ConsensusPathDB—a database for integrating human functional interaction networks

By Atanas Kamburov, C. Wierling, Hans Lehrach, Ralf Herwig. Nucleic Acids Res., 2008

581 citations recorded by the source corpus.

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

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/71e5d9d1a636894564351d3a0cb4cd41c89c20a6

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Citations in the corpus

ConsensusPathDB: toward a more complete picture of cell biology (2010, background): “ConsensusPathDB, which we previously reported in (3), assembles a functional association network from multiple heterogeneous public interaction resources by integrating physical entities based on their accession numbers and functional interactions based on their participants.”
Analyzing and interpreting genome data at the network level with ConsensusPathDB (2016, methodology): “In ConsensusPathDB 7 , we have implemented statistical methods for performing the above tasks by interrogating annotation sets based on molecular interaction information.”
The ConsensusPathDB interaction database: 2013 update (2012, methodology): “Statistical tests are performed with the user-specified metabolite input that are analogous to those described previously in the context of gene set analysis to identify candidate phenotype-associated pathways (7).”
Drug repositioning for non-small cell lung cancer by using machine learning algorithms and topological graph theory (2016, methodology): “In contrast, the Consensus-PathDB (CPDB) [34] resource performs gene set analysis and metabolite set analysis.”
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].”
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored (2010, background): “It is by no means the only such site: related resources that are currently being actively maintained include VisANT (33), GeneMANIA (34), N-Browse (35), I 2 D (36), APID (37), bioPIXIE (38) and ConsensusPathDB (39).”