{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,10]],"date-time":"2026-06-10T02:02:22Z","timestamp":1781056942390,"version":"3.54.1"},"reference-count":52,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2021,11,18]],"date-time":"2021-11-18T00:00:00Z","timestamp":1637193600000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100009708","name":"Novo Nordisk Foundation","doi-asserted-by":"publisher","award":["NNF10CC1016517"],"award-info":[{"award-number":["NNF10CC1016517"]}],"id":[{"id":"10.13039\/501100009708","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><jats:p>The transcriptional regulatory network in prokaryotes controls global gene expression mostly through transcription factors (TFs), which are DNA-binding proteins. Chromatin immunoprecipitation (ChIP) with DNA sequencing methods can identify TF binding sites across the genome, providing a bottom-up, mechanistic understanding of how gene expression is regulated. ChIP provides indispensable evidence toward the goal of acquiring a comprehensive understanding of cellular adaptation and regulation, including condition-specificity. ChIP-derived data's importance and labor-intensiveness motivate its broad dissemination and reuse, which is currently an unmet need in the prokaryotic domain. To fill this gap, we present proChIPdb (prochipdb.org), an information-rich, interactive web database. This website collects public ChIP-seq\/-exo data across several prokaryotes and presents them in dashboards that include curated binding sites, nucleotide-resolution genome viewers, and summary plots such as motif enrichment sequence logos. Users can search for TFs of interest or their target genes, download all data, dashboards, and visuals, and follow external links to understand regulons through biological databases and the literature. This initial release of proChIPdb covers diverse organisms, including most major TFs of Escherichia coli, and can be expanded to support regulon discovery across the prokaryotic domain.<\/jats:p>","DOI":"10.1093\/nar\/gkab1043","type":"journal-article","created":{"date-parts":[[2021,10,16]],"date-time":"2021-10-16T10:07:08Z","timestamp":1634378828000},"page":"D1077-D1084","source":"Crossref","is-referenced-by-count":13,"title":["proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8320-8736","authenticated-orcid":false,"given":"Katherine T","family":"Decker","sequence":"first","affiliation":[{"name":"Department of Bioengineering, University of California, San Diego, La Jolla, CA92093, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8519-1392","authenticated-orcid":false,"given":"Ye","family":"Gao","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California, San Diego, La Jolla, CA92093, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4769-2804","authenticated-orcid":false,"given":"Kevin","family":"Rychel","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California, San Diego, La Jolla, CA92093, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tahani","family":"Al\u00a0Bulushi","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California, San Diego, La Jolla, CA92093, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siddharth\u00a0M","family":"Chauhan","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California, San Diego, La Jolla, CA92093, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Donghyuk","family":"Kim","sequence":"additional","affiliation":[{"name":"School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Byung-Kwan","family":"Cho","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon34141, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2357-6785","authenticated-orcid":false,"given":"Bernhard\u00a0O","family":"Palsson","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California, San Diego, La Jolla, CA92093, USA"},{"name":"Department of Pediatrics, University of California, San Diego, La Jolla, CA92093, USA"},{"name":"Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. 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