title: Pathway and network analysis of cancer genomes.
abstract: Genomic information on tumors from 50 cancer types cataloged by the International Cancer Genome Consortium (ICGC) shows that only a few well-studied driver genes are frequently mutated, in contrast to many infrequently mutated genes that may also contribute to tumor biology. Hence there has been large interest in developing pathway and network analysis methods that group genes and illuminate the processes involved. We provide an overview of these analysis techniques and show where they guide mechanistic and translational investigations.
authors.affiliation: Cellular Signal Integration Group (C-SIG), Technical University of Denmark, Lyngby, Denmark.
authors.forename: Pau
authors.initials: P
authors.lastname: Creixell
authors.affiliation: The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Jüri
authors.initials: J
authors.lastname: Reimand
authors.affiliation: Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
authors.forename: Syed
authors.initials: S
authors.lastname: Haider
authors.affiliation: Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.|Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon, USA.
authors.forename: Guanming
authors.initials: G
authors.lastname: Wu
authors.affiliation: Division of Cancer Genomics, National Cancer Center, Chuo-ku, Tokyo, Japan.
authors.forename: Tatsuhiro
authors.initials: T
authors.lastname: Shibata
authors.affiliation: Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid, Spain.
authors.forename: Miguel
authors.initials: M
authors.lastname: Vazquez
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Ville
authors.initials: V
authors.lastname: Mustonen
authors.affiliation: Research Unit on Biomedical Informatics, University Pompeu Fabra, Barcelona, Spain.
authors.forename: Abel
authors.initials: A
authors.lastname: Gonzalez-Perez
authors.affiliation: Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, Queensland, Australia.
authors.forename: John
authors.initials: J
authors.lastname: Pearson
authors.affiliation: Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
authors.forename: Chris
authors.initials: C
authors.lastname: Sander
authors.affiliation: Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, RI, USA.
authors.forename: Benjamin J
authors.initials: BJ
authors.lastname: Raphael
authors.affiliation: Department of Systems Biology, Harvard Medical School, Boston, MA USA.
authors.forename: Debora S
authors.initials: DS
authors.lastname: Marks
authors.affiliation: Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.|Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada.
authors.forename: B F Francis
authors.initials: BFF
authors.lastname: Ouellette
authors.affiliation: Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid, Spain.
authors.forename: Alfonso
authors.initials: A
authors.lastname: Valencia
authors.affiliation: The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Gary D
authors.initials: GD
authors.lastname: Bader
authors.affiliation: Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.|Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.|Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Paul C
authors.initials: PC
authors.lastname: Boutros
authors.affiliation: Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA.|Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California, USA.
authors.forename: Joshua M
authors.initials: JM
authors.lastname: Stuart
authors.affiliation: Cellular Signal Integration Group (C-SIG), Technical University of Denmark, Lyngby, Denmark.|Biotech Research & Innovation Centre (BRIC), University of Copenhagen (UCPH), DK-2200 Copenhagen, Denmark.
authors.forename: Rune
authors.initials: R
authors.lastname: Linding
authors.affiliation: Research Unit on Biomedical Informatics, University Pompeu Fabra, Barcelona, Spain.|Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.
authors.forename: Nuria
authors.initials: N
authors.lastname: Lopez-Bigas
authors.affiliation: Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.|Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Lincoln D
authors.initials: LD
authors.lastname: Stein
mesh_terms: D053263:Gene Regulatory Networks; D016678:Genome; D006801:Humans; D009369:Neoplasms / Q000235:genetics*; D015398:Signal Transduction / Q000502:physiology*