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Comparative interactomics with Funcoup 2.0
KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
Stockholm University, Science for Life Laboratory.
Stockholm University, Science for Life Laboratory.
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2012 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 40, no D1, D821-D828 p.Article in journal (Refereed) Published
Abstract [en]

FunCoup (http://FunCoup.sbc.su.se) is a database that maintains and visualizes global gene/protein networks of functional coupling that have been constructed by Bayesian integration of diverse high-throughput data. FunCoup achieves high coverage by orthology-based integration of data sources from different model organisms and from different platforms. We here present release 2.0 in which the data sources have been updated and the methodology has been refined. It contains a new data type Genetic Interaction, and three new species: chicken, dog and zebra fish. As FunCoup extensively transfers functional coupling information between species, the new input datasets have considerably improved both coverage and quality of the networks. The number of high-confidence network links has increased dramatically. For instance, the human network has more than eight times as many links above confidence 0.5 as the previous release. FunCoup provides facilities for analysing the conservation of subnetworks in multiple species. We here explain how to do comparative interactomics on the FunCoup website.

Place, publisher, year, edition, pages
2012. Vol. 40, no D1, D821-D828 p.
Keyword [en]
Functional Interaction Networks, Protein Networks, Gene Ontology, Database, Alignment, Unification, Integration, Server, Tool
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:kth:diva-83788DOI: 10.1093/nar/gkr1062ISI: 000298601300123PubMedID: 22110034Scopus ID: 2-s2.0-84862185886OAI: oai:DiVA.org:kth-83788DiVA: diva2:513727
Funder
Swedish Research CouncilSwedish e‐Science Research CenterScience for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20120403

Available from: 2012-04-03 Created: 2012-02-13 Last updated: 2017-12-07Bibliographically approved

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Alexeyenko, AndreyTjärnberg, AndreasGuala, DmitriFrings, OliverSonnhammer, Erik L. L.
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Citation style
  • apa
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