohort = PBTA, N = 51) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA High-grade glioma/astrocytoma EFO_0005543 MONDO_0100342 8.24 3.4 1.02 5.94 8.04 10 19.39 -Low-grade glioma/astrocytoma (cohort = PBTA, N = 237) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Low-grade glioma/astrocytoma EFO_0005543 MONDO_0016685 7.9 3.34 1.63 5.72 7.55 9.61 26.49 -Adipose - Subcutaneous (cohort = GTEx, N = 663) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Subcutaneous UBERON_0002190 12.82 2.87 4.28 10.93 12.52 14.49 31.91 -Adipose - Visceral (Omentum) (cohort = GTEx, N = 541) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Visceral (Omentum) UBERON_0010414 10.51 3.39 2.39 7.84 10.25 12.89 24.23 -Adrenal Gland (cohort = GTEx, N = 258) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Adrenal Gland UBERON_0002369 6.08 1.32 2.22 5.31 6.03 6.91 10.85 -Artery - Aorta (cohort = GTEx, N = 432) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Aorta UBERON_0001496 13.14 2.72 5.41 11.31 12.96 14.79 24.63 -Artery - Coronary (cohort = GTEx, N = 240) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Coronary UBERON_0001621 12.43 3.46 4.44 9.96 11.8 14.15 23.58 -Artery - Tibial (cohort = GTEx, N = 663) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Tibial UBERON_0007610 16.02 3.65 3.67 13.7 15.83 17.99 32.95 -Bladder (cohort = GTEx, N = 21) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Bladder UBERON_0001255 15.52 6.04 6.36 11.79 12.95 20.06 29.41 -Blood (cohort = GTEx, N = 755) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Blood UBERON_0013756 6.38 3.8 0.36 3.73 5.53 7.93 30.85 -Brain - Amygdala (cohort = GTEx, N = 152) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Amygdala UBERON_0001876 5.09 2.49 0.77 3.26 4.67 6.85 12.19 -Brain - Anterior cingulate cortex (BA24) (cohort = GTEx, N = 176) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Anterior cingulate cortex (BA24) UBERON_0009835 7.78 4.2 1.53 4.62 7.13 9.88 24.3 -Brain - Caudate (basal ganglia) (cohort = GTEx, N = 246) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Caudate (basal ganglia) UBERON_0001873 6.87 3.73 0.77 3.89 6.64 9.37 22.01 -Brain - Cerebellum (cohort = GTEx, N = 456) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cerebellum UBERON_0002037 23.77 8.18 4.58 18.59 23.31 28.61 59.09 -Brain - Cortex (cohort = GTEx, N = 255) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cortex UBERON_0001870 8.42 3.06 1.78 6.34 8.39 10.38 20.64 -Brain - Frontal Cortex (BA9) (cohort = GTEx, N = 209) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Frontal Cortex (BA9) UBERON_0009834 11.8 5.24 1.68 7.94 11.98 15.12 32.8 -Brain - Hippocampus (cohort = GTEx, N = 197) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hippocampus UBERON_0001954 5.63 2.99 0.99 3.4 5.13 7.28 17.57 -Brain - Hypothalamus (cohort = GTEx, N = 202) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hypothalamus UBERON_0001898 7.08 3.92 0.84 4.22 6.48 9.27 24.09 -Brain - Nucleus accumbens (basal ganglia) (cohort = GTEx, N = 246) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Nucleus accumbens (basal ganglia) UBERON_0001882 7.97 4.44 0.77 4.76 7.81 10.75 22.12 -Brain - Putamen (basal ganglia) (cohort = GTEx, N = 205) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Putamen (basal ganglia) UBERON_0001874 5.57 3.36 0.77 3.04 5.08 7.41 21.08 -Brain - Spinal cord (cervical c-1) (cohort = GTEx, N = 159) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Spinal cord (cervical c-1) UBERON_0006469 5.98 2.58 1.09 4.28 5.81 7.48 14.2 -Brain - Substantia nigra (cohort = GTEx, N = 139) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Substantia nigra UBERON_0002038 4.69 2.36 1.07 2.9 4.31 6.11 12.65 -Breast - Mammary Tissue (cohort = GTEx, N = 459) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Breast - Mammary Tissue UBERON_0008367 13.52 4.74 4.38 9.63 12.91 16.74 28.59 -Cells - Cultured fibroblasts (cohort = GTEx, N = 504) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cells - Cultured fibroblasts 11.05 2.77 4.75 9.36 10.52 11.93 23.14 -Cells - EBV-transformed lymphocytes (cohort = GTEx, N = 174) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cells - EBV-transformed lymphocytes 16.82 5.02 6.68 13.51 16.31 19.28 40.77 -Cervix - Ectocervix (cohort = GTEx, N = 9) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Ectocervix UBERON_0012249 14.89 4.3 8.52 12.25 14.82 16.37 23.71 -Cervix - Endocervix (cohort = GTEx, N = 10) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Endocervix UBERON_0000458 16.39 2.95 12.68 14.5 15.54 18.15 21.4 -Colon - Sigmoid (cohort = GTEx, N = 373) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Sigmoid UBERON_0001159 12.52 2.95 2.89 10.76 12.66 14.22 23.28 -Colon - Transverse (cohort = GTEx, N = 406) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Transverse UBERON_0001157 8.88 3.67 3.13 5.87 7.91 11.19 21.44 -Esophagus - Gastroesophageal Junction (cohort = GTEx, N = 375) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Gastroesophageal Junction UBERON_0004550 12.04 3.04 4.02 10 11.75 13.82 24.94 -Esophagus - Mucosa (cohort = GTEx, N = 555) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Mucosa UBERON_0006920 7.66 1.85 2.77 6.44 7.44 8.71 18.73 -Esophagus - Muscularis (cohort = GTEx, N = 515) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Muscularis UBERON_0004648 12.05 2.77 4.53 10.2 11.93 13.83 23.34 -Fallopian Tube (cohort = GTEx, N = 9) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Fallopian Tube UBERON_0003889 14.97 3.73 8.41 12.7 16.7 16.96 19.98 -Heart - Atrial Appendage (cohort = GTEx, N = 429) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Atrial Appendage UBERON_0006631 5.31 1.75 1.05 4.12 5.05 6.36 11.83 -Heart - Left Ventricle (cohort = GTEx, N = 432) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Left Ventricle UBERON_0006566 3.35 1.66 0.52 2.43 3.31 4.13 14.39 -Kidney - Cortex (cohort = GTEx, N = 85) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Cortex UBERON_0001225 6.67 4.04 2.38 4.05 5.39 7.58 23 -Kidney - Medulla (cohort = GTEx, N = 4) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Medulla UBERON_0001293 8.9 3.06 5.3 6.99 9.12 11.04 12.07 -Liver (cohort = GTEx, N = 226) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Liver UBERON_0001114 3.63 0.95 1.15 2.97 3.53 4.22 7.74 -Lung (cohort = GTEx, N = 578) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Lung UBERON_0008952 16.39 4.91 6.11 12.79 15.59 18.8 37.04 -Minor Salivary Gland (cohort = GTEx, N = 162) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Minor Salivary Gland UBERON_0006330 8.57 2.06 3.73 7.14 8.49 9.87 14.97 -Muscle - Skeletal (cohort = GTEx, N = 803) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Muscle - Skeletal UBERON_0011907 4.85 1.84 1 3.56 4.56 5.74 14.81 -Nerve - Tibial (cohort = GTEx, N = 619) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Nerve - Tibial UBERON_0001323 16.83 3.21 8.21 14.73 16.65 18.47 46.67 -Ovary (cohort = GTEx, N = 180) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Ovary UBERON_0000992 17.3 3.94 8.23 14.5 16.94 19.15 32.61 -Pancreas (cohort = GTEx, N = 328) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Pancreas UBERON_0001150 4.44 1.49 1.83 3.43 4.19 5.08 15.2 -Pituitary (cohort = GTEx, N = 283) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Pituitary UBERON_0000007 15.06 3.21 6.49 13.16 14.88 16.56 27.8 -Prostate (cohort = GTEx, N = 245) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Prostate UBERON_0002367 13.59 3.43 5.21 10.97 13.49 15.78 26.64 -Skin - Not Sun Exposed (Suprapubic) (cohort = GTEx, N = 604) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Not Sun Exposed (Suprapubic) UBERON_0036149 13.63 3.14 5.81 11.49 13.68 15.46 28.18 -Skin - Sun Exposed (Lower leg) (cohort = GTEx, N = 701) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Sun Exposed (Lower leg) UBERON_0004264 14.29 3.23 5.23 12.1 14.05 16.32 25.49 -Small Intestine - Terminal Ileum (cohort = GTEx, N = 187) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Small Intestine - Terminal Ileum UBERON_0001211 9.85 4.2 3.46 6.53 8.97 11.98 25.59 -Spleen (cohort = GTEx, N = 241) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Spleen UBERON_0002106 10.3 3.13 3.4 8.18 9.55 11.69 20.61 -Stomach (cohort = GTEx, N = 359) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Stomach UBERON_0000945 8.41 3.06 3.57 6.25 7.64 10.02 21.83 -Testis (cohort = GTEx, N = 361) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Testis UBERON_0000473 20.57 3.47 13.28 17.95 20.28 22.95 30.33 -Thyroid (cohort = GTEx, N = 653) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Thyroid UBERON_0002046 18.4 4.17 4.99 15.65 17.94 20.71 37.77 -Uterus (cohort = GTEx, N = 142) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Uterus UBERON_0000995 17.86 4.4 10.39 14.66 17.04 21 37.98 -Vagina (cohort = GTEx, N = 156) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Vagina UBERON_0000996 13.63 3.72 6.02 10.65 13.57 16.66 22.92 diff --git a/tests/results/test-tpm-gene-disease-gtex-ENSG00000157764-EFO_0007206.tsv b/tests/results/test-tpm-gene-disease-gtex-ENSG00000157764-EFO_0007206.tsv deleted file mode 100644 index a02b01d..0000000 --- a/tests/results/test-tpm-gene-disease-gtex-ENSG00000157764-EFO_0007206.tsv +++ /dev/null @@ -1,56 +0,0 @@ -x_labels Gene_Ensembl_ID Gene_symbol PMTL cohort Disease GTEx_tissue_subgroup EFO MONDO GTEx_tissue_subgroup_UBERON TPM_mean TPM_sd TPM_min TPM_25th_percentile TPM_median TPM_75th_percentile TPM_max -Choroid plexus carcinoma (cohort = PBTA, N = 4) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Choroid plexus carcinoma EFO_0007206 MONDO_0016718 5.78 2.77 3.39 4.07 5.04 6.76 9.66 -Choroid plexus cyst (cohort = PBTA, N = 1) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Choroid plexus cyst EFO_0007206 1.46 1.46 1.46 1.46 1.46 1.46 -Adipose - Subcutaneous (cohort = GTEx, N = 663) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Subcutaneous UBERON_0002190 12.82 2.87 4.28 10.93 12.52 14.49 31.91 -Adipose - Visceral (Omentum) (cohort = GTEx, N = 541) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Visceral (Omentum) UBERON_0010414 10.51 3.39 2.39 7.84 10.25 12.89 24.23 -Adrenal Gland (cohort = GTEx, N = 258) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Adrenal Gland UBERON_0002369 6.08 1.32 2.22 5.31 6.03 6.91 10.85 -Artery - Aorta (cohort = GTEx, N = 432) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Aorta UBERON_0001496 13.14 2.72 5.41 11.31 12.96 14.79 24.63 -Artery - Coronary (cohort = GTEx, N = 240) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Coronary UBERON_0001621 12.43 3.46 4.44 9.96 11.8 14.15 23.58 -Artery - Tibial (cohort = GTEx, N = 663) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Tibial UBERON_0007610 16.02 3.65 3.67 13.7 15.83 17.99 32.95 -Bladder (cohort = GTEx, N = 21) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Bladder UBERON_0001255 15.52 6.04 6.36 11.79 12.95 20.06 29.41 -Blood (cohort = GTEx, N = 755) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Blood UBERON_0013756 6.38 3.8 0.36 3.73 5.53 7.93 30.85 -Brain - Amygdala (cohort = GTEx, N = 152) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Amygdala UBERON_0001876 5.09 2.49 0.77 3.26 4.67 6.85 12.19 -Brain - Anterior cingulate cortex (BA24) (cohort = GTEx, N = 176) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Anterior cingulate cortex (BA24) UBERON_0009835 7.78 4.2 1.53 4.62 7.13 9.88 24.3 -Brain - Caudate (basal ganglia) (cohort = GTEx, N = 246) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Caudate (basal ganglia) UBERON_0001873 6.87 3.73 0.77 3.89 6.64 9.37 22.01 -Brain - Cerebellum (cohort = GTEx, N = 456) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cerebellum UBERON_0002037 23.77 8.18 4.58 18.59 23.31 28.61 59.09 -Brain - Cortex (cohort = GTEx, N = 255) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cortex UBERON_0001870 8.42 3.06 1.78 6.34 8.39 10.38 20.64 -Brain - Frontal Cortex (BA9) (cohort = GTEx, N = 209) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Frontal Cortex (BA9) UBERON_0009834 11.8 5.24 1.68 7.94 11.98 15.12 32.8 -Brain - Hippocampus (cohort = GTEx, N = 197) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hippocampus UBERON_0001954 5.63 2.99 0.99 3.4 5.13 7.28 17.57 -Brain - Hypothalamus (cohort = GTEx, N = 202) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hypothalamus UBERON_0001898 7.08 3.92 0.84 4.22 6.48 9.27 24.09 -Brain - Nucleus accumbens (basal ganglia) (cohort = GTEx, N = 246) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Nucleus accumbens (basal ganglia) UBERON_0001882 7.97 4.44 0.77 4.76 7.81 10.75 22.12 -Brain - Putamen (basal ganglia) (cohort = GTEx, N = 205) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Putamen (basal ganglia) UBERON_0001874 5.57 3.36 0.77 3.04 5.08 7.41 21.08 -Brain - Spinal cord (cervical c-1) (cohort = GTEx, N = 159) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Spinal cord (cervical c-1) UBERON_0006469 5.98 2.58 1.09 4.28 5.81 7.48 14.2 -Brain - Substantia nigra (cohort = GTEx, N = 139) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Substantia nigra UBERON_0002038 4.69 2.36 1.07 2.9 4.31 6.11 12.65 -Breast - Mammary Tissue (cohort = GTEx, N = 459) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Breast - Mammary Tissue UBERON_0008367 13.52 4.74 4.38 9.63 12.91 16.74 28.59 -Cells - Cultured fibroblasts (cohort = GTEx, N = 504) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cells - Cultured fibroblasts 11.05 2.77 4.75 9.36 10.52 11.93 23.14 -Cells - EBV-transformed lymphocytes (cohort = GTEx, N = 174) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cells - EBV-transformed lymphocytes 16.82 5.02 6.68 13.51 16.31 19.28 40.77 -Cervix - Ectocervix (cohort = GTEx, N = 9) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Ectocervix UBERON_0012249 14.89 4.3 8.52 12.25 14.82 16.37 23.71 -Cervix - Endocervix (cohort = GTEx, N = 10) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Endocervix UBERON_0000458 16.39 2.95 12.68 14.5 15.54 18.15 21.4 -Colon - Sigmoid (cohort = GTEx, N = 373) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Sigmoid UBERON_0001159 12.52 2.95 2.89 10.76 12.66 14.22 23.28 -Colon - Transverse (cohort = GTEx, N = 406) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Transverse UBERON_0001157 8.88 3.67 3.13 5.87 7.91 11.19 21.44 -Esophagus - Gastroesophageal Junction (cohort = GTEx, N = 375) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Gastroesophageal Junction UBERON_0004550 12.04 3.04 4.02 10 11.75 13.82 24.94 -Esophagus - Mucosa (cohort = GTEx, N = 555) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Mucosa UBERON_0006920 7.66 1.85 2.77 6.44 7.44 8.71 18.73 -Esophagus - Muscularis (cohort = GTEx, N = 515) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Muscularis UBERON_0004648 12.05 2.77 4.53 10.2 11.93 13.83 23.34 -Fallopian Tube (cohort = GTEx, N = 9) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Fallopian Tube UBERON_0003889 14.97 3.73 8.41 12.7 16.7 16.96 19.98 -Heart - Atrial Appendage (cohort = GTEx, N = 429) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Atrial Appendage UBERON_0006631 5.31 1.75 1.05 4.12 5.05 6.36 11.83 -Heart - Left Ventricle (cohort = GTEx, N = 432) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Left Ventricle UBERON_0006566 3.35 1.66 0.52 2.43 3.31 4.13 14.39 -Kidney - Cortex (cohort = GTEx, N = 85) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Cortex UBERON_0001225 6.67 4.04 2.38 4.05 5.39 7.58 23 -Kidney - Medulla (cohort = GTEx, N = 4) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Medulla UBERON_0001293 8.9 3.06 5.3 6.99 9.12 11.04 12.07 -Liver (cohort = GTEx, N = 226) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Liver UBERON_0001114 3.63 0.95 1.15 2.97 3.53 4.22 7.74 -Lung (cohort = GTEx, N = 578) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Lung UBERON_0008952 16.39 4.91 6.11 12.79 15.59 18.8 37.04 -Minor Salivary Gland (cohort = GTEx, N = 162) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Minor Salivary Gland UBERON_0006330 8.57 2.06 3.73 7.14 8.49 9.87 14.97 -Muscle - Skeletal (cohort = GTEx, N = 803) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Muscle - Skeletal UBERON_0011907 4.85 1.84 1 3.56 4.56 5.74 14.81 -Nerve - Tibial (cohort = GTEx, N = 619) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Nerve - Tibial UBERON_0001323 16.83 3.21 8.21 14.73 16.65 18.47 46.67 -Ovary (cohort = GTEx, N = 180) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Ovary UBERON_0000992 17.3 3.94 8.23 14.5 16.94 19.15 32.61 -Pancreas (cohort = GTEx, N = 328) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Pancreas UBERON_0001150 4.44 1.49 1.83 3.43 4.19 5.08 15.2 -Pituitary (cohort = GTEx, N = 283) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Pituitary UBERON_0000007 15.06 3.21 6.49 13.16 14.88 16.56 27.8 -Prostate (cohort = GTEx, N = 245) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Prostate UBERON_0002367 13.59 3.43 5.21 10.97 13.49 15.78 26.64 -Skin - Not Sun Exposed (Suprapubic) (cohort = GTEx, N = 604) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Not Sun Exposed (Suprapubic) UBERON_0036149 13.63 3.14 5.81 11.49 13.68 15.46 28.18 -Skin - Sun Exposed (Lower leg) (cohort = GTEx, N = 701) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Sun Exposed (Lower leg) UBERON_0004264 14.29 3.23 5.23 12.1 14.05 16.32 25.49 -Small Intestine - Terminal Ileum (cohort = GTEx, N = 187) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Small Intestine - Terminal Ileum UBERON_0001211 9.85 4.2 3.46 6.53 8.97 11.98 25.59 -Spleen (cohort = GTEx, N = 241) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Spleen UBERON_0002106 10.3 3.13 3.4 8.18 9.55 11.69 20.61 -Stomach (cohort = GTEx, N = 359) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Stomach UBERON_0000945 8.41 3.06 3.57 6.25 7.64 10.02 21.83 -Testis (cohort = GTEx, N = 361) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Testis UBERON_0000473 20.57 3.47 13.28 17.95 20.28 22.95 30.33 -Thyroid (cohort = GTEx, N = 653) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Thyroid UBERON_0002046 18.4 4.17 4.99 15.65 17.94 20.71 37.77 -Uterus (cohort = GTEx, N = 142) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Uterus UBERON_0000995 17.86 4.4 10.39 14.66 17.04 21 37.98 -Vagina (cohort = GTEx, N = 156) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Vagina UBERON_0000996 13.63 3.72 6.02 10.65 13.57 16.66 22.92 diff --git a/tests/results/test-tpm-gene-disease-gtex-ENSG00000157764-MONDO_0016680.tsv b/tests/results/test-tpm-gene-disease-gtex-ENSG00000157764-MONDO_0016680.tsv new file mode 100644 index 0000000..4eb0df5 --- /dev/null +++ b/tests/results/test-tpm-gene-disease-gtex-ENSG00000157764-MONDO_0016680.tsv @@ -0,0 +1,55 @@ +x_labels Gene_Ensembl_ID Gene_symbol PMTL Dataset Disease GTEx_tissue_subgroup EFO MONDO GTEx_tissue_subgroup_UBERON TPM_mean TPM_sd TPM_min TPM_25th_percentile TPM_median TPM_75th_percentile TPM_max +High-grade glioma/astrocytoma (Dataset = PBTA, N = 51) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA High-grade glioma/astrocytoma MONDO_0016680 MONDO_0100342 8.24 3.4 1.02 5.94 8.04 10 19.39 +Adipose - Subcutaneous (Dataset = GTEx, N = 663) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Subcutaneous UBERON_0002190 12.82 2.87 4.28 10.93 12.52 14.49 31.91 +Adipose - Visceral (Omentum) (Dataset = GTEx, N = 541) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Visceral (Omentum) UBERON_0010414 10.51 3.39 2.39 7.84 10.25 12.89 24.23 +Adrenal Gland (Dataset = GTEx, N = 258) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Adrenal Gland UBERON_0002369 6.08 1.32 2.22 5.31 6.03 6.91 10.85 +Artery - Aorta (Dataset = GTEx, N = 432) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Aorta UBERON_0001496 13.14 2.72 5.41 11.31 12.96 14.79 24.63 +Artery - Coronary (Dataset = GTEx, N = 240) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Coronary UBERON_0001621 12.43 3.46 4.44 9.96 11.8 14.15 23.58 +Artery - Tibial (Dataset = GTEx, N = 663) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Tibial UBERON_0007610 16.02 3.65 3.67 13.7 15.83 17.99 32.95 +Bladder (Dataset = GTEx, N = 21) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Bladder UBERON_0001255 15.52 6.04 6.36 11.79 12.95 20.06 29.41 +Blood (Dataset = GTEx, N = 755) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Blood UBERON_0013756 6.38 3.8 0.36 3.73 5.53 7.93 30.85 +Brain - Amygdala (Dataset = GTEx, N = 152) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Amygdala UBERON_0001876 5.09 2.49 0.77 3.26 4.67 6.85 12.19 +Brain - Anterior cingulate cortex (BA24) (Dataset = GTEx, N = 176) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Anterior cingulate cortex (BA24) UBERON_0009835 7.78 4.2 1.53 4.62 7.13 9.88 24.3 +Brain - Caudate (basal ganglia) (Dataset = GTEx, N = 246) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Caudate (basal ganglia) UBERON_0001873 6.87 3.73 0.77 3.89 6.64 9.37 22.01 +Brain - Cerebellum (Dataset = GTEx, N = 456) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cerebellum UBERON_0002037 23.77 8.18 4.58 18.59 23.31 28.61 59.09 +Brain - Cortex (Dataset = GTEx, N = 255) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cortex UBERON_0001870 8.42 3.06 1.78 6.34 8.39 10.38 20.64 +Brain - Frontal Cortex (BA9) (Dataset = GTEx, N = 209) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Frontal Cortex (BA9) UBERON_0009834 11.8 5.24 1.68 7.94 11.98 15.12 32.8 +Brain - Hippocampus (Dataset = GTEx, N = 197) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hippocampus UBERON_0001954 5.63 2.99 0.99 3.4 5.13 7.28 17.57 +Brain - Hypothalamus (Dataset = GTEx, N = 202) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hypothalamus UBERON_0001898 7.08 3.92 0.84 4.22 6.48 9.27 24.09 +Brain - Nucleus accumbens (basal ganglia) (Dataset = GTEx, N = 246) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Nucleus accumbens (basal ganglia) UBERON_0001882 7.97 4.44 0.77 4.76 7.81 10.75 22.12 +Brain - Putamen (basal ganglia) (Dataset = GTEx, N = 205) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Putamen (basal ganglia) UBERON_0001874 5.57 3.36 0.77 3.04 5.08 7.41 21.08 +Brain - Spinal cord (cervical c-1) (Dataset = GTEx, N = 159) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Spinal cord (cervical c-1) UBERON_0006469 5.98 2.58 1.09 4.28 5.81 7.48 14.2 +Brain - Substantia nigra (Dataset = GTEx, N = 139) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Substantia nigra UBERON_0002038 4.69 2.36 1.07 2.9 4.31 6.11 12.65 +Breast - Mammary Tissue (Dataset = GTEx, N = 459) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Breast - Mammary Tissue UBERON_0008367 13.52 4.74 4.38 9.63 12.91 16.74 28.59 +Cells - Cultured fibroblasts (Dataset = GTEx, N = 504) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cells - Cultured fibroblasts 11.05 2.77 4.75 9.36 10.52 11.93 23.14 +Cells - EBV-transformed lymphocytes (Dataset = GTEx, N = 174) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cells - EBV-transformed lymphocytes 16.82 5.02 6.68 13.51 16.31 19.28 40.77 +Cervix - Ectocervix (Dataset = GTEx, N = 9) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Ectocervix UBERON_0012249 14.89 4.3 8.52 12.25 14.82 16.37 23.71 +Cervix - Endocervix (Dataset = GTEx, N = 10) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Endocervix UBERON_0000458 16.39 2.95 12.68 14.5 15.54 18.15 21.4 +Colon - Sigmoid (Dataset = GTEx, N = 373) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Sigmoid UBERON_0001159 12.52 2.95 2.89 10.76 12.66 14.22 23.28 +Colon - Transverse (Dataset = GTEx, N = 406) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Transverse UBERON_0001157 8.88 3.67 3.13 5.87 7.91 11.19 21.44 +Esophagus - Gastroesophageal Junction (Dataset = GTEx, N = 375) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Gastroesophageal Junction UBERON_0004550 12.04 3.04 4.02 10 11.75 13.82 24.94 +Esophagus - Mucosa (Dataset = GTEx, N = 555) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Mucosa UBERON_0006920 7.66 1.85 2.77 6.44 7.44 8.71 18.73 +Esophagus - Muscularis (Dataset = GTEx, N = 515) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Muscularis UBERON_0004648 12.05 2.77 4.53 10.2 11.93 13.83 23.34 +Fallopian Tube (Dataset = GTEx, N = 9) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Fallopian Tube UBERON_0003889 14.97 3.73 8.41 12.7 16.7 16.96 19.98 +Heart - Atrial Appendage (Dataset = GTEx, N = 429) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Atrial Appendage UBERON_0006631 5.31 1.75 1.05 4.12 5.05 6.36 11.83 +Heart - Left Ventricle (Dataset = GTEx, N = 432) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Left Ventricle UBERON_0006566 3.35 1.66 0.52 2.43 3.31 4.13 14.39 +Kidney - Cortex (Dataset = GTEx, N = 85) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Cortex UBERON_0001225 6.67 4.04 2.38 4.05 5.39 7.58 23 +Kidney - Medulla (Dataset = GTEx, N = 4) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Medulla UBERON_0001293 8.9 3.06 5.3 6.99 9.12 11.04 12.07 +Liver (Dataset = GTEx, N = 226) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Liver UBERON_0001114 3.63 0.95 1.15 2.97 3.53 4.22 7.74 +Lung (Dataset = GTEx, N = 578) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Lung UBERON_0008952 16.39 4.91 6.11 12.79 15.59 18.8 37.04 +Minor Salivary Gland (Dataset = GTEx, N = 162) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Minor Salivary Gland UBERON_0006330 8.57 2.06 3.73 7.14 8.49 9.87 14.97 +Muscle - Skeletal (Dataset = GTEx, N = 803) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Muscle - Skeletal UBERON_0011907 4.85 1.84 1 3.56 4.56 5.74 14.81 +Nerve - Tibial (Dataset = GTEx, N = 619) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Nerve - Tibial UBERON_0001323 16.83 3.21 8.21 14.73 16.65 18.47 46.67 +Ovary (Dataset = GTEx, N = 180) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Ovary UBERON_0000992 17.3 3.94 8.23 14.5 16.94 19.15 32.61 +Pancreas (Dataset = GTEx, N = 328) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Pancreas UBERON_0001150 4.44 1.49 1.83 3.43 4.19 5.08 15.2 +Pituitary (Dataset = GTEx, N = 283) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Pituitary UBERON_0000007 15.06 3.21 6.49 13.16 14.88 16.56 27.8 +Prostate (Dataset = GTEx, N = 245) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Prostate UBERON_0002367 13.59 3.43 5.21 10.97 13.49 15.78 26.64 +Skin - Not Sun Exposed (Suprapubic) (Dataset = GTEx, N = 604) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Not Sun Exposed (Suprapubic) UBERON_0036149 13.63 3.14 5.81 11.49 13.68 15.46 28.18 +Skin - Sun Exposed (Lower leg) (Dataset = GTEx, N = 701) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Sun Exposed (Lower leg) UBERON_0004264 14.29 3.23 5.23 12.1 14.05 16.32 25.49 +Small Intestine - Terminal Ileum (Dataset = GTEx, N = 187) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Small Intestine - Terminal Ileum UBERON_0001211 9.85 4.2 3.46 6.53 8.97 11.98 25.59 +Spleen (Dataset = GTEx, N = 241) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Spleen UBERON_0002106 10.3 3.13 3.4 8.18 9.55 11.69 20.61 +Stomach (Dataset = GTEx, N = 359) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Stomach UBERON_0000945 8.41 3.06 3.57 6.25 7.64 10.02 21.83 +Testis (Dataset = GTEx, N = 361) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Testis UBERON_0000473 20.57 3.47 13.28 17.95 20.28 22.95 30.33 +Thyroid (Dataset = GTEx, N = 653) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Thyroid UBERON_0002046 18.4 4.17 4.99 15.65 17.94 20.71 37.77 +Uterus (Dataset = GTEx, N = 142) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Uterus UBERON_0000995 17.86 4.4 10.39 14.66 17.04 21 37.98 +Vagina (Dataset = GTEx, N = 156) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Vagina UBERON_0000996 13.63 3.72 6.02 10.65 13.57 16.66 22.92 diff --git a/tests/results/test-tpm-gene-disease-gtex-ENSG00000157764-MONDO_0016685.tsv b/tests/results/test-tpm-gene-disease-gtex-ENSG00000157764-MONDO_0016685.tsv new file mode 100644 index 0000000..aebae99 --- /dev/null +++ b/tests/results/test-tpm-gene-disease-gtex-ENSG00000157764-MONDO_0016685.tsv @@ -0,0 +1,55 @@ +x_labels Gene_Ensembl_ID Gene_symbol PMTL Dataset Disease GTEx_tissue_subgroup EFO MONDO GTEx_tissue_subgroup_UBERON TPM_mean TPM_sd TPM_min TPM_25th_percentile TPM_median TPM_75th_percentile TPM_max +Low-grade glioma/astrocytoma (Dataset = PBTA, N = 237) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Low-grade glioma/astrocytoma MONDO_0016685 MONDO_0016685 7.9 3.34 1.63 5.72 7.55 9.61 26.49 +Adipose - Subcutaneous (Dataset = GTEx, N = 663) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Subcutaneous UBERON_0002190 12.82 2.87 4.28 10.93 12.52 14.49 31.91 +Adipose - Visceral (Omentum) (Dataset = GTEx, N = 541) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Visceral (Omentum) UBERON_0010414 10.51 3.39 2.39 7.84 10.25 12.89 24.23 +Adrenal Gland (Dataset = GTEx, N = 258) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Adrenal Gland UBERON_0002369 6.08 1.32 2.22 5.31 6.03 6.91 10.85 +Artery - Aorta (Dataset = GTEx, N = 432) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Aorta UBERON_0001496 13.14 2.72 5.41 11.31 12.96 14.79 24.63 +Artery - Coronary (Dataset = GTEx, N = 240) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Coronary UBERON_0001621 12.43 3.46 4.44 9.96 11.8 14.15 23.58 +Artery - Tibial (Dataset = GTEx, N = 663) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Tibial UBERON_0007610 16.02 3.65 3.67 13.7 15.83 17.99 32.95 +Bladder (Dataset = GTEx, N = 21) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Bladder UBERON_0001255 15.52 6.04 6.36 11.79 12.95 20.06 29.41 +Blood (Dataset = GTEx, N = 755) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Blood UBERON_0013756 6.38 3.8 0.36 3.73 5.53 7.93 30.85 +Brain - Amygdala (Dataset = GTEx, N = 152) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Amygdala UBERON_0001876 5.09 2.49 0.77 3.26 4.67 6.85 12.19 +Brain - Anterior cingulate cortex (BA24) (Dataset = GTEx, N = 176) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Anterior cingulate cortex (BA24) UBERON_0009835 7.78 4.2 1.53 4.62 7.13 9.88 24.3 +Brain - Caudate (basal ganglia) (Dataset = GTEx, N = 246) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Caudate (basal ganglia) UBERON_0001873 6.87 3.73 0.77 3.89 6.64 9.37 22.01 +Brain - Cerebellum (Dataset = GTEx, N = 456) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cerebellum UBERON_0002037 23.77 8.18 4.58 18.59 23.31 28.61 59.09 +Brain - Cortex (Dataset = GTEx, N = 255) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cortex UBERON_0001870 8.42 3.06 1.78 6.34 8.39 10.38 20.64 +Brain - Frontal Cortex (BA9) (Dataset = GTEx, N = 209) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Frontal Cortex (BA9) UBERON_0009834 11.8 5.24 1.68 7.94 11.98 15.12 32.8 +Brain - Hippocampus (Dataset = GTEx, N = 197) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hippocampus UBERON_0001954 5.63 2.99 0.99 3.4 5.13 7.28 17.57 +Brain - Hypothalamus (Dataset = GTEx, N = 202) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hypothalamus UBERON_0001898 7.08 3.92 0.84 4.22 6.48 9.27 24.09 +Brain - Nucleus accumbens (basal ganglia) (Dataset = GTEx, N = 246) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Nucleus accumbens (basal ganglia) UBERON_0001882 7.97 4.44 0.77 4.76 7.81 10.75 22.12 +Brain - Putamen (basal ganglia) (Dataset = GTEx, N = 205) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Putamen (basal ganglia) UBERON_0001874 5.57 3.36 0.77 3.04 5.08 7.41 21.08 +Brain - Spinal cord (cervical c-1) (Dataset = GTEx, N = 159) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Spinal cord (cervical c-1) UBERON_0006469 5.98 2.58 1.09 4.28 5.81 7.48 14.2 +Brain - Substantia nigra (Dataset = GTEx, N = 139) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Substantia nigra UBERON_0002038 4.69 2.36 1.07 2.9 4.31 6.11 12.65 +Breast - Mammary Tissue (Dataset = GTEx, N = 459) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Breast - Mammary Tissue UBERON_0008367 13.52 4.74 4.38 9.63 12.91 16.74 28.59 +Cells - Cultured fibroblasts (Dataset = GTEx, N = 504) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cells - Cultured fibroblasts 11.05 2.77 4.75 9.36 10.52 11.93 23.14 +Cells - EBV-transformed lymphocytes (Dataset = GTEx, N = 174) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cells - EBV-transformed lymphocytes 16.82 5.02 6.68 13.51 16.31 19.28 40.77 +Cervix - Ectocervix (Dataset = GTEx, N = 9) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Ectocervix UBERON_0012249 14.89 4.3 8.52 12.25 14.82 16.37 23.71 +Cervix - Endocervix (Dataset = GTEx, N = 10) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Endocervix UBERON_0000458 16.39 2.95 12.68 14.5 15.54 18.15 21.4 +Colon - Sigmoid (Dataset = GTEx, N = 373) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Sigmoid UBERON_0001159 12.52 2.95 2.89 10.76 12.66 14.22 23.28 +Colon - Transverse (Dataset = GTEx, N = 406) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Transverse UBERON_0001157 8.88 3.67 3.13 5.87 7.91 11.19 21.44 +Esophagus - Gastroesophageal Junction (Dataset = GTEx, N = 375) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Gastroesophageal Junction UBERON_0004550 12.04 3.04 4.02 10 11.75 13.82 24.94 +Esophagus - Mucosa (Dataset = GTEx, N = 555) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Mucosa UBERON_0006920 7.66 1.85 2.77 6.44 7.44 8.71 18.73 +Esophagus - Muscularis (Dataset = GTEx, N = 515) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Muscularis UBERON_0004648 12.05 2.77 4.53 10.2 11.93 13.83 23.34 +Fallopian Tube (Dataset = GTEx, N = 9) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Fallopian Tube UBERON_0003889 14.97 3.73 8.41 12.7 16.7 16.96 19.98 +Heart - Atrial Appendage (Dataset = GTEx, N = 429) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Atrial Appendage UBERON_0006631 5.31 1.75 1.05 4.12 5.05 6.36 11.83 +Heart - Left Ventricle (Dataset = GTEx, N = 432) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Left Ventricle UBERON_0006566 3.35 1.66 0.52 2.43 3.31 4.13 14.39 +Kidney - Cortex (Dataset = GTEx, N = 85) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Cortex UBERON_0001225 6.67 4.04 2.38 4.05 5.39 7.58 23 +Kidney - Medulla (Dataset = GTEx, N = 4) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Medulla UBERON_0001293 8.9 3.06 5.3 6.99 9.12 11.04 12.07 +Liver (Dataset = GTEx, N = 226) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Liver UBERON_0001114 3.63 0.95 1.15 2.97 3.53 4.22 7.74 +Lung (Dataset = GTEx, N = 578) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Lung UBERON_0008952 16.39 4.91 6.11 12.79 15.59 18.8 37.04 +Minor Salivary Gland (Dataset = GTEx, N = 162) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Minor Salivary Gland UBERON_0006330 8.57 2.06 3.73 7.14 8.49 9.87 14.97 +Muscle - Skeletal (Dataset = GTEx, N = 803) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Muscle - Skeletal UBERON_0011907 4.85 1.84 1 3.56 4.56 5.74 14.81 +Nerve - Tibial (Dataset = GTEx, N = 619) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Nerve - Tibial UBERON_0001323 16.83 3.21 8.21 14.73 16.65 18.47 46.67 +Ovary (Dataset = GTEx, N = 180) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Ovary UBERON_0000992 17.3 3.94 8.23 14.5 16.94 19.15 32.61 +Pancreas (Dataset = GTEx, N = 328) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Pancreas UBERON_0001150 4.44 1.49 1.83 3.43 4.19 5.08 15.2 +Pituitary (Dataset = GTEx, N = 283) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Pituitary UBERON_0000007 15.06 3.21 6.49 13.16 14.88 16.56 27.8 +Prostate (Dataset = GTEx, N = 245) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Prostate UBERON_0002367 13.59 3.43 5.21 10.97 13.49 15.78 26.64 +Skin - Not Sun Exposed (Suprapubic) (Dataset = GTEx, N = 604) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Not Sun Exposed (Suprapubic) UBERON_0036149 13.63 3.14 5.81 11.49 13.68 15.46 28.18 +Skin - Sun Exposed (Lower leg) (Dataset = GTEx, N = 701) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Sun Exposed (Lower leg) UBERON_0004264 14.29 3.23 5.23 12.1 14.05 16.32 25.49 +Small Intestine - Terminal Ileum (Dataset = GTEx, N = 187) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Small Intestine - Terminal Ileum UBERON_0001211 9.85 4.2 3.46 6.53 8.97 11.98 25.59 +Spleen (Dataset = GTEx, N = 241) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Spleen UBERON_0002106 10.3 3.13 3.4 8.18 9.55 11.69 20.61 +Stomach (Dataset = GTEx, N = 359) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Stomach UBERON_0000945 8.41 3.06 3.57 6.25 7.64 10.02 21.83 +Testis (Dataset = GTEx, N = 361) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Testis UBERON_0000473 20.57 3.47 13.28 17.95 20.28 22.95 30.33 +Thyroid (Dataset = GTEx, N = 653) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Thyroid UBERON_0002046 18.4 4.17 4.99 15.65 17.94 20.71 37.77 +Uterus (Dataset = GTEx, N = 142) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Uterus UBERON_0000995 17.86 4.4 10.39 14.66 17.04 21 37.98 +Vagina (Dataset = GTEx, N = 156) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Vagina UBERON_0000996 13.63 3.72 6.02 10.65 13.57 16.66 22.92 diff --git a/tests/results/test-tpm-gene-disease-gtex-ENSG00000157764-MONDO_0016718.tsv b/tests/results/test-tpm-gene-disease-gtex-ENSG00000157764-MONDO_0016718.tsv new file mode 100644 index 0000000..d31cd43 --- /dev/null +++ b/tests/results/test-tpm-gene-disease-gtex-ENSG00000157764-MONDO_0016718.tsv @@ -0,0 +1,55 @@ +x_labels Gene_Ensembl_ID Gene_symbol PMTL Dataset Disease GTEx_tissue_subgroup EFO MONDO GTEx_tissue_subgroup_UBERON TPM_mean TPM_sd TPM_min TPM_25th_percentile TPM_median TPM_75th_percentile TPM_max +Choroid plexus carcinoma (Dataset = PBTA, N = 4) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Choroid plexus carcinoma MONDO_0016718 MONDO_0016718 5.78 2.77 3.39 4.07 5.04 6.76 9.66 +Adipose - Subcutaneous (Dataset = GTEx, N = 663) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Subcutaneous UBERON_0002190 12.82 2.87 4.28 10.93 12.52 14.49 31.91 +Adipose - Visceral (Omentum) (Dataset = GTEx, N = 541) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Visceral (Omentum) UBERON_0010414 10.51 3.39 2.39 7.84 10.25 12.89 24.23 +Adrenal Gland (Dataset = GTEx, N = 258) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Adrenal Gland UBERON_0002369 6.08 1.32 2.22 5.31 6.03 6.91 10.85 +Artery - Aorta (Dataset = GTEx, N = 432) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Aorta UBERON_0001496 13.14 2.72 5.41 11.31 12.96 14.79 24.63 +Artery - Coronary (Dataset = GTEx, N = 240) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Coronary UBERON_0001621 12.43 3.46 4.44 9.96 11.8 14.15 23.58 +Artery - Tibial (Dataset = GTEx, N = 663) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Tibial UBERON_0007610 16.02 3.65 3.67 13.7 15.83 17.99 32.95 +Bladder (Dataset = GTEx, N = 21) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Bladder UBERON_0001255 15.52 6.04 6.36 11.79 12.95 20.06 29.41 +Blood (Dataset = GTEx, N = 755) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Blood UBERON_0013756 6.38 3.8 0.36 3.73 5.53 7.93 30.85 +Brain - Amygdala (Dataset = GTEx, N = 152) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Amygdala UBERON_0001876 5.09 2.49 0.77 3.26 4.67 6.85 12.19 +Brain - Anterior cingulate cortex (BA24) (Dataset = GTEx, N = 176) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Anterior cingulate cortex (BA24) UBERON_0009835 7.78 4.2 1.53 4.62 7.13 9.88 24.3 +Brain - Caudate (basal ganglia) (Dataset = GTEx, N = 246) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Caudate (basal ganglia) UBERON_0001873 6.87 3.73 0.77 3.89 6.64 9.37 22.01 +Brain - Cerebellum (Dataset = GTEx, N = 456) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cerebellum UBERON_0002037 23.77 8.18 4.58 18.59 23.31 28.61 59.09 +Brain - Cortex (Dataset = GTEx, N = 255) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cortex UBERON_0001870 8.42 3.06 1.78 6.34 8.39 10.38 20.64 +Brain - Frontal Cortex (BA9) (Dataset = GTEx, N = 209) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Frontal Cortex (BA9) UBERON_0009834 11.8 5.24 1.68 7.94 11.98 15.12 32.8 +Brain - Hippocampus (Dataset = GTEx, N = 197) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hippocampus UBERON_0001954 5.63 2.99 0.99 3.4 5.13 7.28 17.57 +Brain - Hypothalamus (Dataset = GTEx, N = 202) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hypothalamus UBERON_0001898 7.08 3.92 0.84 4.22 6.48 9.27 24.09 +Brain - Nucleus accumbens (basal ganglia) (Dataset = GTEx, N = 246) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Nucleus accumbens (basal ganglia) UBERON_0001882 7.97 4.44 0.77 4.76 7.81 10.75 22.12 +Brain - Putamen (basal ganglia) (Dataset = GTEx, N = 205) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Putamen (basal ganglia) UBERON_0001874 5.57 3.36 0.77 3.04 5.08 7.41 21.08 +Brain - Spinal cord (cervical c-1) (Dataset = GTEx, N = 159) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Spinal cord (cervical c-1) UBERON_0006469 5.98 2.58 1.09 4.28 5.81 7.48 14.2 +Brain - Substantia nigra (Dataset = GTEx, N = 139) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Substantia nigra UBERON_0002038 4.69 2.36 1.07 2.9 4.31 6.11 12.65 +Breast - Mammary Tissue (Dataset = GTEx, N = 459) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Breast - Mammary Tissue UBERON_0008367 13.52 4.74 4.38 9.63 12.91 16.74 28.59 +Cells - Cultured fibroblasts (Dataset = GTEx, N = 504) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cells - Cultured fibroblasts 11.05 2.77 4.75 9.36 10.52 11.93 23.14 +Cells - EBV-transformed lymphocytes (Dataset = GTEx, N = 174) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cells - EBV-transformed lymphocytes 16.82 5.02 6.68 13.51 16.31 19.28 40.77 +Cervix - Ectocervix (Dataset = GTEx, N = 9) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Ectocervix UBERON_0012249 14.89 4.3 8.52 12.25 14.82 16.37 23.71 +Cervix - Endocervix (Dataset = GTEx, N = 10) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Endocervix UBERON_0000458 16.39 2.95 12.68 14.5 15.54 18.15 21.4 +Colon - Sigmoid (Dataset = GTEx, N = 373) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Sigmoid UBERON_0001159 12.52 2.95 2.89 10.76 12.66 14.22 23.28 +Colon - Transverse (Dataset = GTEx, N = 406) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Transverse UBERON_0001157 8.88 3.67 3.13 5.87 7.91 11.19 21.44 +Esophagus - Gastroesophageal Junction (Dataset = GTEx, N = 375) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Gastroesophageal Junction UBERON_0004550 12.04 3.04 4.02 10 11.75 13.82 24.94 +Esophagus - Mucosa (Dataset = GTEx, N = 555) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Mucosa UBERON_0006920 7.66 1.85 2.77 6.44 7.44 8.71 18.73 +Esophagus - Muscularis (Dataset = GTEx, N = 515) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Muscularis UBERON_0004648 12.05 2.77 4.53 10.2 11.93 13.83 23.34 +Fallopian Tube (Dataset = GTEx, N = 9) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Fallopian Tube UBERON_0003889 14.97 3.73 8.41 12.7 16.7 16.96 19.98 +Heart - Atrial Appendage (Dataset = GTEx, N = 429) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Atrial Appendage UBERON_0006631 5.31 1.75 1.05 4.12 5.05 6.36 11.83 +Heart - Left Ventricle (Dataset = GTEx, N = 432) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Left Ventricle UBERON_0006566 3.35 1.66 0.52 2.43 3.31 4.13 14.39 +Kidney - Cortex (Dataset = GTEx, N = 85) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Cortex UBERON_0001225 6.67 4.04 2.38 4.05 5.39 7.58 23 +Kidney - Medulla (Dataset = GTEx, N = 4) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Medulla UBERON_0001293 8.9 3.06 5.3 6.99 9.12 11.04 12.07 +Liver (Dataset = GTEx, N = 226) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Liver UBERON_0001114 3.63 0.95 1.15 2.97 3.53 4.22 7.74 +Lung (Dataset = GTEx, N = 578) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Lung UBERON_0008952 16.39 4.91 6.11 12.79 15.59 18.8 37.04 +Minor Salivary Gland (Dataset = GTEx, N = 162) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Minor Salivary Gland UBERON_0006330 8.57 2.06 3.73 7.14 8.49 9.87 14.97 +Muscle - Skeletal (Dataset = GTEx, N = 803) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Muscle - Skeletal UBERON_0011907 4.85 1.84 1 3.56 4.56 5.74 14.81 +Nerve - Tibial (Dataset = GTEx, N = 619) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Nerve - Tibial UBERON_0001323 16.83 3.21 8.21 14.73 16.65 18.47 46.67 +Ovary (Dataset = GTEx, N = 180) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Ovary UBERON_0000992 17.3 3.94 8.23 14.5 16.94 19.15 32.61 +Pancreas (Dataset = GTEx, N = 328) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Pancreas UBERON_0001150 4.44 1.49 1.83 3.43 4.19 5.08 15.2 +Pituitary (Dataset = GTEx, N = 283) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Pituitary UBERON_0000007 15.06 3.21 6.49 13.16 14.88 16.56 27.8 +Prostate (Dataset = GTEx, N = 245) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Prostate UBERON_0002367 13.59 3.43 5.21 10.97 13.49 15.78 26.64 +Skin - Not Sun Exposed (Suprapubic) (Dataset = GTEx, N = 604) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Not Sun Exposed (Suprapubic) UBERON_0036149 13.63 3.14 5.81 11.49 13.68 15.46 28.18 +Skin - Sun Exposed (Lower leg) (Dataset = GTEx, N = 701) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Sun Exposed (Lower leg) UBERON_0004264 14.29 3.23 5.23 12.1 14.05 16.32 25.49 +Small Intestine - Terminal Ileum (Dataset = GTEx, N = 187) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Small Intestine - Terminal Ileum UBERON_0001211 9.85 4.2 3.46 6.53 8.97 11.98 25.59 +Spleen (Dataset = GTEx, N = 241) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Spleen UBERON_0002106 10.3 3.13 3.4 8.18 9.55 11.69 20.61 +Stomach (Dataset = GTEx, N = 359) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Stomach UBERON_0000945 8.41 3.06 3.57 6.25 7.64 10.02 21.83 +Testis (Dataset = GTEx, N = 361) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Testis UBERON_0000473 20.57 3.47 13.28 17.95 20.28 22.95 30.33 +Thyroid (Dataset = GTEx, N = 653) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Thyroid UBERON_0002046 18.4 4.17 4.99 15.65 17.94 20.71 37.77 +Uterus (Dataset = GTEx, N = 142) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Uterus UBERON_0000995 17.86 4.4 10.39 14.66 17.04 21 37.98 +Vagina (Dataset = GTEx, N = 156) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Vagina UBERON_0000996 13.63 3.72 6.02 10.65 13.57 16.66 22.92 diff --git a/tests/results/test-tpm-gene-disease-gtex-ENSG00000157764-Orphanet_178.tsv b/tests/results/test-tpm-gene-disease-gtex-ENSG00000157764-Orphanet_178.tsv new file mode 100644 index 0000000..63a9df0 --- /dev/null +++ b/tests/results/test-tpm-gene-disease-gtex-ENSG00000157764-Orphanet_178.tsv @@ -0,0 +1,55 @@ +x_labels Gene_Ensembl_ID Gene_symbol PMTL Dataset Disease GTEx_tissue_subgroup EFO MONDO GTEx_tissue_subgroup_UBERON TPM_mean TPM_sd TPM_min TPM_25th_percentile TPM_median TPM_75th_percentile TPM_max +Chordoma (Dataset = PBTA, N = 3) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) PBTA Chordoma Orphanet_178 MONDO_0008978 3.45 0.51 2.95 3.18 3.42 3.7 3.97 +Adipose - Subcutaneous (Dataset = GTEx, N = 663) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Subcutaneous UBERON_0002190 12.82 2.87 4.28 10.93 12.52 14.49 31.91 +Adipose - Visceral (Omentum) (Dataset = GTEx, N = 541) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Visceral (Omentum) UBERON_0010414 10.51 3.39 2.39 7.84 10.25 12.89 24.23 +Adrenal Gland (Dataset = GTEx, N = 258) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Adrenal Gland UBERON_0002369 6.08 1.32 2.22 5.31 6.03 6.91 10.85 +Artery - Aorta (Dataset = GTEx, N = 432) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Aorta UBERON_0001496 13.14 2.72 5.41 11.31 12.96 14.79 24.63 +Artery - Coronary (Dataset = GTEx, N = 240) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Coronary UBERON_0001621 12.43 3.46 4.44 9.96 11.8 14.15 23.58 +Artery - Tibial (Dataset = GTEx, N = 663) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Tibial UBERON_0007610 16.02 3.65 3.67 13.7 15.83 17.99 32.95 +Bladder (Dataset = GTEx, N = 21) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Bladder UBERON_0001255 15.52 6.04 6.36 11.79 12.95 20.06 29.41 +Blood (Dataset = GTEx, N = 755) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Blood UBERON_0013756 6.38 3.8 0.36 3.73 5.53 7.93 30.85 +Brain - Amygdala (Dataset = GTEx, N = 152) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Amygdala UBERON_0001876 5.09 2.49 0.77 3.26 4.67 6.85 12.19 +Brain - Anterior cingulate cortex (BA24) (Dataset = GTEx, N = 176) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Anterior cingulate cortex (BA24) UBERON_0009835 7.78 4.2 1.53 4.62 7.13 9.88 24.3 +Brain - Caudate (basal ganglia) (Dataset = GTEx, N = 246) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Caudate (basal ganglia) UBERON_0001873 6.87 3.73 0.77 3.89 6.64 9.37 22.01 +Brain - Cerebellum (Dataset = GTEx, N = 456) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cerebellum UBERON_0002037 23.77 8.18 4.58 18.59 23.31 28.61 59.09 +Brain - Cortex (Dataset = GTEx, N = 255) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cortex UBERON_0001870 8.42 3.06 1.78 6.34 8.39 10.38 20.64 +Brain - Frontal Cortex (BA9) (Dataset = GTEx, N = 209) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Frontal Cortex (BA9) UBERON_0009834 11.8 5.24 1.68 7.94 11.98 15.12 32.8 +Brain - Hippocampus (Dataset = GTEx, N = 197) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hippocampus UBERON_0001954 5.63 2.99 0.99 3.4 5.13 7.28 17.57 +Brain - Hypothalamus (Dataset = GTEx, N = 202) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hypothalamus UBERON_0001898 7.08 3.92 0.84 4.22 6.48 9.27 24.09 +Brain - Nucleus accumbens (basal ganglia) (Dataset = GTEx, N = 246) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Nucleus accumbens (basal ganglia) UBERON_0001882 7.97 4.44 0.77 4.76 7.81 10.75 22.12 +Brain - Putamen (basal ganglia) (Dataset = GTEx, N = 205) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Putamen (basal ganglia) UBERON_0001874 5.57 3.36 0.77 3.04 5.08 7.41 21.08 +Brain - Spinal cord (cervical c-1) (Dataset = GTEx, N = 159) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Spinal cord (cervical c-1) UBERON_0006469 5.98 2.58 1.09 4.28 5.81 7.48 14.2 +Brain - Substantia nigra (Dataset = GTEx, N = 139) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Substantia nigra UBERON_0002038 4.69 2.36 1.07 2.9 4.31 6.11 12.65 +Breast - Mammary Tissue (Dataset = GTEx, N = 459) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Breast - Mammary Tissue UBERON_0008367 13.52 4.74 4.38 9.63 12.91 16.74 28.59 +Cells - Cultured fibroblasts (Dataset = GTEx, N = 504) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cells - Cultured fibroblasts 11.05 2.77 4.75 9.36 10.52 11.93 23.14 +Cells - EBV-transformed lymphocytes (Dataset = GTEx, N = 174) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cells - EBV-transformed lymphocytes 16.82 5.02 6.68 13.51 16.31 19.28 40.77 +Cervix - Ectocervix (Dataset = GTEx, N = 9) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Ectocervix UBERON_0012249 14.89 4.3 8.52 12.25 14.82 16.37 23.71 +Cervix - Endocervix (Dataset = GTEx, N = 10) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Endocervix UBERON_0000458 16.39 2.95 12.68 14.5 15.54 18.15 21.4 +Colon - Sigmoid (Dataset = GTEx, N = 373) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Sigmoid UBERON_0001159 12.52 2.95 2.89 10.76 12.66 14.22 23.28 +Colon - Transverse (Dataset = GTEx, N = 406) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Transverse UBERON_0001157 8.88 3.67 3.13 5.87 7.91 11.19 21.44 +Esophagus - Gastroesophageal Junction (Dataset = GTEx, N = 375) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Gastroesophageal Junction UBERON_0004550 12.04 3.04 4.02 10 11.75 13.82 24.94 +Esophagus - Mucosa (Dataset = GTEx, N = 555) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Mucosa UBERON_0006920 7.66 1.85 2.77 6.44 7.44 8.71 18.73 +Esophagus - Muscularis (Dataset = GTEx, N = 515) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Muscularis UBERON_0004648 12.05 2.77 4.53 10.2 11.93 13.83 23.34 +Fallopian Tube (Dataset = GTEx, N = 9) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Fallopian Tube UBERON_0003889 14.97 3.73 8.41 12.7 16.7 16.96 19.98 +Heart - Atrial Appendage (Dataset = GTEx, N = 429) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Atrial Appendage UBERON_0006631 5.31 1.75 1.05 4.12 5.05 6.36 11.83 +Heart - Left Ventricle (Dataset = GTEx, N = 432) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Left Ventricle UBERON_0006566 3.35 1.66 0.52 2.43 3.31 4.13 14.39 +Kidney - Cortex (Dataset = GTEx, N = 85) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Cortex UBERON_0001225 6.67 4.04 2.38 4.05 5.39 7.58 23 +Kidney - Medulla (Dataset = GTEx, N = 4) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Medulla UBERON_0001293 8.9 3.06 5.3 6.99 9.12 11.04 12.07 +Liver (Dataset = GTEx, N = 226) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Liver UBERON_0001114 3.63 0.95 1.15 2.97 3.53 4.22 7.74 +Lung (Dataset = GTEx, N = 578) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Lung UBERON_0008952 16.39 4.91 6.11 12.79 15.59 18.8 37.04 +Minor Salivary Gland (Dataset = GTEx, N = 162) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Minor Salivary Gland UBERON_0006330 8.57 2.06 3.73 7.14 8.49 9.87 14.97 +Muscle - Skeletal (Dataset = GTEx, N = 803) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Muscle - Skeletal UBERON_0011907 4.85 1.84 1 3.56 4.56 5.74 14.81 +Nerve - Tibial (Dataset = GTEx, N = 619) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Nerve - Tibial UBERON_0001323 16.83 3.21 8.21 14.73 16.65 18.47 46.67 +Ovary (Dataset = GTEx, N = 180) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Ovary UBERON_0000992 17.3 3.94 8.23 14.5 16.94 19.15 32.61 +Pancreas (Dataset = GTEx, N = 328) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Pancreas UBERON_0001150 4.44 1.49 1.83 3.43 4.19 5.08 15.2 +Pituitary (Dataset = GTEx, N = 283) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Pituitary UBERON_0000007 15.06 3.21 6.49 13.16 14.88 16.56 27.8 +Prostate (Dataset = GTEx, N = 245) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Prostate UBERON_0002367 13.59 3.43 5.21 10.97 13.49 15.78 26.64 +Skin - Not Sun Exposed (Suprapubic) (Dataset = GTEx, N = 604) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Not Sun Exposed (Suprapubic) UBERON_0036149 13.63 3.14 5.81 11.49 13.68 15.46 28.18 +Skin - Sun Exposed (Lower leg) (Dataset = GTEx, N = 701) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Sun Exposed (Lower leg) UBERON_0004264 14.29 3.23 5.23 12.1 14.05 16.32 25.49 +Small Intestine - Terminal Ileum (Dataset = GTEx, N = 187) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Small Intestine - Terminal Ileum UBERON_0001211 9.85 4.2 3.46 6.53 8.97 11.98 25.59 +Spleen (Dataset = GTEx, N = 241) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Spleen UBERON_0002106 10.3 3.13 3.4 8.18 9.55 11.69 20.61 +Stomach (Dataset = GTEx, N = 359) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Stomach UBERON_0000945 8.41 3.06 3.57 6.25 7.64 10.02 21.83 +Testis (Dataset = GTEx, N = 361) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Testis UBERON_0000473 20.57 3.47 13.28 17.95 20.28 22.95 30.33 +Thyroid (Dataset = GTEx, N = 653) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Thyroid UBERON_0002046 18.4 4.17 4.99 15.65 17.94 20.71 37.77 +Uterus (Dataset = GTEx, N = 142) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Uterus UBERON_0000995 17.86 4.4 10.39 14.66 17.04 21 37.98 +Vagina (Dataset = GTEx, N = 156) ENSG00000157764 BRAF Relevant Molecular Target (RMTL version 1.0) GTEx Vagina UBERON_0000996 13.63 3.72 6.02 10.65 13.57 16.66 22.92 diff --git a/tests/results/test-tpm-gene-disease-gtex-ENSG00000213420-EFO_0000621.tsv b/tests/results/test-tpm-gene-disease-gtex-ENSG00000213420-EFO_0000621.tsv index 508a5ec..824e68d 100644 --- a/tests/results/test-tpm-gene-disease-gtex-ENSG00000213420-EFO_0000621.tsv +++ b/tests/results/test-tpm-gene-disease-gtex-ENSG00000213420-EFO_0000621.tsv @@ -1,57 +1,57 @@ -x_labels Gene_Ensembl_ID Gene_symbol PMTL cohort Disease GTEx_tissue_subgroup EFO MONDO GTEx_tissue_subgroup_UBERON TPM_mean TPM_sd TPM_min TPM_25th_percentile TPM_median TPM_75th_percentile TPM_max -Neuroblastoma (cohort = all_cohorts, N = 347) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) all_cohorts Neuroblastoma EFO_0000621 MONDO_0005072 50.05 45.34 0.52 21.65 37 63.88 332.67 -Neuroblastoma (cohort = GMKF, N = 209) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GMKF Neuroblastoma EFO_0000621 MONDO_0005072 27.83 15.74 0.52 17.23 26.63 38.92 73.07 -Neuroblastoma (cohort = TARGET, N = 149) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) TARGET Neuroblastoma EFO_0000621 MONDO_0005072 81.2 53.17 1.2 43.22 72.03 112.68 332.67 -Adipose - Subcutaneous (cohort = GTEx, N = 663) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Subcutaneous UBERON_0002190 1.76 0.82 0.3 1.17 1.66 2.18 5.47 -Adipose - Visceral (Omentum) (cohort = GTEx, N = 541) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Visceral (Omentum) UBERON_0010414 1.2 0.65 0.14 0.71 1.04 1.54 4.09 -Adrenal Gland (cohort = GTEx, N = 258) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Adrenal Gland UBERON_0002369 0.72 0.36 0.18 0.51 0.63 0.86 3.25 -Artery - Aorta (cohort = GTEx, N = 432) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Aorta UBERON_0001496 1.45 0.74 0.35 0.98 1.3 1.69 5.66 -Artery - Coronary (cohort = GTEx, N = 240) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Coronary UBERON_0001621 1.37 0.95 0.17 0.84 1.14 1.63 10.15 -Artery - Tibial (cohort = GTEx, N = 663) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Tibial UBERON_0007610 0.75 0.59 0 0.39 0.61 0.93 6.25 -Bladder (cohort = GTEx, N = 21) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Bladder UBERON_0001255 1.98 1.25 0.73 1.16 1.85 2.11 5.98 -Blood (cohort = GTEx, N = 755) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Blood UBERON_0013756 1.04 1.81 0 0.45 0.8 1.26 45.04 -Brain - Amygdala (cohort = GTEx, N = 152) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Amygdala UBERON_0001876 2.29 0.86 0.21 1.66 2.22 2.84 5.07 -Brain - Anterior cingulate cortex (BA24) (cohort = GTEx, N = 176) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Anterior cingulate cortex (BA24) UBERON_0009835 1.86 0.65 0.28 1.42 1.78 2.16 4.74 -Brain - Caudate (basal ganglia) (cohort = GTEx, N = 246) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Caudate (basal ganglia) UBERON_0001873 1.35 0.5 0.28 0.98 1.35 1.64 3.44 -Brain - Cerebellum (cohort = GTEx, N = 456) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cerebellum UBERON_0002037 3.2 1.91 0.54 2.01 2.78 3.67 15.63 -Brain - Cortex (cohort = GTEx, N = 255) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cortex UBERON_0001870 1.63 0.57 0.45 1.23 1.53 1.95 4.32 -Brain - Frontal Cortex (BA9) (cohort = GTEx, N = 209) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Frontal Cortex (BA9) UBERON_0009834 1.61 0.59 0.42 1.24 1.56 1.84 5.38 -Brain - Hippocampus (cohort = GTEx, N = 197) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hippocampus UBERON_0001954 2.21 1 0.19 1.47 2.09 2.68 5.95 -Brain - Hypothalamus (cohort = GTEx, N = 202) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hypothalamus UBERON_0001898 1.58 0.83 0.19 1 1.45 2 6.24 -Brain - Nucleus accumbens (basal ganglia) (cohort = GTEx, N = 246) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Nucleus accumbens (basal ganglia) UBERON_0001882 1.36 0.69 0.1 0.91 1.28 1.64 6.23 -Brain - Putamen (basal ganglia) (cohort = GTEx, N = 205) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Putamen (basal ganglia) UBERON_0001874 1.32 0.58 0.26 0.92 1.24 1.6 3.86 -Brain - Spinal cord (cervical c-1) (cohort = GTEx, N = 159) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Spinal cord (cervical c-1) UBERON_0006469 3.34 1.52 0.51 2.19 3.2 4.41 6.84 -Brain - Substantia nigra (cohort = GTEx, N = 139) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Substantia nigra UBERON_0002038 1.74 0.96 0.4 1.06 1.59 2.32 6.38 -Breast - Mammary Tissue (cohort = GTEx, N = 459) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Breast - Mammary Tissue UBERON_0008367 2.27 1.62 0.26 1.17 1.88 2.93 15.34 -Cells - Cultured fibroblasts (cohort = GTEx, N = 504) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cells - Cultured fibroblasts 1.3 0.6 0.33 0.94 1.21 1.49 8.06 -Cells - EBV-transformed lymphocytes (cohort = GTEx, N = 174) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cells - EBV-transformed lymphocytes 2.61 1.56 0.43 1.58 2.33 3.11 11.26 -Cervix - Ectocervix (cohort = GTEx, N = 9) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Ectocervix UBERON_0012249 4.63 2.91 2.15 2.94 3.68 4.47 11.61 -Cervix - Endocervix (cohort = GTEx, N = 10) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Endocervix UBERON_0000458 5.14 4.09 2.33 2.93 3.64 4.68 15.63 -Colon - Sigmoid (cohort = GTEx, N = 373) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Sigmoid UBERON_0001159 1.67 0.83 0.29 1.06 1.55 2.1 5.22 -Colon - Transverse (cohort = GTEx, N = 406) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Transverse UBERON_0001157 2.02 0.87 0.34 1.4 1.92 2.48 8.43 -Esophagus - Gastroesophageal Junction (cohort = GTEx, N = 375) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Gastroesophageal Junction UBERON_0004550 1.13 0.61 0.1 0.68 0.99 1.47 4.08 -Esophagus - Mucosa (cohort = GTEx, N = 555) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Mucosa UBERON_0006920 1.16 0.59 0.13 0.74 1.04 1.42 4.14 -Esophagus - Muscularis (cohort = GTEx, N = 515) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Muscularis UBERON_0004648 1.19 0.65 0.16 0.75 1.05 1.55 5.36 -Fallopian Tube (cohort = GTEx, N = 9) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Fallopian Tube UBERON_0003889 3.32 1.75 0.91 2.7 2.8 4 6.78 -Heart - Atrial Appendage (cohort = GTEx, N = 429) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Atrial Appendage UBERON_0006631 0.63 0.36 0.1 0.38 0.56 0.77 2.66 -Heart - Left Ventricle (cohort = GTEx, N = 432) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Left Ventricle UBERON_0006566 0.44 0.42 0.04 0.25 0.34 0.5 6.14 -Kidney - Cortex (cohort = GTEx, N = 85) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Cortex UBERON_0001225 0.66 0.75 0.1 0.27 0.48 0.72 4.74 -Kidney - Medulla (cohort = GTEx, N = 4) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Medulla UBERON_0001293 0.97 0.47 0.48 0.72 0.92 1.17 1.59 -Liver (cohort = GTEx, N = 226) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Liver UBERON_0001114 0.17 0.2 0 0.07 0.12 0.2 2.17 -Lung (cohort = GTEx, N = 578) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Lung UBERON_0008952 1.52 1.01 0.17 0.88 1.31 1.94 13.43 -Minor Salivary Gland (cohort = GTEx, N = 162) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Minor Salivary Gland UBERON_0006330 2.06 1.2 0.5 1.24 1.84 2.49 8.52 -Muscle - Skeletal (cohort = GTEx, N = 803) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Muscle - Skeletal UBERON_0011907 0.45 0.4 0.02 0.22 0.34 0.54 4.2 -Nerve - Tibial (cohort = GTEx, N = 619) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Nerve - Tibial UBERON_0001323 3 1.11 0.62 2.19 2.89 3.62 9.17 -Ovary (cohort = GTEx, N = 180) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Ovary UBERON_0000992 5.42 3.52 1.26 3.25 4.51 6.42 21.19 -Pancreas (cohort = GTEx, N = 328) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Pancreas UBERON_0001150 0.33 0.32 0.01 0.17 0.26 0.39 3.81 -Pituitary (cohort = GTEx, N = 283) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Pituitary UBERON_0000007 2.24 1.12 0.39 1.51 2.04 2.72 8.7 -Prostate (cohort = GTEx, N = 245) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Prostate UBERON_0002367 2.24 1.05 0.5 1.47 2.08 2.7 5.88 -Skin - Not Sun Exposed (Suprapubic) (cohort = GTEx, N = 604) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Not Sun Exposed (Suprapubic) UBERON_0036149 13.99 6.07 1.61 9.51 13.12 17.57 38.26 -Skin - Sun Exposed (Lower leg) (cohort = GTEx, N = 701) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Sun Exposed (Lower leg) UBERON_0004264 10.98 4.54 1.27 7.77 10.5 13.68 27.79 -Small Intestine - Terminal Ileum (cohort = GTEx, N = 187) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Small Intestine - Terminal Ileum UBERON_0001211 2.74 2 0.47 1.2 2.13 3.67 12.23 -Spleen (cohort = GTEx, N = 241) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Spleen UBERON_0002106 3.1 1.43 0.55 2.2 2.8 3.75 12.37 -Stomach (cohort = GTEx, N = 359) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Stomach UBERON_0000945 0.76 0.46 0.09 0.47 0.65 0.9 4.03 -Testis (cohort = GTEx, N = 361) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Testis UBERON_0000473 32.59 10.03 4.54 25.34 32.61 39.41 75.12 -Thyroid (cohort = GTEx, N = 653) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Thyroid UBERON_0002046 1.07 0.6 0.04 0.67 0.95 1.31 5.28 -Uterus (cohort = GTEx, N = 142) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Uterus UBERON_0000995 6.07 4.41 1.15 3.49 4.65 6.87 25.44 -Vagina (cohort = GTEx, N = 156) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Vagina UBERON_0000996 3.16 1.37 0.94 2.13 2.98 3.79 8.56 +x_labels Gene_Ensembl_ID Gene_symbol PMTL Dataset Disease GTEx_tissue_subgroup EFO MONDO GTEx_tissue_subgroup_UBERON TPM_mean TPM_sd TPM_min TPM_25th_percentile TPM_median TPM_75th_percentile TPM_max +Neuroblastoma (Dataset = all_cohorts, N = 347) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) all_cohorts Neuroblastoma EFO_0000621 MONDO_0005072 50.05 45.34 0.52 21.65 37 63.88 332.67 +Neuroblastoma (Dataset = GMKF, N = 209) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GMKF Neuroblastoma EFO_0000621 MONDO_0005072 27.83 15.74 0.52 17.23 26.63 38.92 73.07 +Neuroblastoma (Dataset = TARGET, N = 149) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) TARGET Neuroblastoma EFO_0000621 MONDO_0005072 81.2 53.17 1.2 43.22 72.03 112.68 332.67 +Adipose - Subcutaneous (Dataset = GTEx, N = 663) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Subcutaneous UBERON_0002190 1.76 0.82 0.3 1.17 1.66 2.18 5.47 +Adipose - Visceral (Omentum) (Dataset = GTEx, N = 541) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Visceral (Omentum) UBERON_0010414 1.2 0.65 0.14 0.71 1.04 1.54 4.09 +Adrenal Gland (Dataset = GTEx, N = 258) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Adrenal Gland UBERON_0002369 0.72 0.36 0.18 0.51 0.63 0.86 3.25 +Artery - Aorta (Dataset = GTEx, N = 432) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Aorta UBERON_0001496 1.45 0.74 0.35 0.98 1.3 1.69 5.66 +Artery - Coronary (Dataset = GTEx, N = 240) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Coronary UBERON_0001621 1.37 0.95 0.17 0.84 1.14 1.63 10.15 +Artery - Tibial (Dataset = GTEx, N = 663) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Tibial UBERON_0007610 0.75 0.59 0 0.39 0.61 0.93 6.25 +Bladder (Dataset = GTEx, N = 21) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Bladder UBERON_0001255 1.98 1.25 0.73 1.16 1.85 2.11 5.98 +Blood (Dataset = GTEx, N = 755) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Blood UBERON_0013756 1.04 1.81 0 0.45 0.8 1.26 45.04 +Brain - Amygdala (Dataset = GTEx, N = 152) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Amygdala UBERON_0001876 2.29 0.86 0.21 1.66 2.22 2.84 5.07 +Brain - Anterior cingulate cortex (BA24) (Dataset = GTEx, N = 176) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Anterior cingulate cortex (BA24) UBERON_0009835 1.86 0.65 0.28 1.42 1.78 2.16 4.74 +Brain - Caudate (basal ganglia) (Dataset = GTEx, N = 246) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Caudate (basal ganglia) UBERON_0001873 1.35 0.5 0.28 0.98 1.35 1.64 3.44 +Brain - Cerebellum (Dataset = GTEx, N = 456) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cerebellum UBERON_0002037 3.2 1.91 0.54 2.01 2.78 3.67 15.63 +Brain - Cortex (Dataset = GTEx, N = 255) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cortex UBERON_0001870 1.63 0.57 0.45 1.23 1.53 1.95 4.32 +Brain - Frontal Cortex (BA9) (Dataset = GTEx, N = 209) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Frontal Cortex (BA9) UBERON_0009834 1.61 0.59 0.42 1.24 1.56 1.84 5.38 +Brain - Hippocampus (Dataset = GTEx, N = 197) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hippocampus UBERON_0001954 2.21 1 0.19 1.47 2.09 2.68 5.95 +Brain - Hypothalamus (Dataset = GTEx, N = 202) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hypothalamus UBERON_0001898 1.58 0.83 0.19 1 1.45 2 6.24 +Brain - Nucleus accumbens (basal ganglia) (Dataset = GTEx, N = 246) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Nucleus accumbens (basal ganglia) UBERON_0001882 1.36 0.69 0.1 0.91 1.28 1.64 6.23 +Brain - Putamen (basal ganglia) (Dataset = GTEx, N = 205) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Putamen (basal ganglia) UBERON_0001874 1.32 0.58 0.26 0.92 1.24 1.6 3.86 +Brain - Spinal cord (cervical c-1) (Dataset = GTEx, N = 159) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Spinal cord (cervical c-1) UBERON_0006469 3.34 1.52 0.51 2.19 3.2 4.41 6.84 +Brain - Substantia nigra (Dataset = GTEx, N = 139) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Substantia nigra UBERON_0002038 1.74 0.96 0.4 1.06 1.59 2.32 6.38 +Breast - Mammary Tissue (Dataset = GTEx, N = 459) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Breast - Mammary Tissue UBERON_0008367 2.27 1.62 0.26 1.17 1.88 2.93 15.34 +Cells - Cultured fibroblasts (Dataset = GTEx, N = 504) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cells - Cultured fibroblasts 1.3 0.6 0.33 0.94 1.21 1.49 8.06 +Cells - EBV-transformed lymphocytes (Dataset = GTEx, N = 174) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cells - EBV-transformed lymphocytes 2.61 1.56 0.43 1.58 2.33 3.11 11.26 +Cervix - Ectocervix (Dataset = GTEx, N = 9) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Ectocervix UBERON_0012249 4.63 2.91 2.15 2.94 3.68 4.47 11.61 +Cervix - Endocervix (Dataset = GTEx, N = 10) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Endocervix UBERON_0000458 5.14 4.09 2.33 2.93 3.64 4.68 15.63 +Colon - Sigmoid (Dataset = GTEx, N = 373) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Sigmoid UBERON_0001159 1.67 0.83 0.29 1.06 1.55 2.1 5.22 +Colon - Transverse (Dataset = GTEx, N = 406) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Transverse UBERON_0001157 2.02 0.87 0.34 1.4 1.92 2.48 8.43 +Esophagus - Gastroesophageal Junction (Dataset = GTEx, N = 375) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Gastroesophageal Junction UBERON_0004550 1.13 0.61 0.1 0.68 0.99 1.47 4.08 +Esophagus - Mucosa (Dataset = GTEx, N = 555) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Mucosa UBERON_0006920 1.16 0.59 0.13 0.74 1.04 1.42 4.14 +Esophagus - Muscularis (Dataset = GTEx, N = 515) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Muscularis UBERON_0004648 1.19 0.65 0.16 0.75 1.05 1.55 5.36 +Fallopian Tube (Dataset = GTEx, N = 9) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Fallopian Tube UBERON_0003889 3.32 1.75 0.91 2.7 2.8 4 6.78 +Heart - Atrial Appendage (Dataset = GTEx, N = 429) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Atrial Appendage UBERON_0006631 0.63 0.36 0.1 0.38 0.56 0.77 2.66 +Heart - Left Ventricle (Dataset = GTEx, N = 432) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Left Ventricle UBERON_0006566 0.44 0.42 0.04 0.25 0.34 0.5 6.14 +Kidney - Cortex (Dataset = GTEx, N = 85) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Cortex UBERON_0001225 0.66 0.75 0.1 0.27 0.48 0.72 4.74 +Kidney - Medulla (Dataset = GTEx, N = 4) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Medulla UBERON_0001293 0.97 0.47 0.48 0.72 0.92 1.17 1.59 +Liver (Dataset = GTEx, N = 226) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Liver UBERON_0001114 0.17 0.2 0 0.07 0.12 0.2 2.17 +Lung (Dataset = GTEx, N = 578) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Lung UBERON_0008952 1.52 1.01 0.17 0.88 1.31 1.94 13.43 +Minor Salivary Gland (Dataset = GTEx, N = 162) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Minor Salivary Gland UBERON_0006330 2.06 1.2 0.5 1.24 1.84 2.49 8.52 +Muscle - Skeletal (Dataset = GTEx, N = 803) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Muscle - Skeletal UBERON_0011907 0.45 0.4 0.02 0.22 0.34 0.54 4.2 +Nerve - Tibial (Dataset = GTEx, N = 619) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Nerve - Tibial UBERON_0001323 3 1.11 0.62 2.19 2.89 3.62 9.17 +Ovary (Dataset = GTEx, N = 180) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Ovary UBERON_0000992 5.42 3.52 1.26 3.25 4.51 6.42 21.19 +Pancreas (Dataset = GTEx, N = 328) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Pancreas UBERON_0001150 0.33 0.32 0.01 0.17 0.26 0.39 3.81 +Pituitary (Dataset = GTEx, N = 283) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Pituitary UBERON_0000007 2.24 1.12 0.39 1.51 2.04 2.72 8.7 +Prostate (Dataset = GTEx, N = 245) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Prostate UBERON_0002367 2.24 1.05 0.5 1.47 2.08 