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CancerGeneList

maintain the list of cancer-associated genes

Usage

Currently list of genes of interest are stored in:

  • allonco_no_pipes.csv gene symbols of known onco genes,
  • genes_adverse_event.csv list of genes that associated with adverse events in previous gene therapy trials,
  • mouseonco_gene_no_pipes.csv list of mouse onco genes.

Note

mouseonco_gene_no_pipes.csv was obtained by first downloading gene list from http://variation.osu.edu/rtcgd/, and then process the file with the following command to get rid of special characters.

cut -d, -f2 mouse_onco_gene.csv | awk -F'|' '{print $1}' | perl -lne '~/([a-zA-Z0-9-_\.]*)/; print $1' > mouse_onco_gene_nopipe.csv

source('onco_genes.R')

onco_genes <- get_oncogene_from_file('allonco_no_pipes.csv')
adverse_genes <- get_adverse_event_genes('genes_adverse_event.csv')