title: RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12.
abstract: RegulonDB is the primary database of the major international maintained curation of original literature with experimental knowledge about the elements and interactions of the network of transcriptional regulation in Escherichia coli K-12. This includes mechanistic information about operon organization and their decomposition into transcription units (TUs), promoters and their sigma type, binding sites of specific transcriptional regulators (TRs), their organization into 'regulatory phrases', active and inactive conformations of TRs, as well as terminators and ribosome binding sites. The database is complemented with clearly marked computational predictions of TUs, promoters and binding sites of TRs. The current version has been expanded to include information beyond specific mechanisms aimed at gathering different growth conditions and the associated induced and/or repressed genes. RegulonDB is now linked with Swiss-Prot, with microarray databases, and with a suite of programs to analyze and visualize microarray experiments. We provide a summary of the biological knowledge contained in RegulonDB and describe the major changes in the design of the database. RegulonDB can be accessed on the web at the URL: http://www.cifn.unam.mx/Computational_Biology/regulondb/.
authors.affiliation: Program of Computational Genomics, CIFN, UNAM. A.P. 565-A Cuernavaca, Morelos 62100, Mexico.
authors.forename: Heladia
authors.initials: H
authors.lastname: Salgado
authors.forename: Socorro
authors.initials: S
authors.lastname: Gama-Castro
authors.forename: Agustino
authors.initials: A
authors.lastname: Martínez-Antonio
authors.forename: Edgar
authors.initials: E
authors.lastname: Díaz-Peredo
authors.forename: Fabiola
authors.initials: F
authors.lastname: Sánchez-Solano
authors.forename: Martín
authors.initials: M
authors.lastname: Peralta-Gil
authors.forename: Delfino
authors.initials: D
authors.lastname: Garcia-Alonso
authors.forename: Verónica
authors.initials: V
authors.lastname: Jiménez-Jacinto
authors.forename: Alberto
authors.initials: A
authors.lastname: Santos-Zavaleta
authors.forename: César
authors.initials: C
authors.lastname: Bonavides-Martínez
authors.forename: Julio
authors.initials: J
authors.lastname: Collado-Vides
mesh_terms: D016208:Databases, Factual; D030541:Databases, Genetic; D004777:Environment; D004926:Escherichia coli / Q000235:genetics* / Q000254:growth & development*; D015964:Gene Expression Regulation, Bacterial; D016247:Information Storage and Retrieval; D020407:Internet; D009876:Operon / Q000235:genetics*; D018085:Regulon / Q000235:genetics*; D014158:Transcription, Genetic; D014584:User-Computer Interface