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Nucleic Acids Research Advance Access originally published online on October 21, 2008
Nucleic Acids Research 2009 37(Database issue):D623-D628; doi:10.1093/nar/gkn698
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Nucleic Acids Research, 2009, Vol. 37, Database issue D623-D628
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

ConsensusPathDB—a database for integrating human functional interaction networks

Atanas Kamburov*, Christoph Wierling, Hans Lehrach and Ralf Herwig

Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany

*To whom correspondence should be addressed. Tel: +49 30 84131279; Fax: +49 30 84131380; Email: kamburov{at}molgen.mpg.de

Received July 16, 2008. Accepted September 25, 2008.

ConsensusPathDB is a database system for the integration of human functional interactions. Current knowledge of these interactions is dispersed in more than 200 databases, each having a specific focus and data format. ConsensusPathDB currently integrates the content of 12 different interaction databases with heterogeneous foci comprising a total of 26 133 distinct physical entities and 74 289 distinct functional interactions (protein–protein interactions, biochemical reactions, gene regulatory interactions), and covering 1738 pathways. We describe the database schema and the methods used for data integration. Furthermore, we describe the functionality of the ConsensusPathDB web interface, where users can search and visualize interaction networks, upload, modify and expand networks in BioPAX, SBML or PSI-MI format, or carry out over-representation analysis with uploaded identifier lists with respect to substructures derived from the integrated interaction network. The ConsensusPathDB database is available at: http://cpdb.molgen.mpg.de


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