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  ConsensusPathDB 2022: molecular interactions update as a resource for network biology

Kamburov, A., & Herwig, R. (2021). ConsensusPathDB 2022: molecular interactions update as a resource for network biology. Nucleic Acids Research, gkab1128. doi:10.1093/nar/gkab1128.

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Kamburov, Atanas1, Author
Herwig, Ralf2, Author              
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1R&D Digital Technologies Department, Bayer AG, Berlin 13353, Germany, ou_persistent22              
2Bioinformatics (Ralf Herwig), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_2385701              

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 Abstract: Molecular interactions are key drivers of biological function. Providing interaction resources to the research community is important since they allow functional interpretation and network-based analysis of molecular data. ConsensusPathDB (http://consensuspathdb.org) is a meta-database combining interactions of diverse types from 31 public resources for humans, 16 for mice and 14 for yeasts. Using ConsensusPathDB, researchers commonly evaluate lists of genes, proteins and metabolites against sets of molecular interactions defined by pathways, Gene Ontology and network neighborhoods and retrieve complex molecular neighborhoods formed by heterogeneous interaction types. Furthermore, the integrated protein–protein interaction network is used as a basis for propagation methods. Here, we present the 2022 update of ConsensusPathDB, highlighting content growth, additional functionality and improved database stability. For example, the number of human molecular interactions increased to 859 848 connecting 200 499 unique physical entities such as genes/proteins, metabolites and drugs. Furthermore, we integrated regulatory datasets in the form of transcription factor–, microRNA– and enhancer–gene target interactions, thus providing novel functionality in the context of overrepresentation and enrichment analyses. We specifically emphasize the use of the integrated protein–protein interaction network as a scaffold for network inferences, present topological characteristics of the network and discuss strengths and shortcomings of such approaches.

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 Dates: 2021-11-042021-11-25
 Publication Status: Published online
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 Identifiers: DOI: 10.1093/nar/gkab1128
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Title: Nucleic Acids Research
  Other : Nucleic Acids Res.
Source Genre: Journal
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Pages: - Volume / Issue: - Sequence Number: gkab1128 Start / End Page: - Identifier: ISSN: 0301-5610
CoNE: https://pure.mpg.de/cone/journals/resource/1000000000262810