OMEN data set: Tokheim pancancer data set with genome-wide interaction network

OMEN is a Network-based Driver Gene Identification method that exploits Mutual Exclusivity.<br> 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." <em>Proceedings of the National Academy of Sciences</em> 113.50 (2016): 14330-14335.) formatted to be used by OMEN.<br> - [tokheim_pancancer_somatic_coverage_ranks.pl] A file containing gene coverage data (derived from the CADD data) formatted to be used by OMEN.<br> - [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.<br> The resulting network covers 7901 samples, and contains 15.694 nodes and 178.051 edges.OMEN是一种基于网络的驱动基因识别方法，其核心利用了互斥性（Mutual Exclusivity）特性。 本仓库存储了用于展示该方法的泛癌症实验所用数据，具体包括： - [tokheim_pancancer_somatic_CADD.pl] 存储基因-患者对CADD评分概率的文件，数据源自Tokheim、Collin J.等人发表于《美国国家科学院院刊》（*Proceedings of the National Academy of Sciences*）2016年第113卷第50期的论文《Evaluating the evaluation of cancer driver genes》（页码：14330-14335）中的泛癌症数据集，已完成格式化以适配OMEN的使用需求。 - [tokheim_pancancer_somatic_coverage_ranks.pl] 存储基因覆盖度数据的文件，数据源自上述CADD数据集，已完成格式化以适配OMEN的使用需求。 - [network.pl] 存储全基因组互作网络的文件，该网络包含来自Recon X的高质量代谢互作数据，以及来自Intact的经文献手工整理的互作数据。Recon X与Intact的数据均获取自Pathway Commons第8版。 所得网络覆盖7901个样本，包含15694个节点与178051条边。