{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,8]],"date-time":"2026-08-08T12:32:18Z","timestamp":1786192338560,"version":"build-2736575974"},"reference-count":69,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2021,11,25]],"date-time":"2021-11-25T00:00:00Z","timestamp":1637798400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002347","name":"Federal Ministry of Education and Research","doi-asserted-by":"publisher","award":["161L0242A"],"award-info":[{"award-number":["161L0242A"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Commission Horizon 2020 Framework Programme","award":["811034"],"award-info":[{"award-number":["811034"]}]},{"DOI":"10.13039\/501100004189","name":"Max Planck Society","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004189","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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\u2013protein 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\u00a0848 connecting 200\u00a0499 unique physical entities such as genes\/proteins, metabolites and drugs. Furthermore, we integrated regulatory datasets in the form of transcription factor\u2013, microRNA\u2013 and enhancer\u2013gene target interactions, thus providing novel functionality in the context of overrepresentation and enrichment analyses. We specifically emphasize the use of the integrated\u00a0protein\u2013protein interaction network as a scaffold for network inferences, present topological characteristics of the network and discuss strengths and shortcomings of such approaches.<\/jats:p>","DOI":"10.1093\/nar\/gkab1128","type":"journal-article","created":{"date-parts":[[2021,11,5]],"date-time":"2021-11-05T12:23:26Z","timestamp":1636115006000},"page":"D587-D595","source":"Crossref","is-referenced-by-count":136,"title":["ConsensusPathDB 2022:\u00a0molecular interactions update as a resource for network biology"],"prefix":"10.1093","volume":"50","author":[{"given":"Atanas","family":"Kamburov","sequence":"first","affiliation":[{"name":"R&D Digital Technologies Department,\u00a0Bayer AG, Berlin\u00a013353, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9335-1760","authenticated-orcid":false,"given":"Ralf","family":"Herwig","sequence":"additional","affiliation":[{"name":"Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin\u00a014195, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,11,25]]},"reference":[{"key":"2022010507363699800_B1","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1038\/s41586-021-03620-1","article-title":"A roadmap for the human developmental cell atlas","volume":"597","author":"Haniffa","year":"2021","journal-title":"Nature"},{"key":"2022010507363699800_B2","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1016\/j.cell.2018.02.052","article-title":"An integrated TCGA pan-cancer clinical data resource to drive high-quality survival outcome analytics","volume":"173","author":"Liu","year":"2018","journal-title":"Cell"},{"key":"2022010507363699800_B3","doi-asserted-by":"crossref","first-page":"D504","DOI":"10.1093\/nar\/gkj126","article-title":"Pathguide: a pathway resource list","volume":"34","author":"Bader","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2022010507363699800_B4","doi-asserted-by":"crossref","first-page":"1203","DOI":"10.3389\/fgene.2019.01203","article-title":"The impact of pathway database choice on statistical enrichment analysis and predictive modeling","volume":"10","author":"Mubeen","year":"2019","journal-title":"Front. 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