{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,2]],"date-time":"2025-10-02T13:35:01Z","timestamp":1759412101103},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2017,7,29]],"date-time":"2017-07-29T00:00:00Z","timestamp":1501286400000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"the U.S. Department of Energy","award":["#DE-PS02-06ER64304"],"award-info":[{"award-number":["#DE-PS02-06ER64304"]}]},{"name":"the Office of Biological and Environmental Research"},{"name":"National Science Foundation\/EPSCoR","award":["IIA-1355423"],"award-info":[{"award-number":["IIA-1355423"]}]},{"name":"the State of South Dakota Research Innovation Center"},{"name":"the Agriculture Experiment Station of South Dakota State University"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,7,19]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The rapid accumulation of fully sequenced prokaryotic genomes provides unprecedented information for biological studies of bacterial and archaeal organisms in a systematic manner. Operons are the basic functional units for conducting such studies. Here, we review an operon database DOOR (the Database of prOkaryotic OpeRons) that we have previously developed and continue to update. Currently, the database contains 6\u2009975\u2009454 computationally predicted operons in 2072 complete genomes. In addition, the database also contains the following information: (i) transcriptional units for 24 genomes derived using publicly available transcriptomic data; (ii) orthologous gene mapping across genomes; (iii) 6408 cis-regulatory motifs for transcriptional factors of some operons for 203 genomes; (iv) 3\u2009456\u2009718 Rho-independent terminators for 2072 genomes; as well as (v) a suite of tools in support of applications of the predicted operons. In this review, we will explain how such data are computationally derived and demonstrate how they can be used to derive a wide range of higher-level information needed for systems biology studies to tackle complex and fundamental biology questions.<\/jats:p>","DOI":"10.1093\/bib\/bbx088","type":"journal-article","created":{"date-parts":[[2017,7,6]],"date-time":"2017-07-06T19:18:19Z","timestamp":1499368699000},"page":"1568-1577","source":"Crossref","is-referenced-by-count":29,"title":["DOOR: a prokaryotic operon database for genome analyses and functional inference"],"prefix":"10.1093","volume":"20","author":[{"given":"Huansheng","family":"Cao","sequence":"first","affiliation":[]},{"given":"Qin","family":"Ma","sequence":"additional","affiliation":[]},{"given":"Xin","family":"Chen","sequence":"additional","affiliation":[]},{"given":"Ying","family":"Xu","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2017,7,28]]},"reference":[{"key":"2019100807383463800_bbx088-B1","doi-asserted-by":"crossref","first-page":"D507","DOI":"10.1093\/nar\/gkw929","article-title":"IMG\/M: integrated genome and metagenome comparative data analysis system","volume":"45","author":"Chen","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2019100807383463800_bbx088-B2","first-page":"1727","article-title":"The operon: a group of genes with expression coordinated by an operator","volume":"250","author":"Jacob","year":"1960","journal-title":"C R Acad Sci 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