ConsensusPathDB: toward a more complete picture of cell biology
By Atanas Kamburov, K. Pentchev, Hanna Galicka, C. Wierling, Hans Lehrach, Ralf Herwig. 2010
645 citations recorded by the source corpus.
ConsensusPathDB is a meta-database that integrates different types of functional interactions from heterogeneous interaction data resources. Physical protein interactions, metabolic and signaling reactions and gene regulatory interactions are integrated in a seamless functional association network that simultaneously describes multiple functional aspects of genes, proteins, complexes, metabolites, etc. With 155 432 human, 194 480 yeast and 13 648 mouse complex functional interactions (originating from 18 databases on human and eight databases on yeast and mouse interactions each), ConsensusPathDB currently constitutes the most comprehensive publicly available interaction repository for these species. The Web interface at http://cpdb.molgen.mpg.de offers different ways of utilizing these integrated interaction data, in particular with tools for visualization, analysis and interpretation of high-throughput expression data in the light of functional interactions and biological pathways.
Subfields: Molecular Biology
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In Molecular Biology
- Peer Bork
- Lars Juhl Jensen
- C. von Mering
- Damian Szklarczyk
- Michael Kuhn
- Sune Frankild
- Alexander C. J. Roth
- Milan Simonovic
Citations in the corpus
- EgoNet: identification of human disease ego-network modules (2014, methodology): “The ego-network model has been used for network module over-representation analysis in ConsensusPathDB [24].”
- Reactome pathway analysis: a high-performance in-memory approach (2017, methodology): “However, while DAVID and ConsensusPathDB rely on the Simple Object Access Protocol (SOAP) and the Web Service Description Language (WSDL) for their web services, Reactome analysis web service is based on the Representational State Transfer (REST).”
- The ConsensusPathDB interaction database: 2013 update (2012, methodology): “For example, we have previously described a new class of functional gene sets called NESTs (8).”
- Unmasking Transcriptional Heterogeneity in Senescent Cells (2017, background): “Among the main gene ontology (GO) pathways [19, 20] showing altered in senescent cells, “chromatin organization,” “DNA repair,” “membrane trafficking,” and “activation of NF-kappaB” were notable for their known links to senescence and aging (Figure 1C) (Figure 1C) [1, 10, 21, 22].”
- Chipster: user-friendly analysis software for microarray and other high-throughput data (2011, background): “ConsensusPathDB integrates functional interaction data from 20 databases covering protein-protein, metabolic, signalling and gene regulatory interaction networks [26], thus providing a powerful and combinatorial approach to pathway analysis.”
- STRING v9.1: protein-protein interaction networks, with increased coverage and integration (2012, background): “These include GeneMANIA (23), Consensus-PathDB (24), I2D (25), VisANT (26) and, more recently, hPRINT (27), HitPredict (28), IMID (29) and IMP (30).”