title: MUFFINN: cancer gene discovery via network analysis of somatic mutation data.
abstract: A major challenge for distinguishing cancer-causing driver mutations from inconsequential passenger mutations is the long-tail of infrequently mutated genes in cancer genomes. Here, we present and evaluate a method for prioritizing cancer genes accounting not only for mutations in individual genes but also in their neighbors in functional networks, MUFFINN (MUtations For Functional Impact on Network Neighbors). This pathway-centric method shows high sensitivity compared with gene-centric analyses of mutation data. Notably, only a marginal decrease in performance is observed when using 10 % of TCGA patient samples, suggesting the method may potentiate cancer genome projects with small patient populations.
authors.affiliation: Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea.
authors.forename: Ara
authors.initials: A
authors.lastname: Cho
authors.affiliation: Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea.
authors.forename: Jung Eun
authors.initials: JE
authors.lastname: Shim
authors.affiliation: Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea.
authors.forename: Eiru
authors.initials: E
authors.lastname: Kim
authors.affiliation: EMBL-CRG Systems Biology Unit, Centre for Genomic Regulation (CRG), 08003, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.|Division of Electronics, Rudjer Boskovic Institute, 10000, Zagreb, Croatia.
authors.forename: Fran
authors.initials: F
authors.lastname: Supek
authors.affiliation: EMBL-CRG Systems Biology Unit, Centre for Genomic Regulation (CRG), 08003, Barcelona, Spain. ben.lehner@crg.eu.|Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain. ben.lehner@crg.eu.
authors.forename: Ben
authors.initials: B
authors.lastname: Lehner
authors.affiliation: Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea. insuklee@yonsei.ac.kr.
authors.forename: Insuk
authors.initials: I
authors.lastname: Lee
mesh_terms: D019295:Computational Biology; D004252:DNA Mutational Analysis / Q000379:methods*; D030541:Databases, Genetic; D015894:Genome, Human; D006801:Humans; D009154:Mutation; D009363:Neoplasm Proteins / Q000235:genetics*; D009369:Neoplasms / Q000235:genetics*; D009857:Oncogenes / Q000235:genetics; D015398:Signal Transduction / Q000235:genetics*; D012984:Software
chemical_list: D009363:Neoplasm Proteins
keywords: Cancer gene prediction; Cancer genomes; Cancer somatic mutation; Functional gene network; Mutation frequency; Pathway-centric analysis