2.7 5.88 +Skin - Not Sun Exposed (Suprapubic) (Dataset = GTEx, N = 604) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Not Sun Exposed (Suprapubic) UBERON_0036149 13.99 6.07 1.61 9.51 13.12 17.57 38.26 +Skin - Sun Exposed (Lower leg) (Dataset = GTEx, N = 701) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Sun Exposed (Lower leg) UBERON_0004264 10.98 4.54 1.27 7.77 10.5 13.68 27.79 +Small Intestine - Terminal Ileum (Dataset = GTEx, N = 187) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Small Intestine - Terminal Ileum UBERON_0001211 2.74 2 0.47 1.2 2.13 3.67 12.23 +Spleen (Dataset = GTEx, N = 241) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Spleen UBERON_0002106 3.1 1.43 0.55 2.2 2.8 3.75 12.37 +Stomach (Dataset = GTEx, N = 359) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Stomach UBERON_0000945 0.76 0.46 0.09 0.47 0.65 0.9 4.03 +Testis (Dataset = GTEx, N = 361) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Testis UBERON_0000473 32.59 10.03 4.54 25.34 32.61 39.41 75.12 +Thyroid (Dataset = GTEx, N = 653) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Thyroid UBERON_0002046 1.07 0.6 0.04 0.67 0.95 1.31 5.28 +Uterus (Dataset = GTEx, N = 142) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Uterus UBERON_0000995 6.07 4.41 1.15 3.49 4.65 6.87 25.44 +Vagina (Dataset = GTEx, N = 156) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Vagina UBERON_0000996 3.16 1.37 0.94 2.13 2.98 3.79 8.56 diff --git a/tests/results/test-tpm-gene-disease-gtex-ENSG00000213420-EFO_0005543.tsv b/tests/results/test-tpm-gene-disease-gtex-ENSG00000213420-EFO_0005543.tsv deleted file mode 100644 index 9e24626..0000000 --- a/tests/results/test-tpm-gene-disease-gtex-ENSG00000213420-EFO_0005543.tsv +++ /dev/null @@ -1,56 +0,0 @@ -x_labels Gene_Ensembl_ID Gene_symbol PMTL cohort Disease GTEx_tissue_subgroup EFO MONDO GTEx_tissue_subgroup_UBERON TPM_mean TPM_sd TPM_min TPM_25th_percentile TPM_median TPM_75th_percentile TPM_max -High-grade glioma/astrocytoma (cohort = PBTA, N = 51) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA High-grade glioma/astrocytoma EFO_0005543 MONDO_0100342 11.23 14 0.15 2.74 5.66 14.88 59.91 -Low-grade glioma/astrocytoma (cohort = PBTA, N = 237) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Low-grade glioma/astrocytoma EFO_0005543 MONDO_0016685 2.88 2.14 0.17 1.27 2.48 4.11 12.52 -Adipose - Subcutaneous (cohort = GTEx, N = 663) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Subcutaneous UBERON_0002190 1.76 0.82 0.3 1.17 1.66 2.18 5.47 -Adipose - Visceral (Omentum) (cohort = GTEx, N = 541) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Visceral (Omentum) UBERON_0010414 1.2 0.65 0.14 0.71 1.04 1.54 4.09 -Adrenal Gland (cohort = GTEx, N = 258) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Adrenal Gland UBERON_0002369 0.72 0.36 0.18 0.51 0.63 0.86 3.25 -Artery - Aorta (cohort = GTEx, N = 432) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Aorta UBERON_0001496 1.45 0.74 0.35 0.98 1.3 1.69 5.66 -Artery - Coronary (cohort = GTEx, N = 240) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Coronary UBERON_0001621 1.37 0.95 0.17 0.84 1.14 1.63 10.15 -Artery - Tibial (cohort = GTEx, N = 663) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Tibial UBERON_0007610 0.75 0.59 0 0.39 0.61 0.93 6.25 -Bladder (cohort = GTEx, N = 21) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Bladder UBERON_0001255 1.98 1.25 0.73 1.16 1.85 2.11 5.98 -Blood (cohort = GTEx, N = 755) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Blood UBERON_0013756 1.04 1.81 0 0.45 0.8 1.26 45.04 -Brain - Amygdala (cohort = GTEx, N = 152) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Amygdala UBERON_0001876 2.29 0.86 0.21 1.66 2.22 2.84 5.07 -Brain - Anterior cingulate cortex (BA24) (cohort = GTEx, N = 176) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Anterior cingulate cortex (BA24) UBERON_0009835 1.86 0.65 0.28 1.42 1.78 2.16 4.74 -Brain - Caudate (basal ganglia) (cohort = GTEx, N = 246) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Caudate (basal ganglia) UBERON_0001873 1.35 0.5 0.28 0.98 1.35 1.64 3.44 -Brain - Cerebellum (cohort = GTEx, N = 456) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cerebellum UBERON_0002037 3.2 1.91 0.54 2.01 2.78 3.67 15.63 -Brain - Cortex (cohort = GTEx, N = 255) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cortex UBERON_0001870 1.63 0.57 0.45 1.23 1.53 1.95 4.32 -Brain - Frontal Cortex (BA9) (cohort = GTEx, N = 209) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Frontal Cortex (BA9) UBERON_0009834 1.61 0.59 0.42 1.24 1.56 1.84 5.38 -Brain - Hippocampus (cohort = GTEx, N = 197) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hippocampus UBERON_0001954 2.21 1 0.19 1.47 2.09 2.68 5.95 -Brain - Hypothalamus (cohort = GTEx, N = 202) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hypothalamus UBERON_0001898 1.58 0.83 0.19 1 1.45 2 6.24 -Brain - Nucleus accumbens (basal ganglia) (cohort = GTEx, N = 246) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Nucleus accumbens (basal ganglia) UBERON_0001882 1.36 0.69 0.1 0.91 1.28 1.64 6.23 -Brain - Putamen (basal ganglia) (cohort = GTEx, N = 205) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Putamen (basal ganglia) UBERON_0001874 1.32 0.58 0.26 0.92 1.24 1.6 3.86 -Brain - Spinal cord (cervical c-1) (cohort = GTEx, N = 159) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Spinal cord (cervical c-1) UBERON_0006469 3.34 1.52 0.51 2.19 3.2 4.41 6.84 -Brain - Substantia nigra (cohort = GTEx, N = 139) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Substantia nigra UBERON_0002038 1.74 0.96 0.4 1.06 1.59 2.32 6.38 -Breast - Mammary Tissue (cohort = GTEx, N = 459) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Breast - Mammary Tissue UBERON_0008367 2.27 1.62 0.26 1.17 1.88 2.93 15.34 -Cells - Cultured fibroblasts (cohort = GTEx, N = 504) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cells - Cultured fibroblasts 1.3 0.6 0.33 0.94 1.21 1.49 8.06 -Cells - EBV-transformed lymphocytes (cohort = GTEx, N = 174) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cells - EBV-transformed lymphocytes 2.61 1.56 0.43 1.58 2.33 3.11 11.26 -Cervix - Ectocervix (cohort = GTEx, N = 9) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Ectocervix UBERON_0012249 4.63 2.91 2.15 2.94 3.68 4.47 11.61 -Cervix - Endocervix (cohort = GTEx, N = 10) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Endocervix UBERON_0000458 5.14 4.09 2.33 2.93 3.64 4.68 15.63 -Colon - Sigmoid (cohort = GTEx, N = 373) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Sigmoid UBERON_0001159 1.67 0.83 0.29 1.06 1.55 2.1 5.22 -Colon - Transverse (cohort = GTEx, N = 406) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Transverse UBERON_0001157 2.02 0.87 0.34 1.4 1.92 2.48 8.43 -Esophagus - Gastroesophageal Junction (cohort = GTEx, N = 375) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Gastroesophageal Junction UBERON_0004550 1.13 0.61 0.1 0.68 0.99 1.47 4.08 -Esophagus - Mucosa (cohort = GTEx, N = 555) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Mucosa UBERON_0006920 1.16 0.59 0.13 0.74 1.04 1.42 4.14 -Esophagus - Muscularis (cohort = GTEx, N = 515) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Muscularis UBERON_0004648 1.19 0.65 0.16 0.75 1.05 1.55 5.36 -Fallopian Tube (cohort = GTEx, N = 9) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Fallopian Tube UBERON_0003889 3.32 1.75 0.91 2.7 2.8 4 6.78 -Heart - Atrial Appendage (cohort = GTEx, N = 429) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Atrial Appendage UBERON_0006631 0.63 0.36 0.1 0.38 0.56 0.77 2.66 -Heart - Left Ventricle (cohort = GTEx, N = 432) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Left Ventricle UBERON_0006566 0.44 0.42 0.04 0.25 0.34 0.5 6.14 -Kidney - Cortex (cohort = GTEx, N = 85) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Cortex UBERON_0001225 0.66 0.75 0.1 0.27 0.48 0.72 4.74 -Kidney - Medulla (cohort = GTEx, N = 4) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Medulla UBERON_0001293 0.97 0.47 0.48 0.72 0.92 1.17 1.59 -Liver (cohort = GTEx, N = 226) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Liver UBERON_0001114 0.17 0.2 0 0.07 0.12 0.2 2.17 -Lung (cohort = GTEx, N = 578) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Lung UBERON_0008952 1.52 1.01 0.17 0.88 1.31 1.94 13.43 -Minor Salivary Gland (cohort = GTEx, N = 162) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Minor Salivary Gland UBERON_0006330 2.06 1.2 0.5 1.24 1.84 2.49 8.52 -Muscle - Skeletal (cohort = GTEx, N = 803) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Muscle - Skeletal UBERON_0011907 0.45 0.4 0.02 0.22 0.34 0.54 4.2 -Nerve - Tibial (cohort = GTEx, N = 619) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Nerve - Tibial UBERON_0001323 3 1.11 0.62 2.19 2.89 3.62 9.17 -Ovary (cohort = GTEx, N = 180) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Ovary UBERON_0000992 5.42 3.52 1.26 3.25 4.51 6.42 21.19 -Pancreas (cohort = GTEx, N = 328) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Pancreas UBERON_0001150 0.33 0.32 0.01 0.17 0.26 0.39 3.81 -Pituitary (cohort = GTEx, N = 283) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Pituitary UBERON_0000007 2.24 1.12 0.39 1.51 2.04 2.72 8.7 -Prostate (cohort = GTEx, N = 245) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Prostate UBERON_0002367 2.24 1.05 0.5 1.47 2.08 2.7 5.88 -Skin - Not Sun Exposed (Suprapubic) (cohort = GTEx, N = 604) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Not Sun Exposed (Suprapubic) UBERON_0036149 13.99 6.07 1.61 9.51 13.12 17.57 38.26 -Skin - Sun Exposed (Lower leg) (cohort = GTEx, N = 701) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Sun Exposed (Lower leg) UBERON_0004264 10.98 4.54 1.27 7.77 10.5 13.68 27.79 -Small Intestine - Terminal Ileum (cohort = GTEx, N = 187) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Small Intestine - Terminal Ileum UBERON_0001211 2.74 2 0.47 1.2 2.13 3.67 12.23 -Spleen (cohort = GTEx, N = 241) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Spleen UBERON_0002106 3.1 1.43 0.55 2.2 2.8 3.75 12.37 -Stomach (cohort = GTEx, N = 359) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Stomach UBERON_0000945 0.76 0.46 0.09 0.47 0.65 0.9 4.03 -Testis (cohort = GTEx, N = 361) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Testis UBERON_0000473 32.59 10.03 4.54 25.34 32.61 39.41 75.12 -Thyroid (cohort = GTEx, N = 653) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Thyroid UBERON_0002046 1.07 0.6 0.04 0.67 0.95 1.31 5.28 -Uterus (cohort = GTEx, N = 142) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Uterus UBERON_0000995 6.07 4.41 1.15 3.49 4.65 6.87 25.44 -Vagina (cohort = GTEx, N = 156) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Vagina UBERON_0000996 3.16 1.37 0.94 2.13 2.98 3.79 8.56 diff --git a/tests/results/test-tpm-gene-disease-gtex-ENSG00000213420-EFO_0007206.tsv b/tests/results/test-tpm-gene-disease-gtex-ENSG00000213420-EFO_0007206.tsv deleted file mode 100644 index 9398a89..0000000 --- a/tests/results/test-tpm-gene-disease-gtex-ENSG00000213420-EFO_0007206.tsv +++ /dev/null @@ -1,56 +0,0 @@ -x_labels Gene_Ensembl_ID Gene_symbol PMTL cohort Disease GTEx_tissue_subgroup EFO MONDO GTEx_tissue_subgroup_UBERON TPM_mean TPM_sd TPM_min TPM_25th_percentile TPM_median TPM_75th_percentile TPM_max -Choroid plexus carcinoma (cohort = PBTA, N = 4) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Choroid plexus carcinoma EFO_0007206 MONDO_0016718 12.53 11.31 2.74 3.27 10.87 20.14 25.64 -Choroid plexus cyst (cohort = PBTA, N = 1) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Choroid plexus cyst EFO_0007206 0.04 0.04 0.04 0.04 0.04 0.04 -Adipose - Subcutaneous (cohort = GTEx, N = 663) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Subcutaneous UBERON_0002190 1.76 0.82 0.3 1.17 1.66 2.18 5.47 -Adipose - Visceral (Omentum) (cohort = GTEx, N = 541) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Visceral (Omentum) UBERON_0010414 1.2 0.65 0.14 0.71 1.04 1.54 4.09 -Adrenal Gland (cohort = GTEx, N = 258) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Adrenal Gland UBERON_0002369 0.72 0.36 0.18 0.51 0.63 0.86 3.25 -Artery - Aorta (cohort = GTEx, N = 432) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Aorta UBERON_0001496 1.45 0.74 0.35 0.98 1.3 1.69 5.66 -Artery - Coronary (cohort = GTEx, N = 240) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Coronary UBERON_0001621 1.37 0.95 0.17 0.84 1.14 1.63 10.15 -Artery - Tibial (cohort = GTEx, N = 663) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Tibial UBERON_0007610 0.75 0.59 0 0.39 0.61 0.93 6.25 -Bladder (cohort = GTEx, N = 21) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Bladder UBERON_0001255 1.98 1.25 0.73 1.16 1.85 2.11 5.98 -Blood (cohort = GTEx, N = 755) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Blood UBERON_0013756 1.04 1.81 0 0.45 0.8 1.26 45.04 -Brain - Amygdala (cohort = GTEx, N = 152) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Amygdala UBERON_0001876 2.29 0.86 0.21 1.66 2.22 2.84 5.07 -Brain - Anterior cingulate cortex (BA24) (cohort = GTEx, N = 176) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Anterior cingulate cortex (BA24) UBERON_0009835 1.86 0.65 0.28 1.42 1.78 2.16 4.74 -Brain - Caudate (basal ganglia) (cohort = GTEx, N = 246) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Caudate (basal ganglia) UBERON_0001873 1.35 0.5 0.28 0.98 1.35 1.64 3.44 -Brain - Cerebellum (cohort = GTEx, N = 456) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cerebellum UBERON_0002037 3.2 1.91 0.54 2.01 2.78 3.67 15.63 -Brain - Cortex (cohort = GTEx, N = 255) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cortex UBERON_0001870 1.63 0.57 0.45 1.23 1.53 1.95 4.32 -Brain - Frontal Cortex (BA9) (cohort = GTEx, N = 209) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Frontal Cortex (BA9) UBERON_0009834 1.61 0.59 0.42 1.24 1.56 1.84 5.38 -Brain - Hippocampus (cohort = GTEx, N = 197) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hippocampus UBERON_0001954 2.21 1 0.19 1.47 2.09 2.68 5.95 -Brain - Hypothalamus (cohort = GTEx, N = 202) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hypothalamus UBERON_0001898 1.58 0.83 0.19 1 1.45 2 6.24 -Brain - Nucleus accumbens (basal ganglia) (cohort = GTEx, N = 246) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Nucleus accumbens (basal ganglia) UBERON_0001882 1.36 0.69 0.1 0.91 1.28 1.64 6.23 -Brain - Putamen (basal ganglia) (cohort = GTEx, N = 205) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Putamen (basal ganglia) UBERON_0001874 1.32 0.58 0.26 0.92 1.24 1.6 3.86 -Brain - Spinal cord (cervical c-1) (cohort = GTEx, N = 159) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Spinal cord (cervical c-1) UBERON_0006469 3.34 1.52 0.51 2.19 3.2 4.41 6.84 -Brain - Substantia nigra (cohort = GTEx, N = 139) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Substantia nigra UBERON_0002038 1.74 0.96 0.4 1.06 1.59 2.32 6.38 -Breast - Mammary Tissue (cohort = GTEx, N = 459) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Breast - Mammary Tissue UBERON_0008367 2.27 1.62 0.26 1.17 1.88 2.93 15.34 -Cells - Cultured fibroblasts (cohort = GTEx, N = 504) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cells - Cultured fibroblasts 1.3 0.6 0.33 0.94 1.21 1.49 8.06 -Cells - EBV-transformed lymphocytes (cohort = GTEx, N = 174) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cells - EBV-transformed lymphocytes 2.61 1.56 0.43 1.58 2.33 3.11 11.26 -Cervix - Ectocervix (cohort = GTEx, N = 9) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Ectocervix UBERON_0012249 4.63 2.91 2.15 2.94 3.68 4.47 11.61 -Cervix - Endocervix (cohort = GTEx, N = 10) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Endocervix UBERON_0000458 5.14 4.09 2.33 2.93 3.64 4.68 15.63 -Colon - Sigmoid (cohort = GTEx, N = 373) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Sigmoid UBERON_0001159 1.67 0.83 0.29 1.06 1.55 2.1 5.22 -Colon - Transverse (cohort = GTEx, N = 406) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Transverse UBERON_0001157 2.02 0.87 0.34 1.4 1.92 2.48 8.43 -Esophagus - Gastroesophageal Junction (cohort = GTEx, N = 375) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Gastroesophageal Junction UBERON_0004550 1.13 0.61 0.1 0.68 0.99 1.47 4.08 -Esophagus - Mucosa (cohort = GTEx, N = 555) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Mucosa UBERON_0006920 1.16 0.59 0.13 0.74 1.04 1.42 4.14 -Esophagus - Muscularis (cohort = GTEx, N = 515) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Muscularis UBERON_0004648 1.19 0.65 0.16 0.75 1.05 1.55 5.36 -Fallopian Tube (cohort = GTEx, N = 9) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Fallopian Tube UBERON_0003889 3.32 1.75 0.91 2.7 2.8 4 6.78 -Heart - Atrial Appendage (cohort = GTEx, N = 429) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Atrial Appendage UBERON_0006631 0.63 0.36 0.1 0.38 0.56 0.77 2.66 -Heart - Left Ventricle (cohort = GTEx, N = 432) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Left Ventricle UBERON_0006566 0.44 0.42 0.04 0.25 0.34 0.5 6.14 -Kidney - Cortex (cohort = GTEx, N = 85) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Cortex UBERON_0001225 0.66 0.75 0.1 0.27 0.48 0.72 4.74 -Kidney - Medulla (cohort = GTEx, N = 4) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Medulla UBERON_0001293 0.97 0.47 0.48 0.72 0.92 1.17 1.59 -Liver (cohort = GTEx, N = 226) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Liver UBERON_0001114 0.17 0.2 0 0.07 0.12 0.2 2.17 -Lung (cohort = GTEx, N = 578) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Lung UBERON_0008952 1.52 1.01 0.17 0.88 1.31 1.94 13.43 -Minor Salivary Gland (cohort = GTEx, N = 162) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Minor Salivary Gland UBERON_0006330 2.06 1.2 0.5 1.24 1.84 2.49 8.52 -Muscle - Skeletal (cohort = GTEx, N = 803) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Muscle - Skeletal UBERON_0011907 0.45 0.4 0.02 0.22 0.34 0.54 4.2 -Nerve - Tibial (cohort = GTEx, N = 619) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Nerve - Tibial UBERON_0001323 3 1.11 0.62 2.19 2.89 3.62 9.17 -Ovary (cohort = GTEx, N = 180) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Ovary UBERON_0000992 5.42 3.52 1.26 3.25 4.51 6.42 21.19 -Pancreas (cohort = GTEx, N = 328) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Pancreas UBERON_0001150 0.33 0.32 0.01 0.17 0.26 0.39 3.81 -Pituitary (cohort = GTEx, N = 283) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Pituitary UBERON_0000007 2.24 1.12 0.39 1.51 2.04 2.72 8.7 -Prostate (cohort = GTEx, N = 245) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Prostate UBERON_0002367 2.24 1.05 0.5 1.47 2.08 2.7 5.88 -Skin - Not Sun Exposed (Suprapubic) (cohort = GTEx, N = 604) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Not Sun Exposed (Suprapubic) UBERON_0036149 13.99 6.07 1.61 9.51 13.12 17.57 38.26 -Skin - Sun Exposed (Lower leg) (cohort = GTEx, N = 701) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Sun Exposed (Lower leg) UBERON_0004264 10.98 4.54 1.27 7.77 10.5 13.68 27.79 -Small Intestine - Terminal Ileum (cohort = GTEx, N = 187) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Small Intestine - Terminal Ileum UBERON_0001211 2.74 2 0.47 1.2 2.13 3.67 12.23 -Spleen (cohort = GTEx, N = 241) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Spleen UBERON_0002106 3.1 1.43 0.55 2.2 2.8 3.75 12.37 -Stomach (cohort = GTEx, N = 359) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Stomach UBERON_0000945 0.76 0.46 0.09 0.47 0.65 0.9 4.03 -Testis (cohort = GTEx, N = 361) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Testis UBERON_0000473 32.59 10.03 4.54 25.34 32.61 39.41 75.12 -Thyroid (cohort = GTEx, N = 653) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Thyroid UBERON_0002046 1.07 0.6 0.04 0.67 0.95 1.31 5.28 -Uterus (cohort = GTEx, N = 142) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Uterus UBERON_0000995 6.07 4.41 1.15 3.49 4.65 6.87 25.44 -Vagina (cohort = GTEx, N = 156) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Vagina UBERON_0000996 3.16 1.37 0.94 2.13 2.98 3.79 8.56 diff --git a/tests/results/test-tpm-gene-disease-gtex-ENSG00000213420-MONDO_0016680.tsv b/tests/results/test-tpm-gene-disease-gtex-ENSG00000213420-MONDO_0016680.tsv new file mode 100644 index 0000000..6a180eb --- /dev/null +++ b/tests/results/test-tpm-gene-disease-gtex-ENSG00000213420-MONDO_0016680.tsv @@ -0,0 +1,55 @@ +x_labels Gene_Ensembl_ID Gene_symbol PMTL Dataset Disease GTEx_tissue_subgroup EFO MONDO GTEx_tissue_subgroup_UBERON TPM_mean TPM_sd TPM_min TPM_25th_percentile TPM_median TPM_75th_percentile TPM_max +High-grade glioma/astrocytoma (Dataset = PBTA, N = 51) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA High-grade glioma/astrocytoma MONDO_0016680 MONDO_0100342 11.23 14 0.15 2.74 5.66 14.88 59.91 +Adipose - Subcutaneous (Dataset = GTEx, N = 663) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Subcutaneous UBERON_0002190 1.76 0.82 0.3 1.17 1.66 2.18 5.47 +Adipose - Visceral (Omentum) (Dataset = GTEx, N = 541) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Visceral (Omentum) UBERON_0010414 1.2 0.65 0.14 0.71 1.04 1.54 4.09 +Adrenal Gland (Dataset = GTEx, N = 258) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Adrenal Gland UBERON_0002369 0.72 0.36 0.18 0.51 0.63 0.86 3.25 +Artery - Aorta (Dataset = GTEx, N = 432) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Aorta UBERON_0001496 1.45 0.74 0.35 0.98 1.3 1.69 5.66 +Artery - Coronary (Dataset = GTEx, N = 240) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Coronary UBERON_0001621 1.37 0.95 0.17 0.84 1.14 1.63 10.15 +Artery - Tibial (Dataset = GTEx, N = 663) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Tibial UBERON_0007610 0.75 0.59 0 0.39 0.61 0.93 6.25 +Bladder (Dataset = GTEx, N = 21) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Bladder UBERON_0001255 1.98 1.25 0.73 1.16 1.85 2.11 5.98 +Blood (Dataset = GTEx, N = 755) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Blood UBERON_0013756 1.04 1.81 0 0.45 0.8 1.26 45.04 +Brain - Amygdala (Dataset = GTEx, N = 152) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Amygdala UBERON_0001876 2.29 0.86 0.21 1.66 2.22 2.84 5.07 +Brain - Anterior cingulate cortex (BA24) (Dataset = GTEx, N = 176) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Anterior cingulate cortex (BA24) UBERON_0009835 1.86 0.65 0.28 1.42 1.78 2.16 4.74 +Brain - Caudate (basal ganglia) (Dataset = GTEx, N = 246) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Caudate (basal ganglia) UBERON_0001873 1.35 0.5 0.28 0.98 1.35 1.64 3.44 +Brain - Cerebellum (Dataset = GTEx, N = 456) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cerebellum UBERON_0002037 3.2 1.91 0.54 2.01 2.78 3.67 15.63 +Brain - Cortex (Dataset = GTEx, N = 255) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cortex UBERON_0001870 1.63 0.57 0.45 1.23 1.53 1.95 4.32 +Brain - Frontal Cortex (BA9) (Dataset = GTEx, N = 209) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Frontal Cortex (BA9) UBERON_0009834 1.61 0.59 0.42 1.24 1.56 1.84 5.38 +Brain - Hippocampus (Dataset = GTEx, N = 197) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hippocampus UBERON_0001954 2.21 1 0.19 1.47 2.09 2.68 5.95 +Brain - Hypothalamus (Dataset = GTEx, N = 202) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hypothalamus UBERON_0001898 1.58 0.83 0.19 1 1.45 2 6.24 +Brain - Nucleus accumbens (basal ganglia) (Dataset = GTEx, N = 246) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Nucleus accumbens (basal ganglia) UBERON_0001882 1.36 0.69 0.1 0.91 1.28 1.64 6.23 +Brain - Putamen (basal ganglia) (Dataset = GTEx, N = 205) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Putamen (basal ganglia) UBERON_0001874 1.32 0.58 0.26 0.92 1.24 1.6 3.86 +Brain - Spinal cord (cervical c-1) (Dataset = GTEx, N = 159) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Spinal cord (cervical c-1) UBERON_0006469 3.34 1.52 0.51 2.19 3.2 4.41 6.84 +Brain - Substantia nigra (Dataset = GTEx, N = 139) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Substantia nigra UBERON_0002038 1.74 0.96 0.4 1.06 1.59 2.32 6.38 +Breast - Mammary Tissue (Dataset = GTEx, N = 459) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Breast - Mammary Tissue UBERON_0008367 2.27 1.62 0.26 1.17 1.88 2.93 15.34 +Cells - Cultured fibroblasts (Dataset = GTEx, N = 504) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cells - Cultured fibroblasts 1.3 