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  The ConsensusPathDB interaction database: 2013 update

Kamburov, A., Stelzl, U., Lehrach, H., & Herwig, R. (2013). The ConsensusPathDB interaction database: 2013 update. Nucleic Acids Research (London), 41(Database issue), D793-800. doi:10.1093/nar/gks1055.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-000E-E7B2-8 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-000E-E7B3-6
Genre: Journal Article

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 Creators:
Kamburov, Atanas1, Author              
Stelzl, Ulrich2, Author              
Lehrach, Hans3, Author              
Herwig, Ralf1, Author              
Affiliations:
1Bioinformatics (Ralf Herwig), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479648              
2Molecular Interaction Networks (Ulrich Stelzl), Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479660              
3Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433550              

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 Abstract: Knowledge of the various interactions between molecules in the cell is crucial for understanding cellular processes in health and disease. Currently available interaction databases, being largely complementary to each other, must be integrated to obtain a comprehensive global map of the different types of interactions. We have previously reported the development of an integrative interaction database called ConsensusPathDB (http://ConsensusPathDB.org) that aims to fulfill this task. In this update article, we report its significant progress in terms of interaction content and web interface tools. ConsensusPathDB has grown mainly due to the integration of 12 further databases; it now contains 215 541 unique interactions and 4601 pathways from overall 30 databases. Binary protein interactions are scored with our confidence assessment tool, IntScore. The ConsensusPathDB web interface allows users to take advantage of these integrated interaction and pathway data in different contexts. Recent developments include pathway analysis of metabolite lists, visualization of functional gene/metabolite sets as overlap graphs, gene set analysis based on protein complexes and induced network modules analysis that connects a list of genes through various interaction types. To facilitate the interactive, visual interpretation of interaction and pathway data, we have re-implemented the graph visualization feature of ConsensusPathDB using the Cytoscape.js library.

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Language(s): eng - English
 Dates: 2013-01-01
 Publication Status: Published in print
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 Rev. Method: Peer
 Identifiers: DOI: 10.1093/nar/gks1055
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Title: Nucleic Acids Research (London)
  Other : Nucleic Acids Res
Source Genre: Journal
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Publ. Info: Oxford : Oxford University Press
Pages: - Volume / Issue: 41 (Database issue) Sequence Number: - Start / End Page: D793 - 800 Identifier: ISSN: 0305-1048
CoNE: /journals/resource/110992357379342