title: Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations.
abstract: We present a novel method for the identification of sets of mutually exclusive gene alterations in a given set of genomic profiles. We scan the groups of genes with a common downstream effect on the signaling network, using a mutual exclusivity criterion that ensures that each gene in the group significantly contributes to the mutual exclusivity pattern. We test the method on all available TCGA cancer genomics datasets, and detect multiple previously unreported alterations that show significant mutual exclusivity and are likely to be driver events.
authors.affiliation: Computational Biology Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 460, New York, 10065, USA. mutex@cbio.mskcc.org.
authors.forename: Özgün
authors.initials: Ö
authors.lastname: Babur
authors.affiliation: Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, 10065, USA. gonenm@mskcc.org.
authors.forename: Mithat
authors.initials: M
authors.lastname: Gönen
authors.affiliation: Computational Biology Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 460, New York, 10065, USA. arman@cbio.mskcc.org.|Tri-Institutional Training Program in Computational Biology and Medicine, 1275 York Avenue, New York, 10065, USA. arman@cbio.mskcc.org.
authors.forename: Bülent Arman
authors.initials: BA
authors.lastname: Aksoy
authors.affiliation: Computational Biology Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 460, New York, 10065, USA. schultz@cbio.mskcc.org.
authors.forename: Nikolaus
authors.initials: N
authors.lastname: Schultz
authors.affiliation: Computational Biology Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 460, New York, 10065, USA. ciriello@cbio.mskcc.org.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Ciriello
authors.affiliation: Computational Biology Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 460, New York, 10065, USA. sander@cbio.mskcc.org.
authors.forename: Chris
authors.initials: C
authors.lastname: Sander
authors.affiliation: Computational Biology Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 460, New York, 10065, USA. demir@cbio.mskcc.org.
authors.forename: Emek
authors.initials: E
authors.lastname: Demir
mesh_terms: D001943:Breast Neoplasms / Q000209:etiology / Q000235:genetics* / Q000473:pathology; D019295:Computational Biology; D030541:Databases, Genetic; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D023281:Genomics; D006801:Humans; D009363:Neoplasm Proteins / Q000096:biosynthesis* / Q000235:genetics; D015398:Signal Transduction / Q000235:genetics
chemical_list: D009363:Neoplasm Proteins