0.6 0.33 0.94 1.21 1.49 8.06 +Cells - EBV-transformed lymphocytes (Dataset = GTEx, N = 174) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cells - EBV-transformed lymphocytes 2.61 1.56 0.43 1.58 2.33 3.11 11.26 +Cervix - Ectocervix (Dataset = GTEx, N = 9) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Ectocervix UBERON_0012249 4.63 2.91 2.15 2.94 3.68 4.47 11.61 +Cervix - Endocervix (Dataset = GTEx, N = 10) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Endocervix UBERON_0000458 5.14 4.09 2.33 2.93 3.64 4.68 15.63 +Colon - Sigmoid (Dataset = GTEx, N = 373) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Sigmoid UBERON_0001159 1.67 0.83 0.29 1.06 1.55 2.1 5.22 +Colon - Transverse (Dataset = GTEx, N = 406) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Transverse UBERON_0001157 2.02 0.87 0.34 1.4 1.92 2.48 8.43 +Esophagus - Gastroesophageal Junction (Dataset = GTEx, N = 375) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Gastroesophageal Junction UBERON_0004550 1.13 0.61 0.1 0.68 0.99 1.47 4.08 +Esophagus - Mucosa (Dataset = GTEx, N = 555) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Mucosa UBERON_0006920 1.16 0.59 0.13 0.74 1.04 1.42 4.14 +Esophagus - Muscularis (Dataset = GTEx, N = 515) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Muscularis UBERON_0004648 1.19 0.65 0.16 0.75 1.05 1.55 5.36 +Fallopian Tube (Dataset = GTEx, N = 9) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Fallopian Tube UBERON_0003889 3.32 1.75 0.91 2.7 2.8 4 6.78 +Heart - Atrial Appendage (Dataset = GTEx, N = 429) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Atrial Appendage UBERON_0006631 0.63 0.36 0.1 0.38 0.56 0.77 2.66 +Heart - Left Ventricle (Dataset = GTEx, N = 432) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Left Ventricle UBERON_0006566 0.44 0.42 0.04 0.25 0.34 0.5 6.14 +Kidney - Cortex (Dataset = GTEx, N = 85) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Cortex UBERON_0001225 0.66 0.75 0.1 0.27 0.48 0.72 4.74 +Kidney - Medulla (Dataset = GTEx, N = 4) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Medulla UBERON_0001293 0.97 0.47 0.48 0.72 0.92 1.17 1.59 +Liver (Dataset = GTEx, N = 226) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Liver UBERON_0001114 0.17 0.2 0 0.07 0.12 0.2 2.17 +Lung (Dataset = GTEx, N = 578) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Lung UBERON_0008952 1.52 1.01 0.17 0.88 1.31 1.94 13.43 +Minor Salivary Gland (Dataset = GTEx, N = 162) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Minor Salivary Gland UBERON_0006330 2.06 1.2 0.5 1.24 1.84 2.49 8.52 +Muscle - Skeletal (Dataset = GTEx, N = 803) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Muscle - Skeletal UBERON_0011907 0.45 0.4 0.02 0.22 0.34 0.54 4.2 +Nerve - Tibial (Dataset = GTEx, N = 619) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Nerve - Tibial UBERON_0001323 3 1.11 0.62 2.19 2.89 3.62 9.17 +Ovary (Dataset = GTEx, N = 180) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Ovary UBERON_0000992 5.42 3.52 1.26 3.25 4.51 6.42 21.19 +Pancreas (Dataset = GTEx, N = 328) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Pancreas UBERON_0001150 0.33 0.32 0.01 0.17 0.26 0.39 3.81 +Pituitary (Dataset = GTEx, N = 283) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Pituitary UBERON_0000007 2.24 1.12 0.39 1.51 2.04 2.72 8.7 +Prostate (Dataset = GTEx, N = 245) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Prostate UBERON_0002367 2.24 1.05 0.5 1.47 2.08 2.7 5.88 +Skin - Not Sun Exposed (Suprapubic) (Dataset = GTEx, N = 604) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Not Sun Exposed (Suprapubic) UBERON_0036149 13.99 6.07 1.61 9.51 13.12 17.57 38.26 +Skin - Sun Exposed (Lower leg) (Dataset = GTEx, N = 701) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Sun Exposed (Lower leg) UBERON_0004264 10.98 4.54 1.27 7.77 10.5 13.68 27.79 +Small Intestine - Terminal Ileum (Dataset = GTEx, N = 187) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Small Intestine - Terminal Ileum UBERON_0001211 2.74 2 0.47 1.2 2.13 3.67 12.23 +Spleen (Dataset = GTEx, N = 241) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Spleen UBERON_0002106 3.1 1.43 0.55 2.2 2.8 3.75 12.37 +Stomach (Dataset = GTEx, N = 359) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Stomach UBERON_0000945 0.76 0.46 0.09 0.47 0.65 0.9 4.03 +Testis (Dataset = GTEx, N = 361) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Testis UBERON_0000473 32.59 10.03 4.54 25.34 32.61 39.41 75.12 +Thyroid (Dataset = GTEx, N = 653) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Thyroid UBERON_0002046 1.07 0.6 0.04 0.67 0.95 1.31 5.28 +Uterus (Dataset = GTEx, N = 142) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Uterus UBERON_0000995 6.07 4.41 1.15 3.49 4.65 6.87 25.44 +Vagina (Dataset = GTEx, N = 156) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Vagina UBERON_0000996 3.16 1.37 0.94 2.13 2.98 3.79 8.56 diff --git a/tests/results/test-tpm-gene-disease-gtex-ENSG00000213420-MONDO_0016685.tsv b/tests/results/test-tpm-gene-disease-gtex-ENSG00000213420-MONDO_0016685.tsv new file mode 100644 index 0000000..65dbafe --- /dev/null +++ b/tests/results/test-tpm-gene-disease-gtex-ENSG00000213420-MONDO_0016685.tsv @@ -0,0 +1,55 @@ +x_labels Gene_Ensembl_ID Gene_symbol PMTL Dataset Disease GTEx_tissue_subgroup EFO MONDO GTEx_tissue_subgroup_UBERON TPM_mean TPM_sd TPM_min TPM_25th_percentile TPM_median TPM_75th_percentile TPM_max +Low-grade glioma/astrocytoma (Dataset = PBTA, N = 237) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Low-grade glioma/astrocytoma MONDO_0016685 MONDO_0016685 2.88 2.14 0.17 1.27 2.48 4.11 12.52 +Adipose - Subcutaneous (Dataset = GTEx, N = 663) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Subcutaneous UBERON_0002190 1.76 0.82 0.3 1.17 1.66 2.18 5.47 +Adipose - Visceral (Omentum) (Dataset = GTEx, N = 541) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Visceral (Omentum) UBERON_0010414 1.2 0.65 0.14 0.71 1.04 1.54 4.09 +Adrenal Gland (Dataset = GTEx, N = 258) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Adrenal Gland UBERON_0002369 0.72 0.36 0.18 0.51 0.63 0.86 3.25 +Artery - Aorta (Dataset = GTEx, N = 432) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Aorta UBERON_0001496 1.45 0.74 0.35 0.98 1.3 1.69 5.66 +Artery - Coronary (Dataset = GTEx, N = 240) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Coronary UBERON_0001621 1.37 0.95 0.17 0.84 1.14 1.63 10.15 +Artery - Tibial (Dataset = GTEx, N = 663) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Tibial UBERON_0007610 0.75 0.59 0 0.39 0.61 0.93 6.25 +Bladder (Dataset = GTEx, N = 21) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Bladder UBERON_0001255 1.98 1.25 0.73 1.16 1.85 2.11 5.98 +Blood (Dataset = GTEx, N = 755) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Blood UBERON_0013756 1.04 1.81 0 0.45 0.8 1.26 45.04 +Brain - Amygdala (Dataset = GTEx, N = 152) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Amygdala UBERON_0001876 2.29 0.86 0.21 1.66 2.22 2.84 5.07 +Brain - Anterior cingulate cortex (BA24) (Dataset = GTEx, N = 176) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Anterior cingulate cortex (BA24) UBERON_0009835 1.86 0.65 0.28 1.42 1.78 2.16 4.74 +Brain - Caudate (basal ganglia) (Dataset = GTEx, N = 246) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Caudate (basal ganglia) UBERON_0001873 1.35 0.5 0.28 0.98 1.35 1.64 3.44 +Brain - Cerebellum (Dataset = GTEx, N = 456) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cerebellum UBERON_0002037 3.2 1.91 0.54 2.01 2.78 3.67 15.63 +Brain - Cortex (Dataset = GTEx, N = 255) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cortex UBERON_0001870 1.63 0.57 0.45 1.23 1.53 1.95 4.32 +Brain - Frontal Cortex (BA9) (Dataset = GTEx, N = 209) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Frontal Cortex (BA9) UBERON_0009834 1.61 0.59 0.42 1.24 1.56 1.84 5.38 +Brain - Hippocampus (Dataset = GTEx, N = 197) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hippocampus UBERON_0001954 2.21 1 0.19 1.47 2.09 2.68 5.95 +Brain - Hypothalamus (Dataset = GTEx, N = 202) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hypothalamus UBERON_0001898 1.58 0.83 0.19 1 1.45 2 6.24 +Brain - Nucleus accumbens (basal ganglia) (Dataset = GTEx, N = 246) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Nucleus accumbens (basal ganglia) UBERON_0001882 1.36 0.69 0.1 0.91 1.28 1.64 6.23 +Brain - Putamen (basal ganglia) (Dataset = GTEx, N = 205) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Putamen (basal ganglia) UBERON_0001874 1.32 0.58 0.26 0.92 1.24 1.6 3.86 +Brain - Spinal cord (cervical c-1) (Dataset = GTEx, N = 159) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Spinal cord (cervical c-1) UBERON_0006469 3.34 1.52 0.51 2.19 3.2 4.41 6.84 +Brain - Substantia nigra (Dataset = GTEx, N = 139) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Substantia nigra UBERON_0002038 1.74 0.96 0.4 1.06 1.59 2.32 6.38 +Breast - Mammary Tissue (Dataset = GTEx, N = 459) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Breast - Mammary Tissue UBERON_0008367 2.27 1.62 0.26 1.17 1.88 2.93 15.34 +Cells - Cultured fibroblasts (Dataset = GTEx, N = 504) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cells - Cultured fibroblasts 1.3 0.6 0.33 0.94 1.21 1.49 8.06 +Cells - EBV-transformed lymphocytes (Dataset = GTEx, N = 174) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cells - EBV-transformed lymphocytes 2.61 1.56 0.43 1.58 2.33 3.11 11.26 +Cervix - Ectocervix (Dataset = GTEx, N = 9) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Ectocervix UBERON_0012249 4.63 2.91 2.15 2.94 3.68 4.47 11.61 +Cervix - Endocervix (Dataset = GTEx, N = 10) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Endocervix UBERON_0000458 5.14 4.09 2.33 2.93 3.64 4.68 15.63 +Colon - Sigmoid (Dataset = GTEx, N = 373) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Sigmoid UBERON_0001159 1.67 0.83 0.29 1.06 1.55 2.1 5.22 +Colon - Transverse (Dataset = GTEx, N = 406) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Transverse UBERON_0001157 2.02 0.87 0.34 1.4 1.92 2.48 8.43 +Esophagus - Gastroesophageal Junction (Dataset = GTEx, N = 375) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Gastroesophageal Junction UBERON_0004550 1.13 0.61 0.1 0.68 0.99 1.47 4.08 +Esophagus - Mucosa (Dataset = GTEx, N = 555) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Mucosa UBERON_0006920 1.16 0.59 0.13 0.74 1.04 1.42 4.14 +Esophagus - Muscularis (Dataset = GTEx, N = 515) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Muscularis UBERON_0004648 1.19 0.65 0.16 0.75 1.05 1.55 5.36 +Fallopian Tube (Dataset = GTEx, N = 9) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Fallopian Tube UBERON_0003889 3.32 1.75 0.91 2.7 2.8 4 6.78 +Heart - Atrial Appendage (Dataset = GTEx, N = 429) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Atrial Appendage UBERON_0006631 0.63 0.36 0.1 0.38 0.56 0.77 2.66 +Heart - Left Ventricle (Dataset = GTEx, N = 432) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Left Ventricle UBERON_0006566 0.44 0.42 0.04 0.25 0.34 0.5 6.14 +Kidney - Cortex (Dataset = GTEx, N = 85) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Cortex UBERON_0001225 0.66 0.75 0.1 0.27 0.48 0.72 4.74 +Kidney - Medulla (Dataset = GTEx, N = 4) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Medulla UBERON_0001293 0.97 0.47 0.48 0.72 0.92 1.17 1.59 +Liver (Dataset = GTEx, N = 226) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Liver UBERON_0001114 0.17 0.2 0 0.07 0.12 0.2 2.17 +Lung (Dataset = GTEx, N = 578) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Lung UBERON_0008952 1.52 1.01 0.17 0.88 1.31 1.94 13.43 +Minor Salivary Gland (Dataset = GTEx, N = 162) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Minor Salivary Gland UBERON_0006330 2.06 1.2 0.5 1.24 1.84 2.49 8.52 +Muscle - Skeletal (Dataset = GTEx, N = 803) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Muscle - Skeletal UBERON_0011907 0.45 0.4 0.02 0.22 0.34 0.54 4.2 +Nerve - Tibial (Dataset = GTEx, N = 619) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Nerve - Tibial UBERON_0001323 3 1.11 0.62 2.19 2.89 3.62 9.17 +Ovary (Dataset = GTEx, N = 180) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Ovary UBERON_0000992 5.42 3.52 1.26 3.25 4.51 6.42 21.19 +Pancreas (Dataset = GTEx, N = 328) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Pancreas UBERON_0001150 0.33 0.32 0.01 0.17 0.26 0.39 3.81 +Pituitary (Dataset = GTEx, N = 283) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Pituitary UBERON_0000007 2.24 1.12 0.39 1.51 2.04 2.72 8.7 +Prostate (Dataset = GTEx, N = 245) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Prostate UBERON_0002367 2.24 1.05 0.5 1.47 2.08 2.7 5.88 +Skin - Not Sun Exposed (Suprapubic) (Dataset = GTEx, N = 604) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Not Sun Exposed (Suprapubic) UBERON_0036149 13.99 6.07 1.61 9.51 13.12 17.57 38.26 +Skin - Sun Exposed (Lower leg) (Dataset = GTEx, N = 701) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Sun Exposed (Lower leg) UBERON_0004264 10.98 4.54 1.27 7.77 10.5 13.68 27.79 +Small Intestine - Terminal Ileum (Dataset = GTEx, N = 187) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Small Intestine - Terminal Ileum UBERON_0001211 2.74 2 0.47 1.2 2.13 3.67 12.23 +Spleen (Dataset = GTEx, N = 241) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Spleen UBERON_0002106 3.1 1.43 0.55 2.2 2.8 3.75 12.37 +Stomach (Dataset = GTEx, N = 359) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Stomach UBERON_0000945 0.76 0.46 0.09 0.47 0.65 0.9 4.03 +Testis (Dataset = GTEx, N = 361) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Testis UBERON_0000473 32.59 10.03 4.54 25.34 32.61 39.41 75.12 +Thyroid (Dataset = GTEx, N = 653) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Thyroid UBERON_0002046 1.07 0.6 0.04 0.67 0.95 1.31 5.28 +Uterus (Dataset = GTEx, N = 142) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Uterus UBERON_0000995 6.07 4.41 1.15 3.49 4.65 6.87 25.44 +Vagina (Dataset = GTEx, N = 156) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Vagina UBERON_0000996 3.16 1.37 0.94 2.13 2.98 3.79 8.56 diff --git a/tests/results/test-tpm-gene-disease-gtex-ENSG00000213420-MONDO_0016718.tsv b/tests/results/test-tpm-gene-disease-gtex-ENSG00000213420-MONDO_0016718.tsv new file mode 100644 index 0000000..f8b66f7 --- /dev/null +++ b/tests/results/test-tpm-gene-disease-gtex-ENSG00000213420-MONDO_0016718.tsv @@ -0,0 +1,55 @@ +x_labels Gene_Ensembl_ID Gene_symbol PMTL Dataset Disease GTEx_tissue_subgroup EFO MONDO GTEx_tissue_subgroup_UBERON TPM_mean TPM_sd TPM_min TPM_25th_percentile TPM_median TPM_75th_percentile TPM_max +Choroid plexus carcinoma (Dataset = PBTA, N = 4) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Choroid plexus carcinoma MONDO_0016718 MONDO_0016718 12.53 11.31 2.74 3.27 10.87 20.14 25.64 +Adipose - Subcutaneous (Dataset = GTEx, N = 663) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Subcutaneous UBERON_0002190 1.76 0.82 0.3 1.17 1.66 2.18 5.47 +Adipose - Visceral (Omentum) (Dataset = GTEx, N = 541) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Visceral (Omentum) UBERON_0010414 1.2 0.65 0.14 0.71 1.04 1.54 4.09 +Adrenal Gland (Dataset = GTEx, N = 258) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Adrenal Gland UBERON_0002369 0.72 0.36 0.18 0.51 0.63 0.86 3.25 +Artery - Aorta (Dataset = GTEx, N = 432) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Aorta UBERON_0001496 1.45 0.74 0.35 0.98 1.3 1.69 5.66 +Artery - Coronary (Dataset = GTEx, N = 240) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Coronary UBERON_0001621 1.37 0.95 0.17 0.84 1.14 1.63 10.15 +Artery - Tibial (Dataset = GTEx, N = 663) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Tibial UBERON_0007610 0.75 0.59 0 0.39 0.61 0.93 6.25 +Bladder (Dataset = GTEx, N = 21) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Bladder UBERON_0001255 1.98 1.25 0.73 1.16 1.85 2.11 5.98 +Blood (Dataset = GTEx, N = 755) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Blood UBERON_0013756 1.04 1.81 0 0.45 0.8 1.26 45.04 +Brain - Amygdala (Dataset = GTEx, N = 152) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Amygdala UBERON_0001876 2.29 0.86 0.21 1.66 2.22 2.84 5.07 +Brain - Anterior cingulate cortex (BA24) (Dataset = GTEx, N = 176) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Anterior cingulate cortex (BA24) UBERON_0009835 1.86 0.65 0.28 1.42 1.78 2.16 4.74 +Brain - Caudate (basal ganglia) (Dataset = GTEx, N = 246) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Caudate (basal ganglia) UBERON_0001873 1.35 0.5 0.28 0.98 1.35 1.64 3.44 +Brain - Cerebellum (Dataset = GTEx, N = 456) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cerebellum UBERON_0002037 3.2 1.91 0.54 2.01 2.78 3.67 15.63 +Brain - Cortex (Dataset = GTEx, N = 255) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cortex UBERON_0001870 1.63 0.57 0.45 1.23 1.53 1.95 4.32 +Brain - Frontal Cortex (BA9) (Dataset = GTEx, N = 209) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Frontal Cortex (BA9) UBERON_0009834 1.61 0.59 0.42 1.24 1.56 1.84 5.38 +Brain - Hippocampus (Dataset = GTEx, N = 197) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hippocampus UBERON_0001954 2.21 1 0.19 1.47 2.09 2.68 5.95 +Brain - Hypothalamus (Dataset = GTEx, N = 202) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hypothalamus UBERON_0001898 1.58 0.83 0.19 1 1.45 2 6.24 +Brain - Nucleus accumbens (basal ganglia) (Dataset = GTEx, N = 246) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Nucleus accumbens (basal ganglia) UBERON_0001882 1.36 0.69 0.1 0.91 1.28 1.64 6.23 +Brain - Putamen (basal ganglia) (Dataset = GTEx, N = 205) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Putamen (basal ganglia) UBERON_0001874 1.32 0.58 0.26 0.92 1.24 1.6 3.86 +Brain - Spinal cord (cervical c-1) (Dataset = GTEx, N = 159) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Spinal cord (cervical c-1) UBERON_0006469 3.34 1.52 0.51 2.19 3.2 4.41 6.84 +Brain - Substantia nigra (Dataset = GTEx, N = 139) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Substantia nigra UBERON_0002038 1.74 0.96 0.4 1.06 1.59 2.32 6.38 +Breast - Mammary Tissue (Dataset = GTEx, N = 459) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Breast - Mammary Tissue UBERON_0008367 2.27 1.62 0.26 1.17 1.88 2.93 15.34 +Cells - Cultured fibroblasts (Dataset = GTEx, N = 504) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cells - Cultured fibroblasts 1.3 0.6 0.33 0.94 1.21 1.49 8.06 +Cells - EBV-transformed lymphocytes (Dataset = GTEx, N = 174) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cells - EBV-transformed lymphocytes 2.61 1.56 0.43 1.58 2.33 3.11 11.26 +Cervix - Ectocervix (Dataset = GTEx, N = 9) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Ectocervix UBERON_0012249 4.63 2.91 2.15 2.94 3.68 4.47 11.61 +Cervix - Endocervix (Dataset = GTEx, N = 10) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Endocervix UBERON_0000458 5.14 4.09 2.33 2.93 3.64 4.68 15.63 +Colon - Sigmoid (Dataset = GTEx, N = 373) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Sigmoid UBERON_0001159 1.67 0.83 0.29 1.06 1.55 2.1 5.22 +Colon - Transverse (Dataset = GTEx, N = 406) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Transverse UBERON_0001157 2.02 0.87 0.34 1.4 1.92 2.48 8.43 +Esophagus - Gastroesophageal Junction (Dataset = GTEx, N = 375) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Gastroesophageal Junction UBERON_0004550 1.13 0.61 0.1 0.68 0.99 1.47 4.08 +Esophagus - Mucosa (Dataset = GTEx, N = 555) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Mucosa UBERON_0006920 1.16 0.59 0.13 0.74 1.04 1.42 4.14 +Esophagus - Muscularis (Dataset = GTEx, N = 515) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Muscularis UBERON_0004648 1.19 0.65 0.16 0.75 1.05 1.55 5.36 +Fallopian Tube (Dataset = GTEx, N = 9) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Fallopian Tube UBERON_0003889 3.32 1.75 0.91 2.7 2.8 4 6.78 +Heart - Atrial Appendage (Dataset = GTEx, N = 429) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Atrial Appendage UBERON_0006631 0.63 0.36 0.1 0.38 0.56 0.77 2.66 +Heart - Left Ventricle (Dataset = GTEx, N = 432) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Left Ventricle UBERON_0006566 0.44 0.42 0.04 0.25 0.34 0.5 6.14 +Kidney - Cortex (Dataset = GTEx, N = 85) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Cortex UBERON_0001225 0.66 0.75 0.1 0.27 0.48 0.72 4.74 +Kidney - Medulla (Dataset = GTEx, N = 4) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Medulla UBERON_0001293 0.97 0.47 0.48 0.72 0.92 1.17 1.59 +Liver (Dataset = GTEx, N = 226) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Liver UBERON_0001114 0.17 0.2 0 0.07 0.12 0.2 2.17 +Lung (Dataset = GTEx, N = 578) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Lung UBERON_0008952 1.52 1.01 0.17 0.88 1.31 1.94 13.43 +Minor Salivary Gland (Dataset = GTEx, N = 162) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Minor Salivary Gland UBERON_0006330 2.06 1.2 0.5 1.24 1.84 2.49 8.52 +Muscle - Skeletal (Dataset = GTEx, N = 803) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Muscle - Skeletal UBERON_0011907 0.45 0.4 0.02 0.22 0.34 0.54 4.2 +Nerve - Tibial (Dataset = GTEx, N = 619) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Nerve - Tibial UBERON_0001323 3 1.11 0.62 2.19 2.89 3.62 9.17 +Ovary (Dataset = GTEx, N = 180) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Ovary UBERON_0000992 5.42 3.52 1.26 3.25 4.51 6.42 21.19 +Pancreas (Dataset = GTEx, N = 328) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Pancreas UBERON_0001150 0.33 0.32 0.01 0.17 0.26 0.39 3.81 +Pituitary (Dataset = GTEx, N = 283) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Pituitary UBERON_0000007 2.24 1.12 0.39 1.51 2.04 2.72 8.7 +Prostate (Dataset = GTEx, N = 245) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Prostate UBERON_0002367 2.24 1.05 0.5 1.47 2.08 2.7 5.88 +Skin - Not Sun Exposed (Suprapubic) (Dataset = GTEx, N = 604) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Not Sun Exposed (Suprapubic) UBERON_0036149 13.99 6.07 1.61 9.51 13.12 17.57 38.26 +Skin - Sun Exposed (Lower leg) (Dataset = GTEx, N = 701) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Sun Exposed (Lower leg) UBERON_0004264 10.98 4.54 1.27 7.77 10.5 13.68 27.79 +Small Intestine - Terminal Ileum (Dataset = GTEx, N = 187) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Small Intestine - Terminal Ileum UBERON_0001211 2.74 2 0.47 1.2 2.13 3.67 12.23 +Spleen (Dataset = GTEx, N = 241) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Spleen UBERON_0002106 3.1 1.43 0.55 2.2 2.8 3.75 12.37 +Stomach (Dataset = GTEx, N = 359) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Stomach UBERON_0000945 0.76 0.46 0.09 0.47 0.65 0.9 4.03 +Testis (Dataset = GTEx, N = 361) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Testis UBERON_0000473 32.59 10.03 4.54 25.34 32.61 39.41 75.12 +Thyroid (Dataset = GTEx, N = 653) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Thyroid UBERON_0002046 1.07 0.6 0.04 0.67 0.95 1.31 5.28 +Uterus (Dataset = GTEx, N = 142) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Uterus UBERON_0000995 6.07 4.41 1.15 3.49 4.65 6.87 25.44 +Vagina (Dataset = GTEx, N = 156) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Vagina UBERON_0000996 3.16 1.37 0.94 2.13 2.98 3.79 8.56 diff --git a/tests/results/test-tpm-gene-disease-gtex-ENSG00000213420-Orphanet_178.tsv b/tests/results/test-tpm-gene-disease-gtex-ENSG00000213420-Orphanet_178.tsv new file mode 100644 index 0000000..e9c512a --- /dev/null +++ b/tests/results/test-tpm-gene-disease-gtex-ENSG00000213420-Orphanet_178.tsv @@ -0,0 +1,55 @@ +x_labels Gene_Ensembl_ID Gene_symbol PMTL Dataset Disease GTEx_tissue_subgroup EFO MONDO GTEx_tissue_subgroup_UBERON TPM_mean TPM_sd TPM_min TPM_25th_percentile TPM_median TPM_75th_percentile TPM_max +Chordoma (Dataset = PBTA, N = 3) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) PBTA Chordoma Orphanet_178 MONDO_0008978 0.54 0.12 0.4 0.49 0.58 0.61 0.64 +Adipose - Subcutaneous (Dataset = GTEx, N = 663) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Subcutaneous UBERON_0002190 1.76 0.82 0.3 1.17 1.66 2.18 5.47 +Adipose - Visceral (Omentum) (Dataset = GTEx, N = 541) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Adipose - Visceral (Omentum) UBERON_0010414 1.2 0.65 0.14 0.71 1.04 1.54 4.09 +Adrenal Gland (Dataset = GTEx, N = 258) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Adrenal