RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli
- PMID: 9847141
- PMCID: PMC148096
- DOI: 10.1093/nar/27.1.59
RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli
Abstract
RegulonDB version 2.0, a database on transcriptional regulation and operon organization in Escherichia coli, is now available on the web at the following URL: http://www.cifn.unam. mx/Computational_Biology/regulondb/. In this paper we describe the main computational changes to the database, which include migrating the database to Sybase, providing graphical descriptions of the internal organization of operons and regulons, and direct links to MEDLINE references. The web interface offers searching either by mechanisms of regulation or by operon organization. The results of a search (operon organization, or site collection) are displayed as hypertext, and can also be displayed graphically. In terms of its contents, RegulonDB contains a large number of operons, as well as the absolute position in the completed genome sequence of sites, promoters, and individual genes of E.coli.
Similar articles
-
RegulonDB (version 3.0): transcriptional regulation and operon organization in Escherichia coli K-12.Nucleic Acids Res. 2000 Jan 1;28(1):65-7. doi: 10.1093/nar/28.1.65. Nucleic Acids Res. 2000. PMID: 10592182 Free PMC article.
-
RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12.Nucleic Acids Res. 2004 Jan 1;32(Database issue):D303-6. doi: 10.1093/nar/gkh140. Nucleic Acids Res. 2004. PMID: 14681419 Free PMC article.
-
RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12.Nucleic Acids Res. 2001 Jan 1;29(1):72-4. doi: 10.1093/nar/29.1.72. Nucleic Acids Res. 2001. PMID: 11125053 Free PMC article.
-
The effects of DNA supercoiling on the expression of operons of the ilv regulon of Escherichia coli suggest a physiological rationale for divergently transcribed operons.Mol Microbiol. 2001 Mar;39(5):1109-15. doi: 10.1111/j.1365-2958.2001.02309.x. Mol Microbiol. 2001. PMID: 11251829 Review.
-
Experimental analysis of global gene regulation in Escherichia coli.Prog Nucleic Acid Res Mol Biol. 1996;55:1-86. doi: 10.1016/s0079-6603(08)60189-0. Prog Nucleic Acid Res Mol Biol. 1996. PMID: 8787606 Review. No abstract available.
Cited by
-
Bayesian network expansion identifies new ROS and biofilm regulators.PLoS One. 2010 Mar 3;5(3):e9513. doi: 10.1371/journal.pone.0009513. PLoS One. 2010. PMID: 20209085 Free PMC article.
-
Two novel genes identified by large-scale transcriptomic analysis are essential for biofilm and rugose colony development of Vibrio vulnificus.PLoS Pathog. 2023 Jan 19;19(1):e1011064. doi: 10.1371/journal.ppat.1011064. eCollection 2023 Jan. PLoS Pathog. 2023. PMID: 36656902 Free PMC article.
-
Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using CoryneRegNet.Nat Protoc. 2009;4(6):992-1005. doi: 10.1038/nprot.2009.81. Nat Protoc. 2009. PMID: 19498379
-
CoryneRegNet 6.0--Updated database content, new analysis methods and novel features focusing on community demands.Nucleic Acids Res. 2012 Jan;40(Database issue):D610-4. doi: 10.1093/nar/gkr883. Epub 2011 Nov 12. Nucleic Acids Res. 2012. PMID: 22080556 Free PMC article.
-
RegulonDB (version 3.0): transcriptional regulation and operon organization in Escherichia coli K-12.Nucleic Acids Res. 2000 Jan 1;28(1):65-7. doi: 10.1093/nar/28.1.65. Nucleic Acids Res. 2000. PMID: 10592182 Free PMC article.
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources
