title: Using MEMo to discover mutual exclusivity modules in cancer.
abstract: Although individual tumors show surprisingly diverse genomic alterations, these events tend to occur in a limited number of pathways, and alterations that affect the same pathway tend to not co-occur in the same patient. While pathway analysis has been a powerful tool in cancer genomics, our knowledge of oncogenic pathway modules is incomplete. To systematically identify such modules, we have developed a novel method, Mutual Exclusivity Modules in Cancer (MEMo). The method searches and identifies modules characterized by three properties: (1) member genes are recurrently altered across a set of tumor samples; (2) member genes are known to or are likely to participate in the same biological process; and (3) alteration events within the modules are mutually exclusive. MEMo integrates multiple data types and maps genomic alterations to biological pathways. MEMo's mutual exclusivity uses a statistical model that preserves the number of alterations per gene and per sample. The MEMo software, source code and sample data sets are available for download at: http://cbio.mskcc.org/memo.
authors.affiliation: Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Ciriello
authors.affiliation: Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York.
authors.forename: Ethan
authors.initials: E
authors.lastname: Cerami
authors.affiliation: Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York.
authors.forename: Bulent Arman
authors.initials: BA
authors.lastname: Aksoy
authors.affiliation: Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York.
authors.forename: Chris
authors.initials: C
authors.lastname: Sander
authors.affiliation: Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York.
authors.forename: Nikolaus
authors.initials: N
authors.lastname: Schultz
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003201:Computers; D056915:DNA Copy Number Variations / Q000235:genetics; D053263:Gene Regulatory Networks / Q000235:genetics*; D006801:Humans; D009154:Mutation / Q000235:genetics; D009369:Neoplasms / Q000235:genetics*; D012984:Software