ensmusg_reactome_path_map: Ensembl gene id's and the Reactome pathways - for mouse!

In GeneAccord: Detection of clonally exclusive gene or pathway pairs in a cohort of cancer patients

Description

This is a tibble that contains mappings between mouse ensembl gene id's and reactome pathways. The reactome pathways are from the lowest level in the hierarchy ("Lowest level pathway diagram / Subset of the pathway"), and were obtained by download from the Reactome website (https://reactome.org/download-data; "ENSEMBL to pathways"). The following commands were used: wget https://reactome.org/download/current/Ensembl2Reactome.txt; cat Ensembl2Reactome.txt | grep "Mus musculus" > Ensembl2Reactome_mus_musculus.txt # and then Ensembl2Reactome_mus_musculus_woOmegaSymbol.txt was created from this by just # replacing the greek 'omega'-symbol in pathway "R-MMU-9027604" with the word 'omega'.

Usage

ensmusg_reactome_path_map

Format

A tibble with 28,630 rows and six variables:

ensembl_gene_id

the Ensembl gene id as a character

reactome_pw_id

the Reactome pathway stable identifier

url

The url leading to the pathway graph

reactome_pw_name

the name of the Reactome pathway

evidence_code

the evidence code

species

the species

Source

The tibble was created as follows: library(dplyr); ensmusg_path_map_raw <- read.csv("Ensembl2Reactome_mus_musculus_woOmegaSymbol.txt", header = F, sep = "\t", comment.char = "", check.names = F, skip = 0); stopifnot(dim(ensmusg_path_map_raw)[1] == 28696); stopifnot(dim(ensmusg_path_map_raw)[2] == 6); colnames(ensmusg_path_map_raw) <- c("ensembl_gene_id", "reactome_pw_id", "url", "reactome_pw_name", "evidence_code", "species"); ensmusg_path_map_raw <- dplyr::as.tbl(ensmusg_path_map_raw); ensmusg_reactome_path_map <- filter(filter(ensmusg_path_map_raw, grepl("ENSMUSG", ensmusg_path_map_raw$ensembl_gene_id)), species == "Mus musculus") stopifnot(dim(ensmusg_reactome_path_map)[1] == 28630)

GeneAccord documentation built on Nov. 8, 2020, 8:04 p.m.