Weighted Sampling based Mutual Exclusivity
Mutual exclusivity is a widely recognized property of many cancer drivers. Knowledge about these relationships can provide important insights into cancer drivers, cancer-driving pathways, and cancer subtypes. It can also be used to predict new functional interactions between cancer driving genes and uncover novel cancer drivers. Currently, most of mutual exclusivity analyses are preformed focusing on a limited set of genes in part due to the computational cost required to rigorously compute p-values. To reduce the computing cost and perform less restricted mutual exclusivity analysis, WeSME uses weighted sampling method to estimate p-values while controlling the mutation rates of individual patients and genes similar to the permutation test. A comprehensive mutual exclusivity analysis allows uncovering many mutually exclusive pairs with relatively low mutation rates, which have often been missed in previous analyses.