{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T01:10:31Z","timestamp":1773277831259,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2016,9,30]],"date-time":"2016-09-30T00:00:00Z","timestamp":1475193600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100012551","name":"Applied Basic Research Program of Sichuan Province","doi-asserted-by":"crossref","award":["2015JY0100"],"award-info":[{"award-number":["2015JY0100"]}],"id":[{"id":"10.13039\/100012551","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100012551","name":"Applied Basic Research Program of Sichuan Province","doi-asserted-by":"crossref","award":["LZ-LY-45"],"award-info":[{"award-number":["LZ-LY-45"]}],"id":[{"id":"10.13039\/100012551","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities of China","doi-asserted-by":"crossref","award":["ZYGX2015J144"],"award-info":[{"award-number":["ZYGX2015J144"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities of China","doi-asserted-by":"crossref","award":["ZYGX2015Z006"],"award-info":[{"award-number":["ZYGX2015Z006"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Program for the Top Young Innovative Talents of Higher Learning Institutions of Hebei Province","award":["BJ2014028"],"award-info":[{"award-number":["BJ2014028"]}]},{"name":"Outstanding Youth Foundation of North China University of Science and Technology","award":["JP201502"],"award-info":[{"award-number":["JP201502"]}]},{"DOI":"10.13039\/501100002858","name":"China Postdoctoral Science Foundation","doi-asserted-by":"crossref","award":["No. 2015M582533"],"award-info":[{"award-number":["No. 2015M582533"]}],"id":[{"id":"10.13039\/501100002858","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Scientific Research Foundation of the Education Department of Sichuan Province","award":["11ZB122"],"award-info":[{"award-number":["11ZB122"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>In prokaryotes, the \u03c354 promoters are unique regulatory elements and have attracted much attention because they are in charge of the transcription of carbon and nitrogen-related genes and participate in numerous ancillary processes and environmental responses. All findings on \u03c354 promoters are favorable for a better understanding of their regulatory mechanisms in gene transcription and an accurate discovery of genes missed by the wet experimental evidences. In order to provide an up-to-date, interactive and extensible database for \u03c354 promoter, a free and easy accessed database called Pro54DB (\u03c354 promoter database) was built to collect information of \u03c354 promoter. In the current version, it has stored 210 experimental-confirmed \u03c354 promoters with 297 regulated genes in 43 species manually extracted from 133 publications, which is helpful for researchers in fields of bioinformatics and molecular biology.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>Pro54DB is freely available on the web at http:\/\/lin.uestc.edu.cn\/database\/pro54db with all major browsers supported.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btw630","type":"journal-article","created":{"date-parts":[[2016,9,29]],"date-time":"2016-09-29T19:06:19Z","timestamp":1475175979000},"page":"467-469","source":"Crossref","is-referenced-by-count":89,"title":["Pro54DB: a database for experimentally verified sigma-54 promoters"],"prefix":"10.1093","volume":"33","author":[{"given":"Zhi-Yong","family":"Liang","sequence":"first","affiliation":[{"name":"Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hong-Yan","family":"Lai","sequence":"additional","affiliation":[{"name":"Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huan","family":"Yang","sequence":"additional","affiliation":[{"name":"Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chang-Jian","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hui","family":"Yang","sequence":"additional","affiliation":[{"name":"Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huan-Huan","family":"Wei","sequence":"additional","affiliation":[{"name":"Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xin-Xin","family":"Chen","sequence":"additional","affiliation":[{"name":"Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ya-Wei","family":"Zhao","sequence":"additional","affiliation":[{"name":"Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhen-Dong","family":"Su","sequence":"additional","affiliation":[{"name":"Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wen-Chao","family":"Li","sequence":"additional","affiliation":[{"name":"Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"En-Ze","family":"Deng","sequence":"additional","affiliation":[{"name":"Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hua","family":"Tang","sequence":"additional","affiliation":[{"name":"Department of Pathophysiology, Southwest Medical University, Luzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Chen","sequence":"additional","affiliation":[{"name":"Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China"},{"name":"Department of Physics, School of Sciences, Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hao","family":"Lin","sequence":"additional","affiliation":[{"name":"Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,9,30]]},"reference":[{"key":"2023020204405968100_btw630-B1","doi-asserted-by":"crossref","first-page":"5574","DOI":"10.1128\/jb.179.17.5574-5581.1997","article-title":"A transcriptional activator, FleQ, regulates mucin adhesion and flagellar gene expression in Pseudomonas aeruginosa in a cascade manner","volume":"179","author":"Arora","year":"1997","journal-title":"J. Bacteriol"},{"key":"2023020204405968100_btw630-B2","doi-asserted-by":"crossref","first-page":"4305","DOI":"10.1093\/nar\/27.22.4305","article-title":"Compilation and analysis of sigma(54)-dependent promoter sequences","volume":"27","author":"Barrios","year":"1999","journal-title":"Nucleic Acids Res"},{"key":"2023020204405968100_btw630-B3","doi-asserted-by":"crossref","first-page":"828","DOI":"10.1074\/jbc.M807707200","article-title":"sigma54-promoter discrimination and regulation by ppGpp and DksA","volume":"284","author":"Bernardo","year":"2009","journal-title":"J. Biol. Chem"},{"key":"2023020204405968100_btw630-B4","doi-asserted-by":"crossref","first-page":"D133","DOI":"10.1093\/nar\/gkv1156","article-title":"RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond","volume":"44","author":"Gama-Castro","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023020204405968100_btw630-B5","first-page":"843","article-title":"Expression of the rocDEF operon involved in arginine catabolism in Bacillus subtilis","volume-title":"J. Mol. Biol.","author":"Gardan","year":"1995"},{"key":"2023020204405968100_btw630-B6","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1128\/mr.53.3.367-376.1989","article-title":"Expression of sigma 54 (ntrA)-dependent genes is probably united by a common mechanism","volume":"53","author":"Kustu","year":"1989","journal-title":"Microbiol. Rev"},{"key":"2023020204405968100_btw630-B7","doi-asserted-by":"crossref","first-page":"12961","DOI":"10.1093\/nar\/gku1019","article-title":"iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition","volume":"42","author":"Lin","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023020204405968100_btw630-B8","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1093\/nar\/gkm910","article-title":"DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information","volume":"36","author":"Sierro","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"2023020204405968100_btw630-B9","doi-asserted-by":"crossref","first-page":"538","DOI":"10.1111\/j.1365-2958.2008.06181.x","article-title":"Modus operandi of the bacterial RNA polymerase containing the sigma54 promoter-specificity factor","volume":"68","author":"Wigneshweraraj","year":"2008","journal-title":"Mol. Microbiol"},{"key":"2023020204405968100_btw630-B10","doi-asserted-by":"crossref","first-page":"7680","DOI":"10.1128\/jb.174.23.7680-7688.1992","article-title":"Alginate synthesis in Pseudomonas aeruginosa: environmental regulation of the algC promoter","volume":"174","author":"Zielinski","year":"1992","journal-title":"J. Bacteriol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/3\/467\/49037578\/bioinformatics_33_3_467.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/3\/467\/49037578\/bioinformatics_33_3_467.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T04:44:32Z","timestamp":1675313072000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/3\/467\/2525726"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2016,9,30]]},"references-count":10,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2017,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw630","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,2,1]]},"published":{"date-parts":[[2016,9,30]]}}}