MaxCLK: discovery of cancer driver genes via maximal clique and information entropy of modules

Abstract

Motivation Cancer is caused by the accumulation of somatic mutations in multiple pathways, in which driver mutations are typically of the properties of high coverage and high exclusivity in patients. Identifying cancer driver genes has a pivotal role in understanding the mechanisms of oncogenesis and treatment. Results Here, we introduced MaxCLK, an algorithm for identifying cancer driver genes, which was developed by an integrated analysis of somatic mutation data and protein–protein interaction (PPI) networks and further improved by an information entropy (IE) index. Tested on pancancer and single cancers, MaxCLK outperformed other existing methods with higher accuracy. About pancancer, we predicted 154 driver genes and 787 driver modules. The analysis of co-occurrence and exclusivity between modules and pathways reveals the correlation of their combinations. Overall, our study has deepened the understanding of driver mechanism in PPI topology and found novel driver genes. Availability The source codes for MaxCLK are freely available at https://github.com/ShandongUniversityMasterMa/MaxCLK-main. Supplementary information Supplementary data are available at Bioinformatics online.