Gland UBERON_0002369 0.72 0.36 0.18 0.51 0.63 0.86 3.25 +Artery - Aorta (Dataset = GTEx, N = 432) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Aorta UBERON_0001496 1.45 0.74 0.35 0.98 1.3 1.69 5.66 +Artery - Coronary (Dataset = GTEx, N = 240) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Coronary UBERON_0001621 1.37 0.95 0.17 0.84 1.14 1.63 10.15 +Artery - Tibial (Dataset = GTEx, N = 663) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Artery - Tibial UBERON_0007610 0.75 0.59 0 0.39 0.61 0.93 6.25 +Bladder (Dataset = GTEx, N = 21) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Bladder UBERON_0001255 1.98 1.25 0.73 1.16 1.85 2.11 5.98 +Blood (Dataset = GTEx, N = 755) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Blood UBERON_0013756 1.04 1.81 0 0.45 0.8 1.26 45.04 +Brain - Amygdala (Dataset = GTEx, N = 152) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Amygdala UBERON_0001876 2.29 0.86 0.21 1.66 2.22 2.84 5.07 +Brain - Anterior cingulate cortex (BA24) (Dataset = GTEx, N = 176) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Anterior cingulate cortex (BA24) UBERON_0009835 1.86 0.65 0.28 1.42 1.78 2.16 4.74 +Brain - Caudate (basal ganglia) (Dataset = GTEx, N = 246) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Caudate (basal ganglia) UBERON_0001873 1.35 0.5 0.28 0.98 1.35 1.64 3.44 +Brain - Cerebellum (Dataset = GTEx, N = 456) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cerebellum UBERON_0002037 3.2 1.91 0.54 2.01 2.78 3.67 15.63 +Brain - Cortex (Dataset = GTEx, N = 255) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Cortex UBERON_0001870 1.63 0.57 0.45 1.23 1.53 1.95 4.32 +Brain - Frontal Cortex (BA9) (Dataset = GTEx, N = 209) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Frontal Cortex (BA9) UBERON_0009834 1.61 0.59 0.42 1.24 1.56 1.84 5.38 +Brain - Hippocampus (Dataset = GTEx, N = 197) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hippocampus UBERON_0001954 2.21 1 0.19 1.47 2.09 2.68 5.95 +Brain - Hypothalamus (Dataset = GTEx, N = 202) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Hypothalamus UBERON_0001898 1.58 0.83 0.19 1 1.45 2 6.24 +Brain - Nucleus accumbens (basal ganglia) (Dataset = GTEx, N = 246) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Nucleus accumbens (basal ganglia) UBERON_0001882 1.36 0.69 0.1 0.91 1.28 1.64 6.23 +Brain - Putamen (basal ganglia) (Dataset = GTEx, N = 205) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Putamen (basal ganglia) UBERON_0001874 1.32 0.58 0.26 0.92 1.24 1.6 3.86 +Brain - Spinal cord (cervical c-1) (Dataset = GTEx, N = 159) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Spinal cord (cervical c-1) UBERON_0006469 3.34 1.52 0.51 2.19 3.2 4.41 6.84 +Brain - Substantia nigra (Dataset = GTEx, N = 139) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Brain - Substantia nigra UBERON_0002038 1.74 0.96 0.4 1.06 1.59 2.32 6.38 +Breast - Mammary Tissue (Dataset = GTEx, N = 459) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Breast - Mammary Tissue UBERON_0008367 2.27 1.62 0.26 1.17 1.88 2.93 15.34 +Cells - Cultured fibroblasts (Dataset = GTEx, N = 504) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cells - Cultured fibroblasts 1.3 0.6 0.33 0.94 1.21 1.49 8.06 +Cells - EBV-transformed lymphocytes (Dataset = GTEx, N = 174) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cells - EBV-transformed lymphocytes 2.61 1.56 0.43 1.58 2.33 3.11 11.26 +Cervix - Ectocervix (Dataset = GTEx, N = 9) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Ectocervix UBERON_0012249 4.63 2.91 2.15 2.94 3.68 4.47 11.61 +Cervix - Endocervix (Dataset = GTEx, N = 10) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Cervix - Endocervix UBERON_0000458 5.14 4.09 2.33 2.93 3.64 4.68 15.63 +Colon - Sigmoid (Dataset = GTEx, N = 373) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Sigmoid UBERON_0001159 1.67 0.83 0.29 1.06 1.55 2.1 5.22 +Colon - Transverse (Dataset = GTEx, N = 406) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Colon - Transverse UBERON_0001157 2.02 0.87 0.34 1.4 1.92 2.48 8.43 +Esophagus - Gastroesophageal Junction (Dataset = GTEx, N = 375) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Gastroesophageal Junction UBERON_0004550 1.13 0.61 0.1 0.68 0.99 1.47 4.08 +Esophagus - Mucosa (Dataset = GTEx, N = 555) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Mucosa UBERON_0006920 1.16 0.59 0.13 0.74 1.04 1.42 4.14 +Esophagus - Muscularis (Dataset = GTEx, N = 515) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Esophagus - Muscularis UBERON_0004648 1.19 0.65 0.16 0.75 1.05 1.55 5.36 +Fallopian Tube (Dataset = GTEx, N = 9) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Fallopian Tube UBERON_0003889 3.32 1.75 0.91 2.7 2.8 4 6.78 +Heart - Atrial Appendage (Dataset = GTEx, N = 429) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Atrial Appendage UBERON_0006631 0.63 0.36 0.1 0.38 0.56 0.77 2.66 +Heart - Left Ventricle (Dataset = GTEx, N = 432) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Heart - Left Ventricle UBERON_0006566 0.44 0.42 0.04 0.25 0.34 0.5 6.14 +Kidney - Cortex (Dataset = GTEx, N = 85) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Cortex UBERON_0001225 0.66 0.75 0.1 0.27 0.48 0.72 4.74 +Kidney - Medulla (Dataset = GTEx, N = 4) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Kidney - Medulla UBERON_0001293 0.97 0.47 0.48 0.72 0.92 1.17 1.59 +Liver (Dataset = GTEx, N = 226) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Liver UBERON_0001114 0.17 0.2 0 0.07 0.12 0.2 2.17 +Lung (Dataset = GTEx, N = 578) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Lung UBERON_0008952 1.52 1.01 0.17 0.88 1.31 1.94 13.43 +Minor Salivary Gland (Dataset = GTEx, N = 162) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Minor Salivary Gland UBERON_0006330 2.06 1.2 0.5 1.24 1.84 2.49 8.52 +Muscle - Skeletal (Dataset = GTEx, N = 803) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Muscle - Skeletal UBERON_0011907 0.45 0.4 0.02 0.22 0.34 0.54 4.2 +Nerve - Tibial (Dataset = GTEx, N = 619) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Nerve - Tibial UBERON_0001323 3 1.11 0.62 2.19 2.89 3.62 9.17 +Ovary (Dataset = GTEx, N = 180) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Ovary UBERON_0000992 5.42 3.52 1.26 3.25 4.51 6.42 21.19 +Pancreas (Dataset = GTEx, N = 328) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Pancreas UBERON_0001150 0.33 0.32 0.01 0.17 0.26 0.39 3.81 +Pituitary (Dataset = GTEx, N = 283) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Pituitary UBERON_0000007 2.24 1.12 0.39 1.51 2.04 2.72 8.7 +Prostate (Dataset = GTEx, N = 245) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Prostate UBERON_0002367 2.24 1.05 0.5 1.47 2.08 2.7 5.88 +Skin - Not Sun Exposed (Suprapubic) (Dataset = GTEx, N = 604) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Not Sun Exposed (Suprapubic) UBERON_0036149 13.99 6.07 1.61 9.51 13.12 17.57 38.26 +Skin - Sun Exposed (Lower leg) (Dataset = GTEx, N = 701) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Skin - Sun Exposed (Lower leg) UBERON_0004264 10.98 4.54 1.27 7.77 10.5 13.68 27.79 +Small Intestine - Terminal Ileum (Dataset = GTEx, N = 187) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Small Intestine - Terminal Ileum UBERON_0001211 2.74 2 0.47 1.2 2.13 3.67 12.23 +Spleen (Dataset = GTEx, N = 241) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Spleen UBERON_0002106 3.1 1.43 0.55 2.2 2.8 3.75 12.37 +Stomach (Dataset = GTEx, N = 359) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Stomach UBERON_0000945 0.76 0.46 0.09 0.47 0.65 0.9 4.03 +Testis (Dataset = GTEx, N = 361) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Testis UBERON_0000473 32.59 10.03 4.54 25.34 32.61 39.41 75.12 +Thyroid (Dataset = GTEx, N = 653) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Thyroid UBERON_0002046 1.07 0.6 0.04 0.67 0.95 1.31 5.28 +Uterus (Dataset = GTEx, N = 142) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Uterus UBERON_0000995 6.07 4.41 1.15 3.49 4.65 6.87 25.44 +Vagina (Dataset = GTEx, N = 156) ENSG00000213420 GPC2 Relevant Molecular Target (RMTL version 1.0) GTEx Vagina UBERON_0000996 3.16 1.37 0.94 2.13 2.98 3.79 8.56 diff --git a/tests/results/test-tpm-gene-disease-gtex-ENSG00000273032-EFO_0000621.tsv b/tests/results/test-tpm-gene-disease-gtex-ENSG00000273032-EFO_0000621.tsv index 4c9dc3d..545e454 100644 --- a/tests/results/test-tpm-gene-disease-gtex-ENSG00000273032-EFO_0000621.tsv +++ b/tests/results/test-tpm-gene-disease-gtex-ENSG00000273032-EFO_0000621.tsv @@ -1,57 +1,57 @@ -x_labels Gene_Ensembl_ID Gene_symbol PMTL cohort Disease GTEx_tissue_subgroup EFO MONDO GTEx_tissue_subgroup_UBERON TPM_mean TPM_sd TPM_min TPM_25th_percentile TPM_median TPM_75th_percentile TPM_max -Neuroblastoma (cohort = all_cohorts, N = 347) ENSG00000273032 DGCR5 all_cohorts Neuroblastoma EFO_0000621 MONDO_0005072 2.92 2.35 0 1.28 2.34 3.95 15.96 -Neuroblastoma (cohort = GMKF, N = 209) ENSG00000273032 DGCR5 GMKF Neuroblastoma EFO_0000621 MONDO_0005072 2.81 2.26 0 1.13 2.28 4.02 14.69 -Neuroblastoma (cohort = TARGET, N = 149) ENSG00000273032 DGCR5 TARGET Neuroblastoma EFO_0000621 MONDO_0005072 3.11 2.44 0.04 1.67 2.49 3.86 15.96 -Adipose - Subcutaneous (cohort = GTEx, N = 663) ENSG00000273032 DGCR5 GTEx Adipose - Subcutaneous UBERON_0002190 0.06 0.13 0 0.01 0.03 0.06 2.11 -Adipose - Visceral (Omentum) (cohort = GTEx, N = 541) ENSG00000273032 DGCR5 GTEx Adipose - Visceral (Omentum) UBERON_0010414 0.21 0.23 0 0.06 0.12 0.28 1.61 -Adrenal Gland (cohort = GTEx, N = 258) ENSG00000273032 DGCR5 GTEx Adrenal Gland UBERON_0002369 4.53 3.59 0.56 2.39 3.57 5.24 23.56 -Artery - Aorta (cohort = GTEx, N = 432) ENSG00000273032 DGCR5 GTEx Artery - Aorta UBERON_0001496 0.04 0.06 0 0.01 0.02 0.06 0.44 -Artery - Coronary (cohort = GTEx, N = 240) ENSG00000273032 DGCR5 GTEx Artery - Coronary UBERON_0001621 0.08 0.07 0 0.02 0.06 0.1 0.41 -Artery - Tibial (cohort = GTEx, N = 663) ENSG00000273032 DGCR5 GTEx Artery - Tibial UBERON_0007610 0.04 0.07 0 0.01 0.03 0.05 0.94 -Bladder (cohort = GTEx, N = 21) ENSG00000273032 DGCR5 GTEx Bladder UBERON_0001255 0.07 0.09 0 0.02 0.03 0.08 0.4 -Blood (cohort = GTEx, N = 755) ENSG00000273032 DGCR5 GTEx Blood UBERON_0013756 0.02 0.03 0 0 0.01 0.02 0.4 -Brain - Amygdala (cohort = GTEx, N = 152) ENSG00000273032 DGCR5 GTEx Brain - Amygdala UBERON_0001876 11.71 7.2 0.37 5.81 10 17.75 30.48 -Brain - Anterior cingulate cortex (BA24) (cohort = GTEx, N = 176) ENSG00000273032 DGCR5 GTEx Brain - Anterior cingulate cortex (BA24) UBERON_0009835 18.87 9.98 1.32 11.13 18.3 25.76 48.81 -Brain - Caudate (basal ganglia) (cohort = GTEx, N = 246) ENSG00000273032 DGCR5 GTEx Brain - Caudate (basal ganglia) UBERON_0001873 12.28 7.36 0.72 6.42 11.88 17.36 41.57 -Brain - Cerebellum (cohort = GTEx, N = 456) ENSG00000273032 DGCR5 GTEx Brain - Cerebellum UBERON_0002037 56.26 24.93 5.23 39.74 55.93 69.55 146.2 -Brain - Cortex (cohort = GTEx, N = 255) ENSG00000273032 DGCR5 GTEx Brain - Cortex UBERON_0001870 24.57 11 2.6 16.95 23.86 32.13 61.87 -Brain - Frontal Cortex (BA9) (cohort = GTEx, N = 209) ENSG00000273032 DGCR5 GTEx Brain - Frontal Cortex (BA9) UBERON_0009834 25.17 12.51 1.46 16.42 25.07 32.04 58.68 -Brain - Hippocampus (cohort = GTEx, N = 197) ENSG00000273032 DGCR5 GTEx Brain - Hippocampus UBERON_0001954 10.25 7.18 0.92 4.53 9.09 14.1 38.19 -Brain - Hypothalamus (cohort = GTEx, N = 202) ENSG00000273032 DGCR5 GTEx Brain - Hypothalamus UBERON_0001898 7.58 5.37 0.35 3.88 6.54 10.4 48.05 -Brain - Nucleus accumbens (basal ganglia) (cohort = GTEx, N = 246) ENSG00000273032 DGCR5 GTEx Brain - Nucleus accumbens (basal ganglia) UBERON_0001882 16.22 8.7 0.88 9.01 16.66 22.12 38.1 -Brain - Putamen (basal ganglia) (cohort = GTEx, N = 205) ENSG00000273032 DGCR5 GTEx Brain - Putamen (basal ganglia) UBERON_0001874 9.2 6.12 0.47 4.46 8.4 12.65 30.49 -Brain - Spinal cord (cervical c-1) (cohort = GTEx, N = 159) ENSG00000273032 DGCR5 GTEx Brain - Spinal cord (cervical c-1) UBERON_0006469 2.29 2.08 0.22 0.87 1.69 3.11 12.93 -Brain - Substantia nigra (cohort = GTEx, N = 139) ENSG00000273032 DGCR5 GTEx Brain - Substantia nigra UBERON_0002038 4.56 3.83 0.41 1.95 3.44 6.47 23.99 -Breast - Mammary Tissue (cohort = GTEx, N = 459) ENSG00000273032 DGCR5 GTEx Breast - Mammary Tissue UBERON_0008367 0.28 0.56 0 0.04 0.14 0.36 7.24 -Cells - Cultured fibroblasts (cohort = GTEx, N = 504) ENSG00000273032 DGCR5 GTEx Cells - Cultured fibroblasts 0.03 0.05 0 0 0.02 0.04 0.47 -Cells - EBV-transformed lymphocytes (cohort = GTEx, N = 174) ENSG00000273032 DGCR5 GTEx Cells - EBV-transformed lymphocytes 0.02 0.04 0 0 0.01 0.02 0.29 -Cervix - Ectocervix (cohort = GTEx, N = 9) ENSG00000273032 DGCR5 GTEx Cervix - Ectocervix UBERON_0012249 0.09 0.09 0 0.02 0.06 0.16 0.28 -Cervix - Endocervix (cohort = GTEx, N = 10) ENSG00000273032 DGCR5 GTEx Cervix - Endocervix UBERON_0000458 0.11 0.09 0.01 0.07 0.09 0.13 0.28 -Colon - Sigmoid (cohort = GTEx, N = 373) ENSG00000273032 DGCR5 GTEx Colon - Sigmoid UBERON_0001159 0.16 0.11 0 0.08 0.13 0.21 0.67 -Colon - Transverse (cohort = GTEx, N = 406) ENSG00000273032 DGCR5 GTEx Colon - Transverse UBERON_0001157 0.09 0.09 0 0.03 0.06 0.13 0.72 -Esophagus - Gastroesophageal Junction (cohort = GTEx, N = 375) ENSG00000273032 DGCR5 GTEx Esophagus - Gastroesophageal Junction UBERON_0004550 0.09 0.08 0 0.03 0.07 0.12 0.57 -Esophagus - Mucosa (cohort = GTEx, N = 555) ENSG00000273032 DGCR5 GTEx Esophagus - Mucosa UBERON_0006920 0.24 0.16 0 0.13 0.21 0.31 1.27 -Esophagus - Muscularis (cohort = GTEx, N = 515) ENSG00000273032 DGCR5 GTEx Esophagus - Muscularis UBERON_0004648 0.09 0.09 0 0.03 0.07 0.12 0.87 -Fallopian Tube (cohort = GTEx, N = 9) ENSG00000273032 DGCR5 GTEx Fallopian Tube UBERON_0003889 0.08 0.04 0.03 0.06 0.07 0.11 0.17 -Heart - Atrial Appendage (cohort = GTEx, N = 429) ENSG00000273032 DGCR5 GTEx Heart - Atrial Appendage UBERON_0006631 0.08 0.1 0 0.03 0.06 0.09 1.61 -Heart - Left Ventricle (cohort = GTEx, N = 432) ENSG00000273032 DGCR5 GTEx Heart - Left Ventricle UBERON_0006566 0.02 0.03 0 0.01 0.01 0.02 0.39 -Kidney - Cortex (cohort = GTEx, N = 85) ENSG00000273032 DGCR5 GTEx Kidney - Cortex UBERON_0001225 0.71 0.71 0.07 0.26 0.47 0.82 3.82 -Kidney - Medulla (cohort = GTEx, N = 4) ENSG00000273032 DGCR5 GTEx Kidney - Medulla UBERON_0001293 0.22 0.17 0.11 0.11 0.14 0.25 0.46 -Liver (cohort = GTEx, N = 226) ENSG00000273032 DGCR5 GTEx Liver UBERON_0001114 3.46 2.75 0.21 1.75 2.82 4.16 18.26 -Lung (cohort = GTEx, N = 578) ENSG00000273032 DGCR5 GTEx Lung UBERON_0008952 0.15 0.14 0 0.07 0.11 0.18 1.23 -Minor Salivary Gland (cohort = GTEx, N = 162) ENSG00000273032 DGCR5 GTEx Minor Salivary Gland UBERON_0006330 0.26 0.17 0.04 0.15 0.23 0.33 1.09 -Muscle - Skeletal (cohort = GTEx, N = 803) ENSG00000273032 DGCR5 GTEx Muscle - Skeletal UBERON_0011907 0.05 0.07 0 0.01 0.03 0.06 1.14 -Nerve - Tibial (cohort = GTEx, N = 619) ENSG00000273032 DGCR5 GTEx Nerve - Tibial UBERON_0001323 0.45 0.45 0 0.2 0.32 0.53 4.76 -Ovary (cohort = GTEx, N = 180) ENSG00000273032 DGCR5 GTEx Ovary UBERON_0000992 0.13 0.18 0 0.04 0.09 0.15 1.41 -Pancreas (cohort = GTEx, N = 328) ENSG00000273032 DGCR5 GTEx Pancreas UBERON_0001150 5.93 3.19 0.37 3.65 5.33 7.46 21.53 -Pituitary (cohort = GTEx, N = 283) ENSG00000273032 DGCR5 GTEx Pituitary UBERON_0000007 7.08 4.15 0.79 4.85 6.38 8.8 51.15 -Prostate (cohort = GTEx, N = 245) ENSG00000273032 DGCR5 GTEx Prostate UBERON_0002367 0.36 0.32 0 0.15 0.29 0.46 2.29 -Skin - Not Sun Exposed (Suprapubic) (cohort = GTEx, N = 604) ENSG00000273032 DGCR5 GTEx Skin - Not Sun Exposed (Suprapubic) UBERON_0036149 1.17 0.72 0.17 0.73 1.01 1.44 7.86 -Skin - Sun Exposed (Lower leg) (cohort = GTEx, N = 701) ENSG00000273032 DGCR5 GTEx Skin - Sun Exposed (Lower leg) UBERON_0004264 1.29 0.79 0.06 0.81 1.14 1.55 8.59 -Small Intestine - Terminal Ileum (cohort = GTEx, N = 187) ENSG00000273032 DGCR5 GTEx Small Intestine - Terminal Ileum UBERON_0001211 0.08 0.07 0 0.04 0.07 0.11 0.44 -Spleen (cohort = GTEx, N = 241) ENSG00000273032 DGCR5 GTEx Spleen UBERON_0002106 0.47 0.42 0.01 0.22 0.35 0.56 3.24 -Stomach (cohort = GTEx, N = 359) ENSG00000273032 DGCR5 GTEx Stomach UBERON_0000945 0.09 0.1 0 0.03 0.07 0.12 0.94 -Testis (cohort = GTEx, N = 361) ENSG00000273032 DGCR5 GTEx Testis UBERON_0000473 1.47 0.48 0.58 1.16 1.39 1.72 3.33 -Thyroid (cohort = GTEx, N = 653) ENSG00000273032 DGCR5 GTEx Thyroid UBERON_0002046 0.55 0.76 0 0.23 0.38 0.63 12 -Uterus (cohort = GTEx, N = 142) ENSG00000273032 DGCR5 GTEx Uterus UBERON_0000995 0.12 0.19 0 0.03 0.07 0.13 1.34 -Vagina (cohort = GTEx, N = 156) ENSG00000273032 DGCR5 GTEx Vagina UBERON_0000996 0.25 0.23 0 0.08 0.18 0.35 1.4 +x_labels Gene_Ensembl_ID Gene_symbol PMTL Dataset Disease GTEx_tissue_subgroup EFO MONDO GTEx_tissue_subgroup_UBERON TPM_mean TPM_sd TPM_min TPM_25th_percentile TPM_median TPM_75th_percentile TPM_max +Neuroblastoma (Dataset = all_cohorts, N = 347) ENSG00000273032 DGCR5 all_cohorts Neuroblastoma EFO_0000621 MONDO_0005072 2.92 2.35 0 1.28 2.34 3.95 15.96 +Neuroblastoma (Dataset = GMKF, N = 209) ENSG00000273032 DGCR5 GMKF Neuroblastoma EFO_0000621 MONDO_0005072 2.81 2.26 0 1.13 2.28 4.02 14.69 +Neuroblastoma (Dataset = TARGET, N = 149) ENSG00000273032 DGCR5 TARGET Neuroblastoma EFO_0000621 MONDO_0005072 3.11 2.44 0.04 1.67 2.49 3.86 15.96 +Adipose - Subcutaneous (Dataset = GTEx, N = 663) ENSG00000273032 DGCR5 GTEx Adipose - Subcutaneous UBERON_0002190 0.06 0.13 0 0.01 0.03 0.06 2.11 +Adipose - Visceral (Omentum) (Dataset = GTEx, N = 541) ENSG00000273032 DGCR5 GTEx Adipose - Visceral (Omentum) UBERON_0010414 0.21 0.23 0 0.06 0.12 0.28 1.61 +Adrenal Gland (Dataset = GTEx, N = 258) ENSG00000273032 DGCR5 GTEx Adrenal Gland UBERON_0002369 4.53 3.59 0.56 2.39 3.57 5.24 23.56 +Artery - Aorta (Dataset = GTEx, N = 432) ENSG00000273032 DGCR5 GTEx Artery - Aorta UBERON_0001496 0.04 0.06 0 0.01 0.02 0.06 0.44 +Artery - Coronary (Dataset = GTEx, N = 240) ENSG00000273032 DGCR5 GTEx Artery - Coronary UBERON_0001621 0.08 0.07 0 0.02 0.06 0.1 0.41 +Artery - Tibial (Dataset = GTEx, N = 663) ENSG00000273032 DGCR5 GTEx Artery - Tibial UBERON_0007610 0.04 0.07 0 0.01 0.03 0.05 0.94 +Bladder (Dataset = GTEx, N = 21) ENSG00000273032 DGCR5 GTEx Bladder UBERON_0001255 0.07 0.09 0 0.02 0.03 0.08 0.4 +Blood (Dataset = GTEx, N = 755) ENSG00000273032 DGCR5 GTEx Blood UBERON_0013756 0.02 0.03 0 0 0.01 0.02 0.4 +Brain - Amygdala (Dataset = GTEx, N = 152) ENSG00000273032 DGCR5 GTEx Brain - Amygdala UBERON_0001876 11.71 7.2 0.37 5.81 10 17.75 30.48 +Brain - Anterior cingulate cortex (BA24) (Dataset = GTEx, N = 176) ENSG00000273032 DGCR5 GTEx Brain - Anterior cingulate cortex (BA24) UBERON_0009835 18.87 9.98 1.32 11.13 18.3 25.76 48.81 +Brain - Caudate (basal ganglia) (Dataset = GTEx, N = 246) ENSG00000273032 DGCR5 GTEx Brain - Caudate (basal ganglia) UBERON_0001873 12.28 7.36 0.72 6.42 11.88 17.36 41.57 +Brain - Cerebellum (Dataset = GTEx, N = 456) ENSG00000273032 DGCR5 GTEx Brain - Cerebellum UBERON_0002037 56.26 24.93 5.23 39.74 55.93 69.55 146.2 +Brain - Cortex (Dataset = GTEx, N = 255) ENSG00000273032 DGCR5 GTEx Brain - Cortex UBERON_0001870 24.57 11 2.6 16.95 23.86 32.13 61.87 +Brain - Frontal Cortex (BA9) (Dataset = GTEx, N = 209) ENSG00000273032 DGCR5 GTEx Brain - Frontal Cortex (BA9) UBERON_0009834 25.17 12.51 1.46 16.42 25.07 32.04 58.68 +Brain - Hippocampus (Dataset = GTEx, N = 197) ENSG00000273032 DGCR5 GTEx Brain - Hippocampus UBERON_0001954 10.25 7.18 0.92 4.53 9.09 14.1 38.19 +Brain - Hypothalamus (Dataset = GTEx, N = 202) ENSG00000273032 DGCR5 GTEx Brain - Hypothalamus UBERON_0001898 7.58 5.37 0.35 3.88 6.54 10.4 48.05 +Brain - Nucleus accumbens (basal ganglia) (Dataset = GTEx, N = 246) ENSG00000273032 DGCR5 GTEx Brain - Nucleus accumbens (basal ganglia) UBERON_0001882 16.22 8.7 0.88 9.01 16.66 22.12 38.1 +Brain - Putamen (basal ganglia) (Dataset = GTEx, N = 205) ENSG00000273032 DGCR5 GTEx Brain - Putamen (basal ganglia) UBERON_0001874 9.2 6.12 0.47 4.46 8.4 12.65 30.49 +Brain - Spinal cord (cervical c-1) (Dataset = GTEx, N = 159) ENSG00000273032 DGCR5 GTEx Brain - Spinal cord (cervical c-1) UBERON_0006469 2.29 2.08 0.22 0.87 1.69 3.11 12.93 +Brain - Substantia nigra (Dataset = GTEx, N = 139) ENSG00000273032 DGCR5 GTEx Brain - Substantia nigra UBERON_0002038 4.56 3.83 0.41 1.95 3.44 6.47 23.99 +Breast - Mammary Tissue (Dataset = GTEx, N = 459) ENSG00000273032 DGCR5 GTEx Breast - Mammary Tissue UBERON_0008367 0.28 0.56 0 0.04 0.14 0.36 7.24 +Cells - Cultured fibroblasts (Dataset = GTEx, N = 504) ENSG00000273032 DGCR5 GTEx Cells - Cultured fibroblasts 0.03 0.05 0 0 0.02 0.04 0.47 +Cells - EBV-transformed lymphocytes (Dataset = GTEx, N = 174) ENSG00000273032 DGCR5 GTEx Cells - EBV-transformed lymphocytes 0.02 0.04 0 0 0.01 0.02 0.29 +Cervix - Ectocervix (Dataset = GTEx, N = 9) ENSG00000273032 DGCR5 GTEx Cervix - Ectocervix UBERON_0012249 0.09 0.09 0 0.02 0.06 0.16 0.28 +Cervix - Endocervix (Dataset = GTEx, N = 10) ENSG00000273032 DGCR5 GTEx Cervix - Endocervix UBERON_0000458 0.11 0.09 0.01 0.07 0.09 0.13 0.28 +Colon - Sigmoid (Dataset = GTEx, N = 373) ENSG00000273032 DGCR5 GTEx Colon - Sigmoid UBERON_0001159 0.16 0.11 0 0.08 0.13 0.21 0.67 +Colon - Transverse (Dataset = GTEx, N = 406) ENSG00000273032 DGCR5 GTEx Colon - Transverse UBERON_0001157 0.09 0.09 0 0.03 0.06 0.13 0.72 +Esophagus - Gastroesophageal Junction (Dataset = GTEx, N = 375) ENSG00000273032 DGCR5 GTEx Esophagus - Gastroesophageal Junction UBERON_0004550 0.09 0.08 0 0.03 0.07 0.12 0.57 +Esophagus - Mucosa (Dataset = GTEx, N = 555) ENSG00000273032 DGCR5 GTEx Esophagus - Mucosa UBERON_0006920 0.24 0.16 0 0.13 0.21 0.31 1.27 +Esophagus - Muscularis (Dataset = GTEx, N = 515) ENSG00000273032 DGCR5 GTEx Esophagus - Muscularis UBERON_0004648 0.09 0.09 0 0.03 0.07 0.12 0.87 +Fallopian Tube (Dataset = GTEx, N = 9) ENSG00000273032 DGCR5 GTEx Fallopian Tube UBERON_0003889 0.08 0.04 0.03 0.06 0.07 0.11 0.17 +Heart - Atrial Appendage (Dataset = GTEx, N = 429) ENSG00000273032 DGCR5 GTEx Heart - Atrial Appendage UBERON_0006631 0.08 0.1 0 0.03 0.06 0.09 1.61 +Heart - Left Ventricle (Dataset = GTEx, N = 432) ENSG00000273032 DGCR5 GTEx Heart - Left Ventricle UBERON_0006566 0.02 0.03 0 0.01 0.01 0.02 0.39 +Kidney - Cortex (Dataset = GTEx, N = 85) ENSG00000273032 DGCR5 GTEx Kidney - Cortex UBERON_0001225 0.71 0.71 0.07 0.26 0.47 0.82 3.82 +Kidney - Medulla (Dataset = GTEx, N = 4) ENSG00000273032 DGCR5 GTEx Kidney - Medulla UBERON_0001293 0.22 0.17 0.11 0.11 0.14 0.25 0.46 +Liver (Dataset = GTEx, N = 226) ENSG00000273032 DGCR5 GTEx Liver UBERON_0001114 3.46 2.75 0.21 1.75 2.82 4.16 18.26 +Lung (Dataset = GTEx, N = 578) ENSG00000273032 DGCR5 GTEx Lung UBERON_0008952 0.15 0.14 0 0.07 0.11 0.18 1.23 +Minor Salivary Gland (Dataset = GTEx, N = 162) ENSG00000273032 DGCR5 GTEx Minor Salivary Gland UBERON_0006330 0.26 0.17 0.04 0.15 0.23 0.33 1.09 +Muscle - Skeletal (Dataset = GTEx, N = 803) ENSG00000273032 DGCR5 GTEx Muscle - Skeletal UBERON_0011907 0.05 0.07 0 0.01 0.03 0.06 1.14 +Nerve - Tibial (Dataset = GTEx, N = 619) ENSG00000273032 DGCR5 GTEx Nerve - Tibial UBERON_0001323 0.45 0.45 0 0.2 0.32 0.53 4.76 +Ovary (Dataset = GTEx, N = 180) ENSG00000273032 DGCR5 GTEx Ovary UBERON_0000992 0.13 0.18 0 0.04 0.09 0.15 1.41 +Pancreas (Dataset = GTEx, N = 328) ENSG00000273032 DGCR5 GTEx Pancreas UBERON_0001150 5.93 3.19 0.37 3.65 5.33 7.46 21.53 +Pituitary (Dataset = GTEx, N = 283) ENSG00000273032 DGCR5 GTEx Pituitary UBERON_0000007 7.08 4.15 0.79 4.85 6.38 8.8 51.15 +Prostate (Dataset = GTEx, N = 245) ENSG00000273032 DGCR5 GTEx Prostate UBERON_0002367 0.36 0.32 0 0.15 0.29 0.46 2.29 +Skin - Not Sun Exposed (Suprapubic) (Dataset = GTEx, N = 604) ENSG00000273032 DGCR5 GTEx Skin - Not Sun Exposed (Suprapubic) UBERON_0036149 1.17 0.72 0.17 0.73 1.01 1.44 7.86 +Skin - Sun Exposed (Lower leg) (Dataset = GTEx, N = 701) ENSG00000273032 DGCR5 GTEx Skin - Sun Exposed (Lower leg) UBERON_0004264 1.29 0.79 0.06 0.81 1.14 1.55 8.59 +Small Intestine - Terminal Ileum (Dataset = GTEx, N = 187) ENSG00000273032 DGCR5 GTEx Small Intestine - Terminal Ileum UBERON_0001211 0.08 0.07 0 0.04 0.07 0.11 0.44 +Spleen (Dataset = GTEx, N = 241) ENSG00000273032 DGCR5 GTEx Spleen UBERON_0002106 0.47 0.42 0.01 0.22 0.35 0.56 3.24 +Stomach (Dataset = GTEx, N = 359) ENSG00000273032 DGCR5 GTEx Stomach UBERON_0000945 0.09 0.1 0 0.03 0.07 0.12 0.94 +Testis (Dataset = GTEx, N = 361) ENSG00000273032 DGCR5 GTEx Testis UBERON_0000473 1.47 0.48 0.58 1.16 1.39 1.72 3.33 +Thyroid (Dataset = GTEx, N = 653) ENSG00000273032 DGCR5 GTEx Thyroid UBERON_0002046 0.55 0.76 0 0.23 0.38 0.63 12 +Uterus (Dataset = GTEx, N = 142) ENSG00000273032 DGCR5 GTEx Uterus UBERON_0000995 0.12 0.19 0 