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Applied to single\u2010cell data, such analyses provide mechanistic insights into individual cells and their interactions. However, knowledge of intercellular communication is scarce, scattered across resources, and not linked to intracellular processes. To address this gap, we combined over 100 resources covering interactions and roles of proteins in inter\u2010 and intracellular signaling, as well as transcriptional and post\u2010transcriptional regulation. We added protein complex information and annotations on function, localization, and role in diseases for each protein. The resource is available for human, and via homology translation for mouse and rat. The data are accessible via\n                    <jats:italic>OmniPath<\/jats:italic>\n                    \u2019s web service (\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/omnipathdb.org\/\" ext-link-type=\"uri\">https:\/\/omnipathdb.org\/<\/jats:ext-link>\n                    ), a Cytoscape plug\u2010in, and packages in R\/Bioconductor and Python, providing access options for computational and experimental scientists. We created workflows with tutorials to facilitate the analysis of cell\u2013cell interactions and affected downstream intracellular signaling processes.\n                    <jats:italic>OmniPath<\/jats:italic>\n                    provides a single access point to knowledge spanning intra\u2010 and intercellular processes for data analysis, as we demonstrate in applications studying SARS\u2010CoV\u20102 infection and ulcerative colitis.\n                  <\/jats:p>","DOI":"10.15252\/msb.20209923","type":"journal-article","created":{"date-parts":[[2021,3,22]],"date-time":"2021-03-22T05:27:31Z","timestamp":1616390851000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":416,"title":["Integrated intra\u2010 and intercellular signaling knowledge for multicellular omics analysis"],"prefix":"10.1038","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7249-9379","authenticated-orcid":false,"given":"D\u00e9nes","family":"T\u00fcrei","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5482-9023","authenticated-orcid":false,"given":"Alberto","family":"Valdeolivas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lejla","family":"Gul","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7022-1437","authenticated-orcid":false,"given":"Nicol\u00e0s","family":"Palacio\u2010Escat","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2433-6380","authenticated-orcid":false,"given":"Michal","family":"Klein","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9111-4593","authenticated-orcid":false,"given":"Olga","family":"Ivanova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4903-6237","authenticated-orcid":false,"given":"M\u00e1rton","family":"\u00d6lbei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0776-1182","authenticated-orcid":false,"given":"Attila","family":"G\u00e1bor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2419-1943","authenticated-orcid":false,"given":"Fabian","family":"Theis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9412-6867","authenticated-orcid":false,"given":"Dezs\u0151","family":"M\u00f3dos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1717-996X","authenticated-orcid":false,"given":"Tam\u00e1s","family":"Korcsm\u00e1ros","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8552-8976","authenticated-orcid":false,"given":"Julio","family":"Saez\u2010Rodriguez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,3,22]]},"reference":[{"key":"BFMSB20209923_CR1","first-page":"201920338","volume":"3","author":"S An","year":"2020","unstructured":"An S, Cho S\u2010Y, Kang J, Lee S, Kim H\u2010S, Min D\u2010J, Son E, Cho K\u2010H (2020) Inhibition of 3\u2010phosphoinositide\u2013dependent protein kinase 1 (PDK1) can revert cellular senescence in human dermal fibroblasts. 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