The ConsensusPathDB interaction database: 2013 update

By Atanas Kamburov, Ulrich Stelzl, Hans Lehrach, Ralf Herwig. Nucleic Acids Res., 2012

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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.

Subfields: Computational Theory and Mathematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b7340682cd94e4a40df2823cee68ff166be93f86

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Citations in the corpus

Integrated interactions database: tissue-specific view of the human and model organism interactomes (2015, background): “Online resources, such as iRefWeb (20), STRING (21) and ConsensusPathDB (22), integrate these databases to obtain about 240,000 human PPIs.”
Quantitative and logic modelling of gene and molecular networks (2015, background): “Metaresources such as ConsensusPathDB (56) and Pathguide (57) provide access to a large variety of pathway databases.”
DEOGEN2: prediction and interactive visualization of single amino acid variant deleteriousness in human proteins (2017, methodology): “We updated the snp&Go (13) inspired pathway log-odd score with data from version 31 of ConsensusPathDB (30), which now contains 4012 human pathways and 131 216 proteins.”
Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis (2020, neutral): “So far no resource offers both the intercellular communication annotations and the intracellular pathways and transcriptional regulation knowledge.”
WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research (2017, background): “The use of pathway knowledge in the life sciences is wide-spread, supported by many databases (4–6) as well as integrative resources (7,8).”
Cooperation between Constitutive and Inducible Chemokines Enables T-cell Engraftment and Immune Attack in Solid Tumors (2019, background): “A uthor M anuscript A uthor M anuscript A uthor M anuscript A uthor M anuscript A uthor M anuscript A uthor M anuscript A uthor M anuscript A uthor M anuscript heatmap for gene sets in BioCarta and Wikipathways in the top 202 differentially expressed genes characteristic for the Hi-Hi groups in five”
The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets (2020, methodology): “Frequently used resources include FunCoup (23), GeneMANIA (24), HumanBase / GIANT (25), IMP (26), IID (27), Consensus-PathDB (28) and HumanNet (29).”