Using MEMo to discover mutual exclusivity modules in cancer Journal Article
| Authors: | Ciriello, G.; Cerami, E.; Aksoy, B. A.; Sander, C.; Schultz, N. |
| Article 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. © 2013 by John Wiley & Sons, Inc. |
| Keywords: | gene mutation; somatic mutation; gene deletion; neoplasm; gene amplification; protein p53; homozygosity; genomics; hemizygosity; medical information system; computer program; cancer genomics; copy number variation; cyclin dependent kinase 2; mutual exclusivity; network modules; mutual exclusivity module in cancer |
| Journal Title: | Current Protocols in Bioinformatics |
| Volume: | 41 |
| ISSN: | 1934-3396 |
| Publisher: | John Wiley & Sons |
| Date Published: | 2013-03-01 |
| Start Page: | 8.17.1 |
| End Page: | 8.17.12 |
| Language: | English |
| DOI: | 10.1002/0471250953.bi0817s41 |
| PROVIDER: | scopus |
| PUBMED: | 23504936 |
| PMCID: | PMC5563973 |
| DOI/URL: | |
| Notes: | --- Unit 8.17 - "Export Date: 1 October 2013" - "Source: Scopus" |
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