title: FunCoup 3.0: database of genome-wide functional coupling networks.
abstract: We present an update of the FunCoup database (http://FunCoup.sbc.su.se) of functional couplings, or functional associations, between genes and gene products. Identifying these functional couplings is an important step in the understanding of higher level mechanisms performed by complex cellular processes. FunCoup distinguishes between four classes of couplings: participation in the same signaling cascade, participation in the same metabolic process, co-membership in a protein complex and physical interaction. For each of these four classes, several types of experimental and statistical evidence are combined by Bayesian integration to predict genome-wide functional coupling networks. The FunCoup framework has been completely re-implemented to allow for more frequent future updates. It contains many improvements, such as a regularization procedure to automatically downweight redundant evidences and a novel method to incorporate phylogenetic profile similarity. Several datasets have been updated and new data have been added in FunCoup 3.0. Furthermore, we have developed a new Web site, which provides powerful tools to explore the predicted networks and to retrieve detailed information about the data underlying each prediction.
authors.affiliation: Stockholm Bioinformatics Centre, Science for Life Laboratory, Box 1031, Solna SE-17121, Sweden, Department of Biochemistry and Biophysics, Stockholm University and Swedish eScience Research Center.
authors.forename: Thomas
authors.initials: T
authors.lastname: Schmitt
authors.forename: Christoph
authors.initials: C
authors.lastname: Ogris
authors.forename: Erik L L
authors.initials: EL
authors.lastname: Sonnhammer
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D030541:Databases, Genetic; D053263:Gene Regulatory Networks; D016678:Genome; D006801:Humans; D020407:Internet; D053858:Metabolic Networks and Pathways; D051379:Mice; D046912:Multiprotein Complexes; D010802:Phylogeny; D025941:Protein Interaction Mapping; D051381:Rats; D015398:Signal Transduction; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D046912:Multiprotein Complexes; D014157:Transcription Factors