0.03 0.07 0.13 1.34 +Vagina (Dataset = GTEx, N = 156) ENSG00000273032 DGCR5 GTEx Vagina UBERON_0000996 0.25 0.23 0 0.08 0.18 0.35 1.4 diff --git a/tests/results/test-tpm-gene-disease-gtex-ENSG00000273032-EFO_0005543.tsv b/tests/results/test-tpm-gene-disease-gtex-ENSG00000273032-EFO_0005543.tsv deleted file mode 100644 index 22fb20c..0000000 --- a/tests/results/test-tpm-gene-disease-gtex-ENSG00000273032-EFO_0005543.tsv +++ /dev/null @@ -1,56 +0,0 @@ -x_labels Gene_Ensembl_ID Gene_symbol PMTL cohort Disease GTEx_tissue_subgroup EFO MONDO GTEx_tissue_subgroup_UBERON TPM_mean TPM_sd TPM_min TPM_25th_percentile TPM_median TPM_75th_percentile TPM_max -High-grade glioma/astrocytoma (cohort = PBTA, N = 51) ENSG00000273032 DGCR5 PBTA High-grade glioma/astrocytoma EFO_0005543 MONDO_0100342 1.45 2.63 0.01 0.24 0.7 1.81 17.8 -Low-grade glioma/astrocytoma (cohort = PBTA, N = 237) ENSG00000273032 DGCR5 PBTA Low-grade glioma/astrocytoma EFO_0005543 MONDO_0016685 1.15 1.58 0 0.25 0.6 1.24 10.82 -Adipose - Subcutaneous (cohort = GTEx, N = 663) ENSG00000273032 DGCR5 GTEx Adipose - Subcutaneous UBERON_0002190 0.06 0.13 0 0.01 0.03 0.06 2.11 -Adipose - Visceral (Omentum) (cohort = GTEx, N = 541) ENSG00000273032 DGCR5 GTEx Adipose - Visceral (Omentum) UBERON_0010414 0.21 0.23 0 0.06 0.12 0.28 1.61 -Adrenal Gland (cohort = GTEx, N = 258) ENSG00000273032 DGCR5 GTEx Adrenal Gland UBERON_0002369 4.53 3.59 0.56 2.39 3.57 5.24 23.56 -Artery - Aorta (cohort = GTEx, N = 432) ENSG00000273032 DGCR5 GTEx Artery - Aorta UBERON_0001496 0.04 0.06 0 0.01 0.02 0.06 0.44 -Artery - Coronary (cohort = GTEx, N = 240) ENSG00000273032 DGCR5 GTEx Artery - Coronary UBERON_0001621 0.08 0.07 0 0.02 0.06 0.1 0.41 -Artery - Tibial (cohort = GTEx, N = 663) ENSG00000273032 DGCR5 GTEx Artery - Tibial UBERON_0007610 0.04 0.07 0 0.01 0.03 0.05 0.94 -Bladder (cohort = GTEx, N = 21) ENSG00000273032 DGCR5 GTEx Bladder UBERON_0001255 0.07 0.09 0 0.02 0.03 0.08 0.4 -Blood (cohort = GTEx, N = 755) ENSG00000273032 DGCR5 GTEx Blood UBERON_0013756 0.02 0.03 0 0 0.01 0.02 0.4 -Brain - Amygdala (cohort = GTEx, N = 152) ENSG00000273032 DGCR5 GTEx Brain - Amygdala UBERON_0001876 11.71 7.2 0.37 5.81 10 17.75 30.48 -Brain - Anterior cingulate cortex (BA24) (cohort = GTEx, N = 176) ENSG00000273032 DGCR5 GTEx Brain - Anterior cingulate cortex (BA24) UBERON_0009835 18.87 9.98 1.32 11.13 18.3 25.76 48.81 -Brain - Caudate (basal ganglia) (cohort = GTEx, N = 246) ENSG00000273032 DGCR5 GTEx Brain - Caudate (basal ganglia) UBERON_0001873 12.28 7.36 0.72 6.42 11.88 17.36 41.57 -Brain - Cerebellum (cohort = GTEx, N = 456) ENSG00000273032 DGCR5 GTEx Brain - Cerebellum UBERON_0002037 56.26 24.93 5.23 39.74 55.93 69.55 146.2 -Brain - Cortex (cohort = GTEx, N = 255) ENSG00000273032 DGCR5 GTEx Brain - Cortex UBERON_0001870 24.57 11 2.6 16.95 23.86 32.13 61.87 -Brain - Frontal Cortex (BA9) (cohort = GTEx, N = 209) ENSG00000273032 DGCR5 GTEx Brain - Frontal Cortex (BA9) UBERON_0009834 25.17 12.51 1.46 16.42 25.07 32.04 58.68 -Brain - Hippocampus (cohort = GTEx, N = 197) ENSG00000273032 DGCR5 GTEx Brain - Hippocampus UBERON_0001954 10.25 7.18 0.92 4.53 9.09 14.1 38.19 -Brain - Hypothalamus (cohort = GTEx, N = 202) ENSG00000273032 DGCR5 GTEx Brain - Hypothalamus UBERON_0001898 7.58 5.37 0.35 3.88 6.54 10.4 48.05 -Brain - Nucleus accumbens (basal ganglia) (cohort = GTEx, N = 246) ENSG00000273032 DGCR5 GTEx Brain - Nucleus accumbens (basal ganglia) UBERON_0001882 16.22 8.7 0.88 9.01 16.66 22.12 38.1 -Brain - Putamen (basal ganglia) (cohort = GTEx, N = 205) ENSG00000273032 DGCR5 GTEx Brain - Putamen (basal ganglia) UBERON_0001874 9.2 6.12 0.47 4.46 8.4 12.65 30.49 -Brain - Spinal cord (cervical c-1) (cohort = GTEx, N = 159) ENSG00000273032 DGCR5 GTEx Brain - Spinal cord (cervical c-1) UBERON_0006469 2.29 2.08 0.22 0.87 1.69 3.11 12.93 -Brain - Substantia nigra (cohort = GTEx, N = 139) ENSG00000273032 DGCR5 GTEx Brain - Substantia nigra UBERON_0002038 4.56 3.83 0.41 1.95 3.44 6.47 23.99 -Breast - Mammary Tissue (cohort = GTEx, N = 459) ENSG00000273032 DGCR5 GTEx Breast - Mammary Tissue UBERON_0008367 0.28 0.56 0 0.04 0.14 0.36 7.24 -Cells - Cultured fibroblasts (cohort = GTEx, N = 504) ENSG00000273032 DGCR5 GTEx Cells - Cultured fibroblasts 0.03 0.05 0 0 0.02 0.04 0.47 -Cells - EBV-transformed lymphocytes (cohort = GTEx, N = 174) ENSG00000273032 DGCR5 GTEx Cells - EBV-transformed lymphocytes 0.02 0.04 0 0 0.01 0.02 0.29 -Cervix - Ectocervix (cohort = GTEx, N = 9) ENSG00000273032 DGCR5 GTEx Cervix - Ectocervix UBERON_0012249 0.09 0.09 0 0.02 0.06 0.16 0.28 -Cervix - Endocervix (cohort = GTEx, N = 10) ENSG00000273032 DGCR5 GTEx Cervix - Endocervix UBERON_0000458 0.11 0.09 0.01 0.07 0.09 0.13 0.28 -Colon - Sigmoid (cohort = GTEx, N = 373) ENSG00000273032 DGCR5 GTEx Colon - Sigmoid UBERON_0001159 0.16 0.11 0 0.08 0.13 0.21 0.67 -Colon - Transverse (cohort = GTEx, N = 406) ENSG00000273032 DGCR5 GTEx Colon - Transverse UBERON_0001157 0.09 0.09 0 0.03 0.06 0.13 0.72 -Esophagus - Gastroesophageal Junction (cohort = GTEx, N = 375) ENSG00000273032 DGCR5 GTEx Esophagus - Gastroesophageal Junction UBERON_0004550 0.09 0.08 0 0.03 0.07 0.12 0.57 -Esophagus - Mucosa (cohort = GTEx, N = 555) ENSG00000273032 DGCR5 GTEx Esophagus - Mucosa UBERON_0006920 0.24 0.16 0 0.13 0.21 0.31 1.27 -Esophagus - Muscularis (cohort = GTEx, N = 515) ENSG00000273032 DGCR5 GTEx Esophagus - Muscularis UBERON_0004648 0.09 0.09 0 0.03 0.07 0.12 0.87 -Fallopian Tube (cohort = GTEx, N = 9) ENSG00000273032 DGCR5 GTEx Fallopian Tube UBERON_0003889 0.08 0.04 0.03 0.06 0.07 0.11 0.17 -Heart - Atrial Appendage (cohort = GTEx, N = 429) ENSG00000273032 DGCR5 GTEx Heart - Atrial Appendage UBERON_0006631 0.08 0.1 0 0.03 0.06 0.09 1.61 -Heart - Left Ventricle (cohort = GTEx, N = 432) ENSG00000273032 DGCR5 GTEx Heart - Left Ventricle UBERON_0006566 0.02 0.03 0 0.01 0.01 0.02 0.39 -Kidney - Cortex (cohort = GTEx, N = 85) ENSG00000273032 DGCR5 GTEx Kidney - Cortex UBERON_0001225 0.71 0.71 0.07 0.26 0.47 0.82 3.82 -Kidney - Medulla (cohort = GTEx, N = 4) ENSG00000273032 DGCR5 GTEx Kidney - Medulla UBERON_0001293 0.22 0.17 0.11 0.11 0.14 0.25 0.46 -Liver (cohort = GTEx, N = 226) ENSG00000273032 DGCR5 GTEx Liver UBERON_0001114 3.46 2.75 0.21 1.75 2.82 4.16 18.26 -Lung (cohort = GTEx, N = 578) ENSG00000273032 DGCR5 GTEx Lung UBERON_0008952 0.15 0.14 0 0.07 0.11 0.18 1.23 -Minor Salivary Gland (cohort = GTEx, N = 162) ENSG00000273032 DGCR5 GTEx Minor Salivary Gland UBERON_0006330 0.26 0.17 0.04 0.15 0.23 0.33 1.09 -Muscle - Skeletal (cohort = GTEx, N = 803) ENSG00000273032 DGCR5 GTEx Muscle - Skeletal UBERON_0011907 0.05 0.07 0 0.01 0.03 0.06 1.14 -Nerve - Tibial (cohort = GTEx, N = 619) ENSG00000273032 DGCR5 GTEx Nerve - Tibial UBERON_0001323 0.45 0.45 0 0.2 0.32 0.53 4.76 -Ovary (cohort = GTEx, N = 180) ENSG00000273032 DGCR5 GTEx Ovary UBERON_0000992 0.13 0.18 0 0.04 0.09 0.15 1.41 -Pancreas (cohort = GTEx, N = 328) ENSG00000273032 DGCR5 GTEx Pancreas UBERON_0001150 5.93 3.19 0.37 3.65 5.33 7.46 21.53 -Pituitary (cohort = GTEx, N = 283) ENSG00000273032 DGCR5 GTEx Pituitary UBERON_0000007 7.08 4.15 0.79 4.85 6.38 8.8 51.15 -Prostate (cohort = GTEx, N = 245) ENSG00000273032 DGCR5 GTEx Prostate UBERON_0002367 0.36 0.32 0 0.15 0.29 0.46 2.29 -Skin - Not Sun Exposed (Suprapubic) (cohort = GTEx, N = 604) ENSG00000273032 DGCR5 GTEx Skin - Not Sun Exposed (Suprapubic) UBERON_0036149 1.17 0.72 0.17 0.73 1.01 1.44 7.86 -Skin - Sun Exposed (Lower leg) (cohort = GTEx, N = 701) ENSG00000273032 DGCR5 GTEx Skin - Sun Exposed (Lower leg) UBERON_0004264 1.29 0.79 0.06 0.81 1.14 1.55 8.59 -Small Intestine - Terminal Ileum (cohort = GTEx, N = 187) ENSG00000273032 DGCR5 GTEx Small Intestine - Terminal Ileum UBERON_0001211 0.08 0.07 0 0.04 0.07 0.11 0.44 -Spleen (cohort = GTEx, N = 241) ENSG00000273032 DGCR5 GTEx Spleen UBERON_0002106 0.47 0.42 0.01 0.22 0.35 0.56 3.24 -Stomach (cohort = GTEx, N = 359) ENSG00000273032 DGCR5 GTEx Stomach UBERON_0000945 0.09 0.1 0 0.03 0.07 0.12 0.94 -Testis (cohort = GTEx, N = 361) ENSG00000273032 DGCR5 GTEx Testis UBERON_0000473 1.47 0.48 0.58 1.16 1.39 1.72 3.33 -Thyroid (cohort = GTEx, N = 653) ENSG00000273032 DGCR5 GTEx Thyroid UBERON_0002046 0.55 0.76 0 0.23 0.38 0.63 12 -Uterus (cohort = GTEx, N = 142) ENSG00000273032 DGCR5 GTEx Uterus UBERON_0000995 0.12 0.19 0 0.03 0.07 0.13 1.34 -Vagina (cohort = GTEx, N = 156) ENSG00000273032 DGCR5 GTEx Vagina UBERON_0000996 0.25 0.23 0 0.08 0.18 0.35 1.4 diff --git a/tests/results/test-tpm-gene-disease-gtex-ENSG00000273032-EFO_0007206.tsv b/tests/results/test-tpm-gene-disease-gtex-ENSG00000273032-EFO_0007206.tsv deleted file mode 100644 index c846040..0000000 --- a/tests/results/test-tpm-gene-disease-gtex-ENSG00000273032-EFO_0007206.tsv +++ /dev/null @@ -1,56 +0,0 @@ -x_labels Gene_Ensembl_ID Gene_symbol PMTL cohort Disease GTEx_tissue_subgroup EFO MONDO GTEx_tissue_subgroup_UBERON TPM_mean TPM_sd TPM_min TPM_25th_percentile TPM_median TPM_75th_percentile TPM_max -Choroid plexus carcinoma (cohort = PBTA, N = 4) ENSG00000273032 DGCR5 PBTA Choroid plexus carcinoma EFO_0007206 MONDO_0016718 0.55 0.17 0.37 0.44 0.52 0.64 0.77 -Choroid plexus cyst (cohort = PBTA, N = 1) ENSG00000273032 DGCR5 PBTA Choroid plexus cyst EFO_0007206 0.25 0.25 0.25 0.25 0.25 0.25 -Adipose - Subcutaneous (cohort = GTEx, N = 663) ENSG00000273032 DGCR5 GTEx Adipose - Subcutaneous UBERON_0002190 0.06 0.13 0 0.01 0.03 0.06 2.11 -Adipose - Visceral (Omentum) (cohort = GTEx, N = 541) ENSG00000273032 DGCR5 GTEx Adipose - Visceral (Omentum) UBERON_0010414 0.21 0.23 0 0.06 0.12 0.28 1.61 -Adrenal Gland (cohort = GTEx, N = 258) ENSG00000273032 DGCR5 GTEx Adrenal Gland UBERON_0002369 4.53 3.59 0.56 2.39 3.57 5.24 23.56 -Artery - Aorta (cohort = GTEx, N = 432) ENSG00000273032 DGCR5 GTEx Artery - Aorta UBERON_0001496 0.04 0.06 0 0.01 0.02 0.06 0.44 -Artery - Coronary (cohort = GTEx, N = 240) ENSG00000273032 DGCR5 GTEx Artery - Coronary UBERON_0001621 0.08 0.07 0 0.02 0.06 0.1 0.41 -Artery - Tibial (cohort = GTEx, N = 663) ENSG00000273032 DGCR5 GTEx Artery - Tibial UBERON_0007610 0.04 0.07 0 0.01 0.03 0.05 0.94 -Bladder (cohort = GTEx, N = 21) ENSG00000273032 DGCR5 GTEx Bladder UBERON_0001255 0.07 0.09 0 0.02 0.03 0.08 0.4 -Blood (cohort = GTEx, N = 755) ENSG00000273032 DGCR5 GTEx Blood UBERON_0013756 0.02 0.03 0 0 0.01 0.02 0.4 -Brain - Amygdala (cohort = GTEx, N = 152) ENSG00000273032 DGCR5 GTEx Brain - Amygdala UBERON_0001876 11.71 7.2 0.37 5.81 10 17.75 30.48 -Brain - Anterior cingulate cortex (BA24) (cohort = GTEx, N = 176) ENSG00000273032 DGCR5 GTEx Brain - Anterior cingulate cortex (BA24) UBERON_0009835 18.87 9.98 1.32 11.13 18.3 25.76 48.81 -Brain - Caudate (basal ganglia) (cohort = GTEx, N = 246) ENSG00000273032 DGCR5 GTEx Brain - Caudate (basal ganglia) UBERON_0001873 12.28 7.36 0.72 6.42 11.88 17.36 41.57 -Brain - Cerebellum (cohort = GTEx, N = 456) ENSG00000273032 DGCR5 GTEx Brain - Cerebellum UBERON_0002037 56.26 24.93 5.23 39.74 55.93 69.55 146.2 -Brain - Cortex (cohort = GTEx, N = 255) ENSG00000273032 DGCR5 GTEx Brain - Cortex UBERON_0001870 24.57 11 2.6 16.95 23.86 32.13 61.87 -Brain - Frontal Cortex (BA9) (cohort = GTEx, N = 209) ENSG00000273032 DGCR5 GTEx Brain - Frontal Cortex (BA9) UBERON_0009834 25.17 12.51 1.46 16.42 25.07 32.04 58.68 -Brain - Hippocampus (cohort = GTEx, N = 197) ENSG00000273032 DGCR5 GTEx Brain - Hippocampus UBERON_0001954 10.25 7.18 0.92 4.53 9.09 14.1 38.19 -Brain - Hypothalamus (cohort = GTEx, N = 202) ENSG00000273032 DGCR5 GTEx Brain - Hypothalamus UBERON_0001898 7.58 5.37 0.35 3.88 6.54 10.4 48.05 -Brain - Nucleus accumbens (basal ganglia) (cohort = GTEx, N = 246) ENSG00000273032 DGCR5 GTEx Brain - Nucleus accumbens (basal ganglia) UBERON_0001882 16.22 8.7 0.88 9.01 16.66 22.12 38.1 -Brain - Putamen (basal ganglia) (cohort = GTEx, N = 205) ENSG00000273032 DGCR5 GTEx Brain - Putamen (basal ganglia) UBERON_0001874 9.2 6.12 0.47 4.46 8.4 12.65 30.49 -Brain - Spinal cord (cervical c-1) (cohort = GTEx, N = 159) ENSG00000273032 DGCR5 GTEx Brain - Spinal cord (cervical c-1) UBERON_0006469 2.29 2.08 0.22 0.87 1.69 3.11 12.93 -Brain - Substantia nigra (cohort = GTEx, N = 139) ENSG00000273032 DGCR5 GTEx Brain - Substantia nigra UBERON_0002038 4.56 3.83 0.41 1.95 3.44 6.47 23.99 -Breast - Mammary Tissue (cohort = GTEx, N = 459) ENSG00000273032 DGCR5 GTEx Breast - Mammary Tissue UBERON_0008367 0.28 0.56 0 0.04 0.14 0.36 7.24 -Cells - Cultured fibroblasts (cohort = GTEx, N = 504) ENSG00000273032 DGCR5 GTEx Cells - Cultured fibroblasts 0.03 0.05 0 0 0.02 0.04 0.47 -Cells - EBV-transformed lymphocytes (cohort = GTEx, N = 174) ENSG00000273032 DGCR5 GTEx Cells - EBV-transformed lymphocytes 0.02 0.04 0 0 0.01 0.02 0.29 -Cervix - Ectocervix (cohort = GTEx, N = 9) ENSG00000273032 DGCR5 GTEx Cervix - Ectocervix UBERON_0012249 0.09 0.09 0 0.02 0.06 0.16 0.28 -Cervix - Endocervix (cohort = GTEx, N = 10) ENSG00000273032 DGCR5 GTEx Cervix - Endocervix UBERON_0000458 0.11 0.09 0.01 0.07 0.09 0.13 0.28 -Colon - Sigmoid (cohort = GTEx, N = 373) ENSG00000273032 DGCR5 GTEx Colon - Sigmoid UBERON_0001159 0.16 0.11 0 0.08 0.13 0.21 0.67 -Colon - Transverse (cohort = GTEx, N = 406) ENSG00000273032 DGCR5 GTEx Colon - Transverse UBERON_0001157 0.09 0.09 0 0.03 0.06 0.13 0.72 -Esophagus - Gastroesophageal Junction (cohort = GTEx, N = 375) ENSG00000273032 DGCR5 GTEx Esophagus - Gastroesophageal Junction UBERON_0004550 0.09 0.08 0 0.03 0.07 0.12 0.57 -Esophagus - Mucosa (cohort = GTEx, N = 555) ENSG00000273032 DGCR5 GTEx Esophagus - Mucosa UBERON_0006920 0.24 0.16 0 0.13 0.21 0.31 1.27 -Esophagus - Muscularis (cohort = GTEx, N = 515) ENSG00000273032 DGCR5 GTEx Esophagus - Muscularis UBERON_0004648 0.09 0.09 0 0.03 0.07 0.12 0.87 -Fallopian Tube (cohort = GTEx, N = 9) ENSG00000273032 DGCR5 GTEx Fallopian Tube UBERON_0003889 0.08 0.04 0.03 0.06 0.07 0.11 0.17 -Heart - Atrial Appendage (cohort = GTEx, N = 429) ENSG00000273032 DGCR5 GTEx Heart - Atrial Appendage UBERON_0006631 0.08 0.1 0 0.03 0.06 0.09 1.61 -Heart - Left Ventricle (cohort = GTEx, N = 432) ENSG00000273032 DGCR5 GTEx Heart - Left Ventricle UBERON_0006566 0.02 0.03 0 0.01 0.01 0.02 0.39 -Kidney - Cortex (cohort = GTEx, N = 85) ENSG00000273032 DGCR5 GTEx Kidney - Cortex UBERON_0001225 0.71 0.71 0.07 0.26 0.47 0.82 3.82 -Kidney - Medulla (cohort = GTEx, N = 4) ENSG00000273032 DGCR5 GTEx Kidney - Medulla UBERON_0001293 0.22 0.17 0.11 0.11 0.14 0.25 0.46 -Liver (cohort = GTEx, N = 226) ENSG00000273032 DGCR5 GTEx Liver UBERON_0001114 3.46 2.75 0.21 1.75 2.82 4.16 18.26 -Lung (cohort = GTEx, N = 578) ENSG00000273032 DGCR5 GTEx Lung UBERON_0008952 0.15 0.14 0 0.07 0.11 0.18 1.23 -Minor Salivary Gland (cohort = GTEx, N = 162) ENSG00000273032 DGCR5 GTEx Minor Salivary Gland UBERON_0006330 0.26 0.17 0.04 0.15 0.23 0.33 1.09 -Muscle - Skeletal (cohort = GTEx, N = 803) ENSG00000273032 DGCR5 GTEx Muscle - Skeletal UBERON_0011907 0.05 0.07 0 0.01 0.03 0.06 1.14 -Nerve - Tibial (cohort = GTEx, N = 619) ENSG00000273032 DGCR5 GTEx Nerve - Tibial UBERON_0001323 0.45 0.45 0 0.2 0.32 0.53 4.76 -Ovary (cohort = GTEx, N = 180) ENSG00000273032 DGCR5 GTEx Ovary UBERON_0000992 0.13 0.18 0 0.04 0.09 0.15 1.41 -Pancreas (cohort = GTEx, N = 328) ENSG00000273032 DGCR5 GTEx Pancreas UBERON_0001150 5.93 3.19 0.37 3.65 5.33 7.46 21.53 -Pituitary (cohort = GTEx, N = 283) ENSG00000273032 DGCR5 GTEx Pituitary UBERON_0000007 7.08 4.15 0.79 4.85 6.38 8.8 51.15 -Prostate (cohort = GTEx, N = 245) ENSG00000273032 DGCR5 GTEx Prostate UBERON_0002367 0.36 0.32 0 0.15 0.29 0.46 2.29 -Skin - Not Sun Exposed (Suprapubic) (cohort = GTEx, N = 604) ENSG00000273032 DGCR5 GTEx Skin - Not Sun Exposed (Suprapubic) UBERON_0036149 1.17 0.72 0.17 0.73 1.01 1.44 7.86 -Skin - Sun Exposed (Lower leg) (cohort = GTEx, N = 701) ENSG00000273032 DGCR5 GTEx Skin - Sun Exposed (Lower leg) UBERON_0004264 1.29 0.79 0.06 0.81 1.14 1.55 8.59 -Small Intestine - Terminal Ileum (cohort = GTEx, N = 187) ENSG00000273032 DGCR5 GTEx Small Intestine - Terminal Ileum UBERON_0001211 0.08 0.07 0 0.04 0.07 0.11 0.44 -Spleen (cohort = GTEx, N = 241) ENSG00000273032 DGCR5 GTEx Spleen UBERON_0002106 0.47 0.42 0.01 0.22 0.35 0.56 3.24 -Stomach (cohort = GTEx, N = 359) ENSG00000273032 DGCR5 GTEx Stomach UBERON_0000945 0.09 0.1 0 0.03 0.07 0.12 0.94 -Testis (cohort = GTEx, N = 361) ENSG00000273032 DGCR5 GTEx Testis UBERON_0000473 1.47 0.48 0.58 1.16 1.39 1.72 3.33 -Thyroid (cohort = GTEx, N = 653) ENSG00000273032 DGCR5 GTEx Thyroid UBERON_0002046 0.55 0.76 0 0.23 0.38 0.63 12 -Uterus (cohort = GTEx, N = 142) ENSG00000273032 DGCR5 GTEx Uterus UBERON_0000995 0.12 0.19 0 0.03 0.07 0.13 1.34 -Vagina (cohort = GTEx, N = 156) ENSG00000273032 DGCR5 GTEx Vagina UBERON_0000996 0.25 0.23 0 0.08 0.18 0.35 1.4 diff --git a/tests/results/test-tpm-gene-disease-gtex-ENSG00000273032-MONDO_0016680.tsv b/tests/results/test-tpm-gene-disease-gtex-ENSG00000273032-MONDO_0016680.tsv new file mode 100644 index 0000000..7718db0 --- /dev/null +++ b/tests/results/test-tpm-gene-disease-gtex-ENSG00000273032-MONDO_0016680.tsv @@ -0,0 +1,55 @@ +x_labels Gene_Ensembl_ID Gene_symbol PMTL Dataset Disease GTEx_tissue_subgroup EFO MONDO GTEx_tissue_subgroup_UBERON TPM_mean TPM_sd TPM_min TPM_25th_percentile TPM_median TPM_75th_percentile TPM_max +High-grade glioma/astrocytoma (Dataset = PBTA, N = 51) ENSG00000273032 DGCR5 PBTA High-grade glioma/astrocytoma MONDO_0016680 MONDO_0100342 1.45 2.63 0.01 0.24 0.7 1.81 17.8 +Adipose - Subcutaneous (Dataset = GTEx, N = 663) ENSG00000273032 DGCR5 GTEx Adipose - Subcutaneous UBERON_0002190 0.06 0.13 0 0.01 0.03 0.06 2.11 +Adipose - Visceral (Omentum) (Dataset = GTEx, N = 541) ENSG00000273032 DGCR5 GTEx Adipose - Visceral (Omentum) UBERON_0010414 0.21 0.23 0 0.06 0.12 0.28 1.61 +Adrenal Gland (Dataset = GTEx, N = 258) ENSG00000273032 DGCR5 GTEx Adrenal Gland UBERON_0002369 4.53 3.59 0.56 2.39 3.57 5.24 23.56 +Artery - Aorta (Dataset = GTEx, N = 432) ENSG00000273032 DGCR5 GTEx Artery - Aorta UBERON_0001496 0.04 0.06 0 0.01 0.02 0.06 0.44 +Artery - Coronary (Dataset = GTEx, N = 240) ENSG00000273032 DGCR5 GTEx Artery - Coronary UBERON_0001621 0.08 0.07 0 0.02 0.06 0.1 0.41 +Artery - Tibial (Dataset = GTEx, N = 663) ENSG00000273032 DGCR5 GTEx Artery - Tibial UBERON_0007610 0.04 0.07 0 0.01 0.03 0.05 0.94 +Bladder (Dataset = GTEx, N = 21) ENSG00000273032 DGCR5 GTEx Bladder UBERON_0001255 0.07 0.09 0 0.02 0.03 0.08 0.4 +Blood (Dataset = GTEx, N = 755) ENSG00000273032 DGCR5 GTEx Blood UBERON_0013756 0.02 0.03 0 0 0.01 0.02 0.4 +Brain - Amygdala (Dataset = GTEx, N = 152) ENSG00000273032 DGCR5 GTEx Brain - Amygdala UBERON_0001876 11.71 7.2 0.37 5.81 10 17.75 30.48 +Brain - Anterior cingulate cortex (BA24) (Dataset = GTEx, N = 176) ENSG00000273032 DGCR5 GTEx Brain - Anterior cingulate cortex (BA24) UBERON_0009835 18.87 9.98 1.32 11.13 18.3 25.76 48.81 +Brain - Caudate (basal ganglia) (Dataset = GTEx, N = 246) ENSG00000273032 DGCR5 GTEx Brain - Caudate (basal ganglia) UBERON_0001873 12.28 7.36 0.72 6.42 11.88 17.36 41.57 +Brain - Cerebellum (Dataset = GTEx, N = 456) ENSG00000273032 DGCR5 GTEx Brain - Cerebellum UBERON_0002037 56.26 24.93 5.23 39.74 55.93 69.55 146.2 +Brain - Cortex (Dataset = GTEx, N = 255) ENSG00000273032 DGCR5 GTEx Brain - Cortex UBERON_0001870 24.57 11 2.6 16.95 23.86 32.13 61.87 +Brain - Frontal Cortex (BA9) (Dataset = GTEx, N = 209) ENSG00000273032 DGCR5 GTEx Brain - Frontal Cortex (BA9) UBERON_0009834 25.17 12.51 1.46 16.42 25.07 32.04 58.68 +Brain - Hippocampus (Dataset = GTEx, N = 197) ENSG00000273032 DGCR5 GTEx Brain - Hippocampus UBERON_0001954 10.25 7.18 0.92 4.53 9.09 14.1 38.19 +Brain - Hypothalamus (Dataset = GTEx, N = 202) ENSG00000273032 DGCR5 GTEx Brain - Hypothalamus UBERON_0001898 7.58 5.37 0.35 3.88 6.54 10.4 48.05 +Brain - Nucleus accumbens (basal ganglia) (Dataset = GTEx, N = 246) ENSG00000273032 DGCR5 GTEx Brain - Nucleus accumbens (basal ganglia) UBERON_0001882 16.22 8.7 0.88 9.01 16.66 22.12 38.1 +Brain - Putamen (basal ganglia) (Dataset = GTEx, N = 205) ENSG00000273032 DGCR5 GTEx Brain - Putamen (basal ganglia) UBERON_0001874 9.2 6.12 0.47 4.46 8.4 12.65 30.49 +Brain - Spinal cord (cervical c-1) (Dataset = GTEx, N = 159) ENSG00000273032 DGCR5 GTEx Brain - Spinal cord (cervical c-1) UBERON_0006469 2.29 2.08 0.22 0.87 1.69 3.11 12.93 +Brain - Substantia nigra (Dataset = GTEx, N = 139) ENSG00000273032 DGCR5 GTEx Brain - Substantia nigra UBERON_0002038 4.56 3.83 0.41 1.95 3.44 6.47 23.99 +Breast - Mammary Tissue (Dataset = GTEx, N = 459) ENSG00000273032 DGCR5 GTEx Breast - Mammary Tissue UBERON_0008367 0.28 0.56 0 0.04 0.14 0.36 7.24 +Cells - Cultured fibroblasts (Dataset = GTEx, N = 504) ENSG00000273032 DGCR5 GTEx Cells - Cultured fibroblasts 0.03 0.05 0 0 0.02 0.04 0.47 +Cells - EBV-transformed lymphocytes (Dataset = GTEx, N = 174) ENSG00000273032 DGCR5 GTEx Cells - EBV-transformed lymphocytes 0.02 0.04 0 0 0.01 0.02 0.29 +Cervix - Ectocervix (Dataset = GTEx, N = 9) ENSG00000273032 DGCR5 GTEx Cervix - Ectocervix UBERON_0012249 0.09 0.09 0 0.02 0.06 0.16 0.28 +Cervix - Endocervix (Dataset = GTEx, N = 10) ENSG00000273032 DGCR5 GTEx Cervix - Endocervix UBERON_0000458 0.11 0.09 0.01 0.07 0.09 0.13 0.28 +Colon - Sigmoid (Dataset = GTEx, N = 373) ENSG00000273032 DGCR5 GTEx Colon - Sigmoid UBERON_0001159 0.16 0.11 0 0.08 0.13 0.21 0.67 +Colon - Transverse (Dataset = GTEx, N = 406) ENSG00000273032 DGCR5 GTEx Colon - Transverse UBERON_0001157 0.09 0.09 0 0.03 0.06 0.13 0.72 +Esophagus - Gastroesophageal Junction (Dataset = GTEx, N = 375) ENSG00000273032 DGCR5 GTEx Esophagus - Gastroesophageal Junction UBERON_0004550 0.09 0.08 0 0.03 0.07 0.12 0.57 +Esophagus - Mucosa (Dataset = GTEx, N = 555) ENSG00000273032 DGCR5 GTEx Esophagus - Mucosa UBERON_0006920 0.24 0.16 0 0.13 0.21 0.31 1.27 +Esophagus - Muscularis (Dataset = GTEx, N = 515) ENSG00000273032 DGCR5 GTEx Esophagus - Muscularis UBERON_0004648 0.09 0.09 0 0.03 0.07 0.12 0.87 +Fallopian Tube (Dataset = GTEx, N = 9) ENSG00000273032 DGCR5 GTEx Fallopian Tube UBERON_0003889 0.08 0.04 0.03 0.06 0.07 0.11 0.17 +Heart - Atrial Appendage (Dataset = GTEx, N = 429) ENSG00000273032 DGCR5 GTEx Heart - Atrial Appendage UBERON_0006631 0.08 0.1 0 0.03 0.06 0.09 1.61 +Heart - Left Ventricle (Dataset = GTEx, N = 432) ENSG00000273032 DGCR5 GTEx Heart - Left Ventricle UBERON_0006566 0.02 0.03 0 0.01 0.01 0.02 0.39 +Kidney - Cortex (Dataset = GTEx, N = 85) ENSG00000273032 DGCR5 GTEx Kidney - Cortex UBERON_0001225 0.71 0.71 0.07 0.26 0.47 0.82 3.82 +Kidney - Medulla (Dataset = GTEx, N = 4) ENSG00000273032 DGCR5 GTEx Kidney - Medulla UBERON_0001293 0.22 0.17 0.11 0.11 0.14 0.25 0.46 +Liver (Dataset = GTEx, N = 226) ENSG00000273032 DGCR5 GTEx Liver UBERON_0001114 3.46 2.75 0.21 1.75 2.82 4.16 18.26 +Lung (Dataset = GTEx, N = 578) ENSG00000273032 DGCR5 GTEx Lung UBERON_0008952 0.15 0.14 0 0.07 0.11 0.18 1.23 +Minor Salivary Gland (Dataset = GTEx, N = 162) ENSG00000273032 DGCR5 GTEx Minor Salivary Gland UBERON_0006330 0.26 0.17 0.04 0.15 0.23 0.33 1.09 +Muscle - Skeletal (Dataset = GTEx, N = 803) ENSG00000273032 DGCR5 GTEx Muscle - Skeletal UBERON_0011907 0.05 0.07 0 0.01 0.03 0.06 1.14 +Nerve - Tibial (Dataset = GTEx, N = 619) ENSG00000273032 DGCR5 GTEx Nerve - Tibial UBERON_0001323 0.45 0.45 0 0.2 0.32 0.53 4.76 +Ovary (Dataset = GTEx, N = 180) ENSG00000273032 DGCR5 GTEx Ovary UBERON_0000992 0.13 0.18 0 0.04 0.09 0.15 1.41 +Pancreas (Dataset = GTEx, N = 328) ENSG00000273032 DGCR5 GTEx Pancreas UBERON_0001150 5.93 3.19 0.37 3.65 5.33 7.46 21.53 +Pituitary (Dataset = GTEx, N = 283) ENSG00000273032 DGCR5 GTEx Pituitary UBERON_0000007 7.08 4.15 0.79 4.85 6.38 8.8 51.15 +Prostate (Dataset = GTEx, N = 245) ENSG00000273032 DGCR5 GTEx Prostate UBERON_0002367 0.36 0.32 0 0.15 0.29 0.46 2.29 +Skin - Not Sun Exposed (Suprapubic) (Dataset = GTEx, N = 604) ENSG00000273032 DGCR5 GTEx Skin - Not Sun Exposed (Suprapubic) UBERON_0036149 1.17 0.72 0.17 0.73 1.01 1.44 7.86 +Skin - Sun Exposed (Lower leg) (Dataset = GTEx, N = 701) ENSG00000273032 DGCR5 GTEx Skin - Sun Exposed (Lower leg) UBERON_0004264 1.29 0.79 0.06 0.81 1.14 1.55 8.59 +Small Intestine - Terminal Ileum (Dataset = GTEx, N = 187) ENSG00000273032 DGCR5 GTEx Small Intestine - Terminal Ileum UBERON_0001211 0.08 0.07 0 0.04 0.07 0.11 0.44 +Spleen (Dataset = GTEx, N = 241) ENSG00000273032 DGCR5 GTEx Spleen UBERON_0002106 0.47 0.42 0.01 0.22 0.35 0.56 3.24 +Stomach (Dataset = GTEx, N = 359) ENSG00000273032 DGCR5 GTEx Stomach UBERON_0000945 0.09 0.1 0 0.03 0.07 0.12 0.94 +Testis (Dataset = GTEx, N = 361) ENSG00000273032 DGCR5 GTEx Testis UBERON_0000473 1.47 0.48 0.58 1.16 1.39 1.72 3.33 +Thyroid (Dataset = GTEx, N = 653) ENSG00000273032 DGCR5 GTEx Thyroid UBERON_0002046 0.55 0.76 0 0.23 0.38 0.63 12 +Uterus (Dataset = GTEx, N = 142) ENSG00000273032 