OMEN data set: Tokheim pancancer data set with genome-wide interaction network
Authors/Creators
- 1. KU Leuven
- 2. IDLab, IMEC, Gent
Description
OMEN is a Network-based Driver Gene Identification method that exploits Mutual Exclusivity.
This repository stores the data used in a pancancer experiment showcasing this method.
It consists of
- [tokheim_pancancer_somatic_CADD.pl] A file containing CADD probabilities for gene-patient pairs (derived from the pancancer data set in Tokheim, Collin J., et al. "Evaluating the evaluation of cancer driver genes." Proceedings of the National Academy of Sciences 113.50 (2016): 14330-14335.) formatted to be used by OMEN.
- [tokheim_pancancer_somatic_coverage_ranks.pl] A file containing gene coverage data (derived from the CADD data) formatted to be used by OMEN.
- [network.pl] A file containing a genome-wide interaction network consisting of high quality metabolic interactions from Recon X and literature curated interactions from Intact. Recon X and Intact data was acquired from Pathway Commons version 8.
The resulting network covers 7901 samples, and contains 15.694 nodes and 178.051 edges.