MEMo is a method for identifying mutually exclusive driver networks in cancer. The method is freely available below as a Java-based command line tool.
Although individual tumors exhibit a diversity of genomic alterations, many of these events affect a limited number of biological pathways, and alterations that affect the same pathway tend to not co-occur in the same patient. To automatically identify such candidate driver networks from cancer genomics data, we have developed a novel method, Mutually Exclusive Modules in Cancer (MEMo). The method identifies networks defined by three properties: first, member genes are recurrently altered via somatic mutation or copy number changes; second, member genes are likely to participate in the same biological pathway or process, as determined from prior pathway and network knowledge; and third, genomic events within the network exhibit a statistically significant level of mutual exclusivity. Applied to genomic data from the Cancer Genome Atlas (TCGA), the method identifies all known altered pathways in glioblastoma and highlights the striking mutual exclusivity of genomic alterations in the PI3K, P53 and RB pathways. In serous ovarian cancer, we make the novel observation that inactivation of BRCA1 and BRCA2 is mutually exclusive of CCNE1 amplification and RB1 inactivation, suggesting alternative causes of genomic instability in this cancer type.
Ciriello, G., Cerami, E., Sander, C. & Schultz, N. Mutual exclusivity analysis identifies oncogenic network modules. Genome Res 22, 398-406 (2012)