DGCR5 GTEx Uterus UBERON_0000995 0.12 0.19 0 0.03 0.07 0.13 1.34 +Vagina (Dataset = GTEx, N = 156) ENSG00000273032 DGCR5 GTEx Vagina UBERON_0000996 0.25 0.23 0 0.08 0.18 0.35 1.4 diff --git a/tests/results/test-tpm-gene-disease-gtex-ENSG00000273032-MONDO_0016685.tsv b/tests/results/test-tpm-gene-disease-gtex-ENSG00000273032-MONDO_0016685.tsv new file mode 100644 index 0000000..ca63f12 --- /dev/null +++ b/tests/results/test-tpm-gene-disease-gtex-ENSG00000273032-MONDO_0016685.tsv @@ -0,0 +1,55 @@ +x_labels Gene_Ensembl_ID Gene_symbol PMTL Dataset Disease GTEx_tissue_subgroup EFO MONDO GTEx_tissue_subgroup_UBERON TPM_mean TPM_sd TPM_min TPM_25th_percentile TPM_median TPM_75th_percentile TPM_max +Low-grade glioma/astrocytoma (Dataset = PBTA, N = 237) ENSG00000273032 DGCR5 PBTA Low-grade glioma/astrocytoma MONDO_0016685 MONDO_0016685 1.15 1.58 0 0.25 0.6 1.24 10.82 +Adipose - Subcutaneous (Dataset = GTEx, N = 663) ENSG00000273032 DGCR5 GTEx Adipose - Subcutaneous UBERON_0002190 0.06 0.13 0 0.01 0.03 0.06 2.11 +Adipose - Visceral (Omentum) (Dataset = GTEx, N = 541) ENSG00000273032 DGCR5 GTEx Adipose - Visceral (Omentum) UBERON_0010414 0.21 0.23 0 0.06 0.12 0.28 1.61 +Adrenal Gland (Dataset = GTEx, N = 258) ENSG00000273032 DGCR5 GTEx Adrenal Gland UBERON_0002369 4.53 3.59 0.56 2.39 3.57 5.24 23.56 +Artery - Aorta (Dataset = GTEx, N = 432) ENSG00000273032 DGCR5 GTEx Artery - Aorta UBERON_0001496 0.04 0.06 0 0.01 0.02 0.06 0.44 +Artery - Coronary (Dataset = GTEx, N = 240) ENSG00000273032 DGCR5 GTEx Artery - Coronary UBERON_0001621 0.08 0.07 0 0.02 0.06 0.1 0.41 +Artery - Tibial (Dataset = GTEx, N = 663) ENSG00000273032 DGCR5 GTEx Artery - Tibial UBERON_0007610 0.04 0.07 0 0.01 0.03 0.05 0.94 +Bladder (Dataset = GTEx, N = 21) ENSG00000273032 DGCR5 GTEx Bladder UBERON_0001255 0.07 0.09 0 0.02 0.03 0.08 0.4 +Blood (Dataset = GTEx, N = 755) ENSG00000273032 DGCR5 GTEx Blood UBERON_0013756 0.02 0.03 0 0 0.01 0.02 0.4 +Brain - Amygdala (Dataset = GTEx, N = 152) ENSG00000273032 DGCR5 GTEx Brain - Amygdala UBERON_0001876 11.71 7.2 0.37 5.81 10 17.75 30.48 +Brain - Anterior cingulate cortex (BA24) (Dataset = GTEx, N = 176) ENSG00000273032 DGCR5 GTEx Brain - Anterior cingulate cortex (BA24) UBERON_0009835 18.87 9.98 1.32 11.13 18.3 25.76 48.81 +Brain - Caudate (basal ganglia) (Dataset = GTEx, N = 246) ENSG00000273032 DGCR5 GTEx Brain - Caudate (basal ganglia) UBERON_0001873 12.28 7.36 0.72 6.42 11.88 17.36 41.57 +Brain - Cerebellum (Dataset = GTEx, N = 456) ENSG00000273032 DGCR5 GTEx Brain - Cerebellum UBERON_0002037 56.26 24.93 5.23 39.74 55.93 69.55 146.2 +Brain - Cortex (Dataset = GTEx, N = 255) ENSG00000273032 DGCR5 GTEx Brain - Cortex UBERON_0001870 24.57 11 2.6 16.95 23.86 32.13 61.87 +Brain - Frontal Cortex (BA9) (Dataset = GTEx, N = 209) ENSG00000273032 DGCR5 GTEx Brain - Frontal Cortex (BA9) UBERON_0009834 25.17 12.51 1.46 16.42 25.07 32.04 58.68 +Brain - Hippocampus (Dataset = GTEx, N = 197) ENSG00000273032 DGCR5 GTEx Brain - Hippocampus UBERON_0001954 10.25 7.18 0.92 4.53 9.09 14.1 38.19 +Brain - Hypothalamus (Dataset = GTEx, N = 202) ENSG00000273032 DGCR5 GTEx Brain - Hypothalamus UBERON_0001898 7.58 5.37 0.35 3.88 6.54 10.4 48.05 +Brain - Nucleus accumbens (basal ganglia) (Dataset = GTEx, N = 246) ENSG00000273032 DGCR5 GTEx Brain - Nucleus accumbens (basal ganglia) UBERON_0001882 16.22 8.7 0.88 9.01 16.66 22.12 38.1 +Brain - Putamen (basal ganglia) (Dataset = GTEx, N = 205) ENSG00000273032 DGCR5 GTEx Brain - Putamen (basal ganglia) UBERON_0001874 9.2 6.12 0.47 4.46 8.4 12.65 30.49 +Brain - Spinal cord (cervical c-1) (Dataset = GTEx, N = 159) ENSG00000273032 DGCR5 GTEx Brain - Spinal cord (cervical c-1) UBERON_0006469 2.29 2.08 0.22 0.87 1.69 3.11 12.93 +Brain - Substantia nigra (Dataset = GTEx, N = 139) ENSG00000273032 DGCR5 GTEx Brain - Substantia nigra UBERON_0002038 4.56 3.83 0.41 1.95 3.44 6.47 23.99 +Breast - Mammary Tissue (Dataset = GTEx, N = 459) ENSG00000273032 DGCR5 GTEx Breast - Mammary Tissue UBERON_0008367 0.28 0.56 0 0.04 0.14 0.36 7.24 +Cells - Cultured fibroblasts (Dataset = GTEx, N = 504) ENSG00000273032 DGCR5 GTEx Cells - Cultured fibroblasts 0.03 0.05 0 0 0.02 0.04 0.47 +Cells - EBV-transformed lymphocytes (Dataset = GTEx, N = 174) ENSG00000273032 DGCR5 GTEx Cells - EBV-transformed lymphocytes 0.02 0.04 0 0 0.01 0.02 0.29 +Cervix - Ectocervix (Dataset = GTEx, N = 9) ENSG00000273032 DGCR5 GTEx Cervix - Ectocervix UBERON_0012249 0.09 0.09 0 0.02 0.06 0.16 0.28 +Cervix - Endocervix (Dataset = GTEx, N = 10) ENSG00000273032 DGCR5 GTEx Cervix - Endocervix UBERON_0000458 0.11 0.09 0.01 0.07 0.09 0.13 0.28 +Colon - Sigmoid (Dataset = GTEx, N = 373) ENSG00000273032 DGCR5 GTEx Colon - Sigmoid UBERON_0001159 0.16 0.11 0 0.08 0.13 0.21 0.67 +Colon - Transverse (Dataset = GTEx, N = 406) ENSG00000273032 DGCR5 GTEx Colon - Transverse UBERON_0001157 0.09 0.09 0 0.03 0.06 0.13 0.72 +Esophagus - Gastroesophageal Junction (Dataset = GTEx, N = 375) ENSG00000273032 DGCR5 GTEx Esophagus - Gastroesophageal Junction UBERON_0004550 0.09 0.08 0 0.03 0.07 0.12 0.57 +Esophagus - Mucosa (Dataset = GTEx, N = 555) ENSG00000273032 DGCR5 GTEx Esophagus - Mucosa UBERON_0006920 0.24 0.16 0 0.13 0.21 0.31 1.27 +Esophagus - Muscularis (Dataset = GTEx, N = 515) ENSG00000273032 DGCR5 GTEx Esophagus - Muscularis UBERON_0004648 0.09 0.09 0 0.03 0.07 0.12 0.87 +Fallopian Tube (Dataset = GTEx, N = 9) ENSG00000273032 DGCR5 GTEx Fallopian Tube UBERON_0003889 0.08 0.04 0.03 0.06 0.07 0.11 0.17 +Heart - Atrial Appendage (Dataset = GTEx, N = 429) ENSG00000273032 DGCR5 GTEx Heart - Atrial Appendage UBERON_0006631 0.08 0.1 0 0.03 0.06 0.09 1.61 +Heart - Left Ventricle (Dataset = GTEx, N = 432) ENSG00000273032 DGCR5 GTEx Heart - Left Ventricle UBERON_0006566 0.02 0.03 0 0.01 0.01 0.02 0.39 +Kidney - Cortex (Dataset = GTEx, N = 85) ENSG00000273032 DGCR5 GTEx Kidney - Cortex UBERON_0001225 0.71 0.71 0.07 0.26 0.47 0.82 3.82 +Kidney - Medulla (Dataset = GTEx, N = 4) ENSG00000273032 DGCR5 GTEx Kidney - Medulla UBERON_0001293 0.22 0.17 0.11 0.11 0.14 0.25 0.46 +Liver (Dataset = GTEx, N = 226) ENSG00000273032 DGCR5 GTEx Liver UBERON_0001114 3.46 2.75 0.21 1.75 2.82 4.16 18.26 +Lung (Dataset = GTEx, N = 578) ENSG00000273032 DGCR5 GTEx Lung UBERON_0008952 0.15 0.14 0 0.07 0.11 0.18 1.23 +Minor Salivary Gland (Dataset = GTEx, N = 162) ENSG00000273032 DGCR5 GTEx Minor Salivary Gland UBERON_0006330 0.26 0.17 0.04 0.15 0.23 0.33 1.09 +Muscle - Skeletal (Dataset = GTEx, N = 803) ENSG00000273032 DGCR5 GTEx Muscle - Skeletal UBERON_0011907 0.05 0.07 0 0.01 0.03 0.06 1.14 +Nerve - Tibial (Dataset = GTEx, N = 619) ENSG00000273032 DGCR5 GTEx Nerve - Tibial UBERON_0001323 0.45 0.45 0 0.2 0.32 0.53 4.76 +Ovary (Dataset = GTEx, N = 180) ENSG00000273032 DGCR5 GTEx Ovary UBERON_0000992 0.13 0.18 0 0.04 0.09 0.15 1.41 +Pancreas (Dataset = GTEx, N = 328) ENSG00000273032 DGCR5 GTEx Pancreas UBERON_0001150 5.93 3.19 0.37 3.65 5.33 7.46 21.53 +Pituitary (Dataset = GTEx, N = 283) ENSG00000273032 DGCR5 GTEx Pituitary UBERON_0000007 7.08 4.15 0.79 4.85 6.38 8.8 51.15 +Prostate (Dataset = GTEx, N = 245) ENSG00000273032 DGCR5 GTEx Prostate UBERON_0002367 0.36 0.32 0 0.15 0.29 0.46 2.29 +Skin - Not Sun Exposed (Suprapubic) (Dataset = GTEx, N = 604) ENSG00000273032 DGCR5 GTEx Skin - Not Sun Exposed (Suprapubic) UBERON_0036149 1.17 0.72 0.17 0.73 1.01 1.44 7.86 +Skin - Sun Exposed (Lower leg) (Dataset = GTEx, N = 701) ENSG00000273032 DGCR5 GTEx Skin - Sun Exposed (Lower leg) UBERON_0004264 1.29 0.79 0.06 0.81 1.14 1.55 8.59 +Small Intestine - Terminal Ileum (Dataset = GTEx, N = 187) ENSG00000273032 DGCR5 GTEx Small Intestine - Terminal Ileum UBERON_0001211 0.08 0.07 0 0.04 0.07 0.11 0.44 +Spleen (Dataset = GTEx, N = 241) ENSG00000273032 DGCR5 GTEx Spleen UBERON_0002106 0.47 0.42 0.01 0.22 0.35 0.56 3.24 +Stomach (Dataset = GTEx, N = 359) ENSG00000273032 DGCR5 GTEx Stomach UBERON_0000945 0.09 0.1 0 0.03 0.07 0.12 0.94 +Testis (Dataset = GTEx, N = 361) ENSG00000273032 DGCR5 GTEx Testis UBERON_0000473 1.47 0.48 0.58 1.16 1.39 1.72 3.33 +Thyroid (Dataset = GTEx, N = 653) ENSG00000273032 DGCR5 GTEx Thyroid UBERON_0002046 0.55 0.76 0 0.23 0.38 0.63 12 +Uterus (Dataset = GTEx, N = 142) ENSG00000273032 DGCR5 GTEx Uterus UBERON_0000995 0.12 0.19 0 0.03 0.07 0.13 1.34 +Vagina (Dataset = GTEx, N = 156) ENSG00000273032 DGCR5 GTEx Vagina UBERON_0000996 0.25 0.23 0 0.08 0.18 0.35 1.4 diff --git a/tests/results/test-tpm-gene-disease-gtex-ENSG00000273032-MONDO_0016718.tsv b/tests/results/test-tpm-gene-disease-gtex-ENSG00000273032-MONDO_0016718.tsv new file mode 100644 index 0000000..e8c38aa --- /dev/null +++ b/tests/results/test-tpm-gene-disease-gtex-ENSG00000273032-MONDO_0016718.tsv @@ -0,0 +1,55 @@ +x_labels Gene_Ensembl_ID Gene_symbol PMTL Dataset Disease GTEx_tissue_subgroup EFO MONDO GTEx_tissue_subgroup_UBERON TPM_mean TPM_sd TPM_min TPM_25th_percentile TPM_median TPM_75th_percentile TPM_max +Choroid plexus carcinoma (Dataset = PBTA, N = 4) ENSG00000273032 DGCR5 PBTA Choroid plexus carcinoma MONDO_0016718 MONDO_0016718 0.55 0.17 0.37 0.44 0.52 0.64 0.77 +Adipose - Subcutaneous (Dataset = GTEx, N = 663) ENSG00000273032 DGCR5 GTEx Adipose - Subcutaneous UBERON_0002190 0.06 0.13 0 0.01 0.03 0.06 2.11 +Adipose - Visceral (Omentum) (Dataset = GTEx, N = 541) ENSG00000273032 DGCR5 GTEx Adipose - Visceral (Omentum) UBERON_0010414 0.21 0.23 0 0.06 0.12 0.28 1.61 +Adrenal Gland (Dataset = GTEx, N = 258) ENSG00000273032 DGCR5 GTEx Adrenal Gland UBERON_0002369 4.53 3.59 0.56 2.39 3.57 5.24 23.56 +Artery - Aorta (Dataset = GTEx, N = 432) ENSG00000273032 DGCR5 GTEx Artery - Aorta UBERON_0001496 0.04 0.06 0 0.01 0.02 0.06 0.44 +Artery - Coronary (Dataset = GTEx, N = 240) ENSG00000273032 DGCR5 GTEx Artery - Coronary UBERON_0001621 0.08 0.07 0 0.02 0.06 0.1 0.41 +Artery - Tibial (Dataset = GTEx, N = 663) ENSG00000273032 DGCR5 GTEx Artery - Tibial UBERON_0007610 0.04 0.07 0 0.01 0.03 0.05 0.94 +Bladder (Dataset = GTEx, N = 21) ENSG00000273032 DGCR5 GTEx Bladder UBERON_0001255 0.07 0.09 0 0.02 0.03 0.08 0.4 +Blood (Dataset = GTEx, N = 755) ENSG00000273032 DGCR5 GTEx Blood UBERON_0013756 0.02 0.03 0 0 0.01 0.02 0.4 +Brain - Amygdala (Dataset = GTEx, N = 152) ENSG00000273032 DGCR5 GTEx Brain - Amygdala UBERON_0001876 11.71 7.2 0.37 5.81 10 17.75 30.48 +Brain - Anterior cingulate cortex (BA24) (Dataset = GTEx, N = 176) ENSG00000273032 DGCR5 GTEx Brain - Anterior cingulate cortex (BA24) UBERON_0009835 18.87 9.98 1.32 11.13 18.3 25.76 48.81 +Brain - Caudate (basal ganglia) (Dataset = GTEx, N = 246) ENSG00000273032 DGCR5 GTEx Brain - Caudate (basal ganglia) UBERON_0001873 12.28 7.36 0.72 6.42 11.88 17.36 41.57 +Brain - Cerebellum (Dataset = GTEx, N = 456) ENSG00000273032 DGCR5 GTEx Brain - Cerebellum UBERON_0002037 56.26 24.93 5.23 39.74 55.93 69.55 146.2 +Brain - Cortex (Dataset = GTEx, N = 255) ENSG00000273032 DGCR5 GTEx Brain - Cortex UBERON_0001870 24.57 11 2.6 16.95 23.86 32.13 61.87 +Brain - Frontal Cortex (BA9) (Dataset = GTEx, N = 209) ENSG00000273032 DGCR5 GTEx Brain - Frontal Cortex (BA9) UBERON_0009834 25.17 12.51 1.46 16.42 25.07 32.04 58.68 +Brain - Hippocampus (Dataset = GTEx, N = 197) ENSG00000273032 DGCR5 GTEx Brain - Hippocampus UBERON_0001954 10.25 7.18 0.92 4.53 9.09 14.1 38.19 +Brain - Hypothalamus (Dataset = GTEx, N = 202) ENSG00000273032 DGCR5 GTEx Brain - Hypothalamus UBERON_0001898 7.58 5.37 0.35 3.88 6.54 10.4 48.05 +Brain - Nucleus accumbens (basal ganglia) (Dataset = GTEx, N = 246) ENSG00000273032 DGCR5 GTEx Brain - Nucleus accumbens (basal ganglia) UBERON_0001882 16.22 8.7 0.88 9.01 16.66 22.12 38.1 +Brain - Putamen (basal ganglia) (Dataset = GTEx, N = 205) ENSG00000273032 DGCR5 GTEx Brain - Putamen (basal ganglia) UBERON_0001874 9.2 6.12 0.47 4.46 8.4 12.65 30.49 +Brain - Spinal cord (cervical c-1) (Dataset = GTEx, N = 159) ENSG00000273032 DGCR5 GTEx Brain - Spinal cord (cervical c-1) UBERON_0006469 2.29 2.08 0.22 0.87 1.69 3.11 12.93 +Brain - Substantia nigra (Dataset = GTEx, N = 139) ENSG00000273032 DGCR5 GTEx Brain - Substantia nigra UBERON_0002038 4.56 3.83 0.41 1.95 3.44 6.47 23.99 +Breast - Mammary Tissue (Dataset = GTEx, N = 459) ENSG00000273032 DGCR5 GTEx Breast - Mammary Tissue UBERON_0008367 0.28 0.56 0 0.04 0.14 0.36 7.24 +Cells - Cultured fibroblasts (Dataset = GTEx, N = 504) ENSG00000273032 DGCR5 GTEx Cells - Cultured fibroblasts 0.03 0.05 0 0 0.02 0.04 0.47 +Cells - EBV-transformed lymphocytes (Dataset = GTEx, N = 174) ENSG00000273032 DGCR5 GTEx Cells - EBV-transformed lymphocytes 0.02 0.04 0 0 0.01 0.02 0.29 +Cervix - Ectocervix (Dataset = GTEx, N = 9) ENSG00000273032 DGCR5 GTEx Cervix - Ectocervix UBERON_0012249 0.09 0.09 0 0.02 0.06 0.16 0.28 +Cervix - Endocervix (Dataset = GTEx, N = 10) ENSG00000273032 DGCR5 GTEx Cervix - Endocervix UBERON_0000458 0.11 0.09 0.01 0.07 0.09 0.13 0.28 +Colon - Sigmoid (Dataset = GTEx, N = 373) ENSG00000273032 DGCR5 GTEx Colon - Sigmoid UBERON_0001159 0.16 0.11 0 0.08 0.13 0.21 0.67 +Colon - Transverse (Dataset = GTEx, N = 406) ENSG00000273032 DGCR5 GTEx Colon - Transverse UBERON_0001157 0.09 0.09 0 0.03 0.06 0.13 0.72 +Esophagus - Gastroesophageal Junction (Dataset = GTEx, N = 375) ENSG00000273032 DGCR5 GTEx Esophagus - Gastroesophageal Junction UBERON_0004550 0.09 0.08 0 0.03 0.07 0.12 0.57 +Esophagus - Mucosa (Dataset = GTEx, N = 555) ENSG00000273032 DGCR5 GTEx Esophagus - Mucosa UBERON_0006920 0.24 0.16 0 0.13 0.21 0.31 1.27 +Esophagus - Muscularis (Dataset = GTEx, N = 515) ENSG00000273032 DGCR5 GTEx Esophagus - Muscularis UBERON_0004648 0.09 0.09 0 0.03 0.07 0.12 0.87 +Fallopian Tube (Dataset = GTEx, N = 9) ENSG00000273032 DGCR5 GTEx Fallopian Tube UBERON_0003889 0.08 0.04 0.03 0.06 0.07 0.11 0.17 +Heart - Atrial Appendage (Dataset = GTEx, N = 429) ENSG00000273032 DGCR5 GTEx Heart - Atrial Appendage UBERON_0006631 0.08 0.1 0 0.03 0.06 0.09 1.61 +Heart - Left Ventricle (Dataset = GTEx, N = 432) ENSG00000273032 DGCR5 GTEx Heart - Left Ventricle UBERON_0006566 0.02 0.03 0 0.01 0.01 0.02 0.39 +Kidney - Cortex (Dataset = GTEx, N = 85) ENSG00000273032 DGCR5 GTEx Kidney - Cortex UBERON_0001225 0.71 0.71 0.07 0.26 0.47 0.82 3.82 +Kidney - Medulla (Dataset = GTEx, N = 4) ENSG00000273032 DGCR5 GTEx Kidney - Medulla UBERON_0001293 0.22 0.17 0.11 0.11 0.14 0.25 0.46 +Liver (Dataset = GTEx, N = 226) ENSG00000273032 DGCR5 GTEx Liver UBERON_0001114 3.46 2.75 0.21 1.75 2.82 4.16 18.26 +Lung (Dataset = GTEx, N = 578) ENSG00000273032 DGCR5 GTEx Lung UBERON_0008952 0.15 0.14 0 0.07 0.11 0.18 1.23 +Minor Salivary Gland (Dataset = GTEx, N = 162) ENSG00000273032 DGCR5 GTEx Minor Salivary Gland UBERON_0006330 0.26 0.17 0.04 0.15 0.23 0.33 1.09 +Muscle - Skeletal (Dataset = GTEx, N = 803) ENSG00000273032 DGCR5 GTEx Muscle - Skeletal UBERON_0011907 0.05 0.07 0 0.01 0.03 0.06 1.14 +Nerve - Tibial (Dataset = GTEx, N = 619) ENSG00000273032 DGCR5 GTEx Nerve - Tibial UBERON_0001323 0.45 0.45 0 0.2 0.32 0.53 4.76 +Ovary (Dataset = GTEx, N = 180) ENSG00000273032 DGCR5 GTEx Ovary UBERON_0000992 0.13 0.18 0 0.04 0.09 0.15 1.41 +Pancreas (Dataset = GTEx, N = 328) ENSG00000273032 DGCR5 GTEx Pancreas UBERON_0001150 5.93 3.19 0.37 3.65 5.33 7.46 21.53 +Pituitary (Dataset = GTEx, N = 283) ENSG00000273032 DGCR5 GTEx Pituitary UBERON_0000007 7.08 4.15 0.79 4.85 6.38 8.8 51.15 +Prostate (Dataset = GTEx, N = 245) ENSG00000273032 DGCR5 GTEx Prostate UBERON_0002367 0.36 0.32 0 0.15 0.29 0.46 2.29 +Skin - Not Sun Exposed (Suprapubic) (Dataset = GTEx, N = 604) ENSG00000273032 DGCR5 GTEx Skin - Not Sun Exposed (Suprapubic) UBERON_0036149 1.17 0.72 0.17 0.73 1.01 1.44 7.86 +Skin - Sun Exposed (Lower leg) (Dataset = GTEx, N = 701) ENSG00000273032 DGCR5 GTEx Skin - Sun Exposed (Lower leg) UBERON_0004264 1.29 0.79 0.06 0.81 1.14 1.55 8.59 +Small Intestine - Terminal Ileum (Dataset = GTEx, N = 187) ENSG00000273032 DGCR5 GTEx Small Intestine - Terminal Ileum UBERON_0001211 0.08 0.07 0 0.04 0.07 0.11 0.44 +Spleen (Dataset = GTEx, N = 241) ENSG00000273032 DGCR5 GTEx Spleen UBERON_0002106 0.47 0.42 0.01 0.22 0.35 0.56 3.24 +Stomach (Dataset = GTEx, N = 359) ENSG00000273032 DGCR5 GTEx Stomach UBERON_0000945 0.09 0.1 0 0.03 0.07 0.12 0.94 +Testis (Dataset = GTEx, N = 361) ENSG00000273032 DGCR5 GTEx Testis UBERON_0000473 1.47 0.48 0.58 1.16 1.39 1.72 3.33 +Thyroid (Dataset = GTEx, N = 653) ENSG00000273032 DGCR5 GTEx Thyroid UBERON_0002046 0.55 0.76 0 0.23 0.38 0.63 12 +Uterus (Dataset = GTEx, N = 142) ENSG00000273032 DGCR5 GTEx Uterus UBERON_0000995 0.12 0.19 0 0.03 0.07 0.13 1.34 +Vagina (Dataset = GTEx, N = 156) ENSG00000273032 DGCR5 GTEx Vagina UBERON_0000996 0.25 0.23 0 0.08 0.18 0.35 1.4 diff --git a/tests/results/test-tpm-gene-disease-gtex-ENSG00000273032-Orphanet_178.tsv b/tests/results/test-tpm-gene-disease-gtex-ENSG00000273032-Orphanet_178.tsv new file mode 100644 index 0000000..08343f5 --- /dev/null +++ b/tests/results/test-tpm-gene-disease-gtex-ENSG00000273032-Orphanet_178.tsv @@ -0,0 +1,55 @@ +x_labels Gene_Ensembl_ID Gene_symbol PMTL Dataset Disease GTEx_tissue_subgroup EFO MONDO GTEx_tissue_subgroup_UBERON TPM_mean TPM_sd TPM_min TPM_25th_percentile TPM_median TPM_75th_percentile TPM_max +Chordoma (Dataset = PBTA, N = 3) ENSG00000273032 DGCR5 PBTA Chordoma Orphanet_178 MONDO_0008978 0.02 0.01 0.01 0.01 0.02 0.02 0.02 +Adipose - Subcutaneous (Dataset = GTEx, N = 663) ENSG00000273032 DGCR5 GTEx Adipose - Subcutaneous UBERON_0002190 0.06 0.13 0 0.01 0.03 0.06 2.11 +Adipose - Visceral (Omentum) (Dataset = GTEx, N = 541) ENSG00000273032 DGCR5 GTEx Adipose - Visceral (Omentum) UBERON_0010414 0.21 0.23 0 0.06 0.12 0.28 1.61 +Adrenal Gland (Dataset = GTEx, N = 258) ENSG00000273032 DGCR5 GTEx Adrenal Gland UBERON_0002369 4.53 3.59 0.56 2.39 3.57 5.24 23.56 +Artery - Aorta (Dataset = GTEx, N = 432) ENSG00000273032 DGCR5 GTEx Artery - Aorta UBERON_0001496 0.04 0.06 0 0.01 0.02 0.06 0.44 +Artery - Coronary (Dataset = GTEx, N = 240) ENSG00000273032 DGCR5 GTEx Artery - Coronary UBERON_0001621 0.08 0.07 0 0.02 0.06 0.1 0.41 +Artery - Tibial (Dataset = GTEx, N = 663) ENSG00000273032 DGCR5 GTEx Artery - Tibial UBERON_0007610 0.04 0.07 0 0.01 0.03 0.05 0.94 +Bladder (Dataset = GTEx, N = 21) ENSG00000273032 DGCR5 GTEx Bladder UBERON_0001255 0.07 0.09 0 0.02 0.03 0.08 0.4 +Blood (Dataset = GTEx, N = 755) ENSG00000273032 DGCR5 GTEx Blood UBERON_0013756 0.02 0.03 0 0 0.01 0.02 0.4 +Brain - Amygdala (Dataset = GTEx, N = 152) ENSG00000273032 DGCR5 GTEx Brain - Amygdala UBERON_0001876 11.71 7.2 0.37 5.81 10 17.75 30.48 +Brain - Anterior cingulate cortex (BA24) (Dataset = GTEx, N = 176) ENSG00000273032 DGCR5 GTEx Brain - Anterior cingulate cortex (BA24) UBERON_0009835 18.87 9.98 1.32 11.13 18.3 25.76 48.81 +Brain - Caudate (basal ganglia) (Dataset = GTEx, N = 246) ENSG00000273032 DGCR5 GTEx Brain - Caudate (basal ganglia) UBERON_0001873 12.28 7.36 0.72 6.42 11.88 17.36 41.57 +Brain - Cerebellum (Dataset = GTEx, N = 456) ENSG00000273032 DGCR5 GTEx Brain - Cerebellum UBERON_0002037 56.26 24.93 5.23 39.74 55.93 69.55 146.2 +Brain - Cortex (Dataset = GTEx, N = 255) ENSG00000273032 DGCR5 GTEx Brain - Cortex UBERON_0001870 24.57 11 2.6 16.95 23.86 32.13 61.87 +Brain - Frontal Cortex (BA9) (Dataset = GTEx, N = 209) ENSG00000273032 DGCR5 GTEx Brain - Frontal Cortex (BA9) UBERON_0009834 25.17 12.51 1.46 16.42 25.07 32.04 58.68 +Brain - Hippocampus (Dataset = GTEx, N = 197) ENSG00000273032 DGCR5 GTEx Brain - Hippocampus UBERON_0001954 10.25 7.18 0.92 4.53 9.09 14.1 38.19 +Brain - Hypothalamus (Dataset = GTEx, N = 202) ENSG00000273032 DGCR5 GTEx Brain - Hypothalamus UBERON_0001898 7.58 5.37 0.35 3.88 6.54 10.4 48.05 +Brain - Nucleus accumbens (basal ganglia) (Dataset = GTEx, N = 246) ENSG00000273032 DGCR5 GTEx Brain - Nucleus accumbens (basal ganglia) UBERON_0001882 16.22 8.7 0.88 9.01 16.66 22.12 38.1 +Brain - Putamen (basal ganglia) (Dataset = GTEx, N = 205) ENSG00000273032 DGCR5 GTEx Brain - Putamen (basal ganglia) UBERON_0001874 9.2 6.12 0.47 4.46 8.4 12.65 30.49 +Brain - Spinal cord (cervical c-1) (Dataset = GTEx, N = 159) ENSG00000273032 DGCR5 GTEx Brain - Spinal cord (cervical c-1) UBERON_0006469 2.29 2.08 0.22 0.87 1.69 3.11 12.93 +Brain - Substantia nigra (Dataset = GTEx, N = 139) ENSG00000273032 DGCR5 GTEx Brain - Substantia nigra UBERON_0002038 4.56 3.83 0.41 1.95 3.44 6.47 23.99 +Breast - Mammary Tissue (Dataset = GTEx, N = 459) ENSG00000273032 DGCR5 GTEx Breast - Mammary Tissue UBERON_0008367 0.28 0.56 0 0.04 0.14 0.36 7.24 +Cells - Cultured fibroblasts (Dataset = GTEx, N = 504) ENSG00000273032 DGCR5 GTEx Cells - Cultured fibroblasts 0.03 0.05 0 0 0.02 0.04 0.47 +Cells - EBV-transformed lymphocytes (Dataset = GTEx, N = 174) ENSG00000273032 DGCR5 GTEx Cells - EBV-transformed lymphocytes 0.02 0.04 0 0 0.01 0.02 0.29 +Cervix - Ectocervix (Dataset = GTEx, N = 9) ENSG00000273032 DGCR5 GTEx Cervix - Ectocervix UBERON_0012249 0.09 0.09 0 0.02 0.06 0.16 0.28 +Cervix - Endocervix (Dataset = GTEx, N = 10) ENSG00000273032 DGCR5 GTEx Cervix - Endocervix UBERON_0000458 0.11 0.09 0.01 0.07 0.09 0.13 0.28 +Colon - Sigmoid (Dataset = GTEx, N = 373) ENSG00000273032 DGCR5 GTEx Colon - Sigmoid UBERON_0001159 0.16 0.11 0 0.08 0.13 0.21 0.67 +Colon - Transverse (Dataset = GTEx, N = 406) ENSG00000273032 DGCR5 GTEx Colon - Transverse UBERON_0001157 0.09 0.09 0 0.03 0.06 0.13 0.72 +Esophagus - Gastroesophageal Junction (Dataset = GTEx, N = 375) ENSG00000273032 DGCR5 GTEx Esophagus - Gastroesophageal Junction UBERON_0004550 0.09 0.08 0 0.03 0.07 0.12 0.57 +Esophagus - Mucosa (Dataset = GTEx, N = 555) ENSG00000273032 DGCR5 GTEx Esophagus - Mucosa UBERON_0006920 0.24 0.16 0 0.13 0.21 0.31 1.27 +Esophagus - Muscularis (Dataset = GTEx, N = 515) ENSG00000273032 DGCR5 GTEx Esophagus - Muscularis UBERON_0004648 0.09 0.09 0 0.03 0.07 0.12 0.87 +Fallopian Tube (Dataset = GTEx, N = 9) ENSG00000273032 DGCR5 GTEx Fallopian Tube UBERON_0003889 0.08 0.04 0.03 0.06 0.07 0.11 0.17 +Heart - Atrial Appendage (Dataset = GTEx, N = 429) ENSG00000273032 DGCR5 GTEx Heart - Atrial Appendage UBERON_0006631 0.08 0.1 0 0.03 0.06 0.09 1.61 +Heart - Left Ventricle (Dataset = GTEx, N = 432) ENSG00000273032 DGCR5 GTEx Heart - Left Ventricle UBERON_0006566 0.02 0.03 0 0.01 0.01 0.02 0.39 +Kidney - Cortex (Dataset = GTEx, N = 85) ENSG00000273032 DGCR5 GTEx Kidney - Cortex UBERON_0001225 0.71 0.71 0.07 0.26 0.47 0.82 3.82 +Kidney - Medulla (Dataset = GTEx, N = 4) ENSG00000273032 DGCR5 GTEx Kidney - Medulla UBERON_0001293 0.22 0.17 0.11 0.11 0.14 0.25 0.46 +Liver (Dataset = GTEx, N = 226) ENSG00000273032 DGCR5 GTEx Liver UBERON_0001114 3.46 2.75 0.21 1.75 2.82 4.16 18.26 +Lung (Dataset = GTEx, N = 578) ENSG00000273032 DGCR5 GTEx Lung UBERON_0008952 0.15 0.14 0 0.07 0.11 0.18 1.23 +Minor Salivary Gland (Dataset = GTEx, N = 162) ENSG00000273032 DGCR5 GTEx Minor Salivary Gland UBERON_0006330 0.26 0.17 0.04 0.15 0.23 0.33 1.09 +Muscle - Skeletal (Dataset = GTEx, N = 803) ENSG00000273032 DGCR5 GTEx Muscle - Skeletal UBERON_0011907 0.05 0.07 0 0.01 0.03 0.06 1.14 +Nerve - Tibial (Dataset = GTEx, N = 619) ENSG00000273032 DGCR5 GTEx Nerve - Tibial UBERON_0001323 0.45 0.45 0 0.2 0.32 0.53 4.76 +Ovary (Dataset = GTEx, N = 180) ENSG00000273032 DGCR5 GTEx Ovary UBERON_0000992 0.13 0.18 0 0.04 0.09 0.15 1.41 +Pancreas (Dataset = GTEx, N = 328) ENSG00000273032 DGCR5 GTEx Pancreas UBERON_0001150 5.93 3.19 0.37 3.65 5.33 7.46 21.53 +Pituitary (Dataset = GTEx, N = 283) ENSG00000273032 DGCR5 GTEx Pituitary UBERON_0000007 7.08 4.15 0.79 4.85 6.38 8.8 51.15 +Prostate (Dataset = GTEx, N = 245) ENSG00000273032 DGCR5 GTEx Prostate UBERON_0002367 0.36 0.32 0 0.15 0.29 0.46 2.29 +Skin - Not Sun Exposed (Suprapubic) (Dataset = GTEx, N = 604) ENSG00000273032 DGCR5 GTEx Skin - Not Sun Exposed (Suprapubic) UBERON_0036149 1.17 0.72 0.17 0.73 1.01 1.44 7.86 +Skin - Sun Exposed (Lower leg) (Dataset = GTEx, N = 701) ENSG00000273032 DGCR5 GTEx Skin - Sun Exposed (Lower leg) UBERON_0004264 1.29 0.79 0.06 0.81 1.14 1.55 8.59 +Small Intestine - Terminal Ileum (Dataset = GTEx, N = 187) ENSG00000273032 DGCR5 GTEx Small Intestine - Terminal Ileum UBERON_0001211 0.08 0.07 0 0.04 0.07 0.11 0.44 +Spleen (Dataset = GTEx, N = 241) ENSG00000273032 DGCR5 GTEx Spleen UBERON_0002106 0.47 0.42 0.01 0.22 0.35 0.56 3.24 +Stomach (Dataset = GTEx, N = 359) ENSG00000273032 DGCR5 GTEx Stomach UBERON_0000945 0.09 0.1 0 0.03 0.07 0.12 0.94 +Testis (Dataset = GTEx, N = 361) ENSG00000273032 DGCR5 GTEx Testis UBERON_0000473 1.47 0.48 0.58 1.16 1.39 1.72 3.33 +Thyroid (Dataset = GTEx, N = 653) ENSG00000273032 DGCR5 GTEx Thyroid UBERON_0002046 0.55 0.76 0 0.23 0.38 0.63 12 +Uterus (Dataset = GTEx, N = 142) ENSG00000273032 DGCR5 GTEx Uterus UBERON_0000995 0.12 0.19 0 0.03 0.07 0.13 1.34 +Vagina (Dataset = GTEx, N = 156) ENSG00000273032 DGCR5 GTEx Vagina UBERON_0000996 0.25 0.23 0 0.08 0.18 0.35 1.4