Using MEMo to Discover Mutual Exclusivity Modules in Cancer. Issue 1 (1st March 2013)

• Record Type: Journal Article
• Authors: Ciriello, Giovanni; Cerami, Ethan; Aksoy, Bulent Arman; Sander, Chris; Schultz, Nikolaus
• Editors: Baxevanis, Andreas D.; Petsko, Gregory A.; Stein, Lincoln D.; Stormo, Gary D.
• Is Part Of: Current protocols in bioinformatics. Volume 41:Issue 1(2013)
• Page Start: 8.17.1
• Page End: 8.17.12
• Publication Date: 2013-03-01
• Subjects: mutual exclusivity -- network modules -- cancer genomics; Bioinformatics -- Laboratory manuals; Nucleotide sequence -- Laboratory manuals; Amino acid sequence -- Laboratory manuals; Base Sequence; Amino Acid Sequence; Computational Biology -- methods; Databases, Genetic; Proteins -- analysis; Sequence Analysis -- methods; Sequence Homology; Amino acid sequence; Bioinformatics; Nucleotide sequence; Laboratory Manuals; Laboratory manuals; 570.285
• DOI: 10.1002/0471250953.bi0817s41
• Languages: English
• ISSNs: 1934-3396

Abstract

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 . Curr. Protoc. Bioinform . 41:8.17.1‐8.17.12. © 2013 by John Wiley & Sons, Inc.