FunCoup 3.0: Database of functional couplings
(English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962Article in journal (Refereed) Submitted
Gene products are involved in complex cellular processes to perform higher level functions. An important step in the understanding of these functions is to infer a network of functional couplings, or functional associations, between the genes. Here we present an update to the FunCoup database of functional couplings. 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 reimplemented to allow for more frequent future updates. It contains many improvements, such as a regularization procedure to automatically down-weight redundant evidences and a novel heuristic to incorporate phylogenetic profile similarity. Several data sets have been updated and new data has been added in release 3.0. Furthermore we have developed a new website http://FunCoup.sbc.su.se, which provides powerful tools to explore the predicted networks and to retrieve detailed information about the data underlying each prediction.
FunCoup, functional association, functional coupling, network
Bioinformatics and Systems Biology
Research subject Molecular Biology
IdentifiersURN: urn:nbn:se:su:diva-92681OAI: oai:DiVA.org:su-92681DiVA: diva2:644634