{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,4]],"date-time":"2026-02-04T17:36:19Z","timestamp":1770226579850,"version":"3.49.0"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2023,5,19]],"date-time":"2023-05-19T00:00:00Z","timestamp":1684454400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003977","name":"Israel Science Foundation","doi-asserted-by":"publisher","award":["401\/22"],"award-info":[{"award-number":["401\/22"]}],"id":[{"id":"10.13039\/501100003977","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003977","name":"Israel Science Foundation","doi-asserted-by":"publisher","award":["317\/19"],"award-info":[{"award-number":["317\/19"]}],"id":[{"id":"10.13039\/501100003977","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The distinct functions and phenotypes of human tissues and cells derive from the activity of biological processes that varies in a context-dependent manner. Here, we present the Process Activity (ProAct) webserver that estimates the preferential activity of biological processes in tissues, cells, and other contexts. Users can upload a differential gene expression matrix measured across contexts or cells, or use a built-in matrix of differential gene expression in 34 human tissues. Per context, ProAct associates gene ontology (GO) biological processes with estimated preferential activity scores, which are inferred from the input matrix. ProAct visualizes these scores across processes, contexts, and process-associated genes. ProAct also offers potential cell-type annotations for cell subsets, by inferring them from the preferential activity of 2001 cell-type-specific processes. Thus, ProAct output can highlight the distinct functions of tissues and cell types in various contexts, and can enhance cell-type annotation efforts. The ProAct webserver is available at https:\/\/netbio.bgu.ac.il\/ProAct\/.<\/jats:p>","DOI":"10.1093\/nar\/gkad421","type":"journal-article","created":{"date-parts":[[2023,5,19]],"date-time":"2023-05-19T20:23:35Z","timestamp":1684527815000},"page":"W478-W483","source":"Crossref","is-referenced-by-count":4,"title":["ProAct: quantifying the differential activity of biological processes in tissues, cells, and user-defined contexts"],"prefix":"10.1093","volume":"51","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1478-8719","authenticated-orcid":false,"given":"Moran","family":"Sharon","sequence":"first","affiliation":[{"name":"Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev , POB 653 Beer-Sheva 8410501, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gil","family":"Gruber","sequence":"additional","affiliation":[{"name":"Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev , POB 653 Beer-Sheva 8410501, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4324-588X","authenticated-orcid":false,"given":"Chanan M","family":"Argov","sequence":"additional","affiliation":[{"name":"Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev , POB 653 Beer-Sheva 8410501, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Miri","family":"Volozhinsky","sequence":"additional","affiliation":[{"name":"Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev , POB 653 Beer-Sheva 8410501, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8279-7898","authenticated-orcid":false,"given":"Esti","family":"Yeger-Lotem","sequence":"additional","affiliation":[{"name":"Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev , POB 653 Beer-Sheva 8410501, Israel"},{"name":"The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev , POB 653 Beer-Sheva 8410501, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,5,19]]},"reference":[{"key":"2023070505021339700_B1","doi-asserted-by":"crossref","first-page":"1318","DOI":"10.1126\/science.aaz1776","article-title":"The GTEx Consortium atlas of genetic regulatory effects across human tissues","volume":"369","author":"GTEx Consortium","year":"2020","journal-title":"Science"},{"key":"2023070505021339700_B2","doi-asserted-by":"crossref","first-page":"eabl4896","DOI":"10.1126\/science.abl4896","article-title":"The Tabula Sapiens: a multiple-organ, single-cell transcriptomic atlas of humans","volume":"376","author":"Tabula","year":"2022","journal-title":"Science"},{"key":"2023070505021339700_B3","doi-asserted-by":"crossref","first-page":"C47","DOI":"10.1038\/35011540","article-title":"From molecular to modular cell biology","volume":"402","author":"Hartwell","year":"1999","journal-title":"Nature"},{"key":"2023070505021339700_B4","doi-asserted-by":"crossref","first-page":"eabf3067","DOI":"10.1126\/science.abf3067","article-title":"Interpretation of cancer mutations using a multiscale map of protein systems","volume":"374","author":"Zheng","year":"2021","journal-title":"Science"},{"key":"2023070505021339700_B5","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. 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