title: RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions.
abstract: RegulonDB is the internationally recognized reference database of Escherichia coli K-12 offering curated knowledge of the regulatory network and operon organization. It is currently the largest electronically-encoded database of the regulatory network of any free-living organism. We present here the recently launched RegulonDB version 5.0 radically different in content, interface design and capabilities. Continuous curation of original scientific literature provides the evidence behind every single object and feature. This knowledge is complemented with comprehensive computational predictions across the complete genome. Literature-based and predicted data are clearly distinguished in the database. Starting with this version, RegulonDB public releases are synchronized with those of EcoCyc since our curation supports both databases. The complex biology of regulation is simplified in a navigation scheme based on three major streams: genes, operons and regulons. Regulatory knowledge is directly available in every navigation step. Displays combine graphic and textual information and are organized allowing different levels of detail and biological context. This knowledge is the backbone of an integrated system for the graphic display of the network, graphic and tabular microarray comparisons with curated and predicted objects, as well as predictions across bacterial genomes, and predicted networks of functionally related gene products. Access RegulonDB at http://regulondb.ccg.unam.mx.
authors.affiliation: Program of Computational Genomics, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 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: Martín
authors.initials: M
authors.lastname: Peralta-Gil
authors.forename: Edgar
authors.initials: E
authors.lastname: Díaz-Peredo
authors.forename: Fabiola
authors.initials: F
authors.lastname: Sánchez-Solano
authors.forename: Alberto
authors.initials: A
authors.lastname: Santos-Zavaleta
authors.forename: Irma
authors.initials: I
authors.lastname: Martínez-Flores
authors.forename: Verónica
authors.initials: V
authors.lastname: Jiménez-Jacinto
authors.forename: César
authors.initials: C
authors.lastname: Bonavides-Martínez
authors.forename: Juan
authors.initials: J
authors.lastname: Segura-Salazar
authors.forename: Agustino
authors.initials: A
authors.lastname: Martínez-Antonio
authors.forename: Julio
authors.initials: J
authors.lastname: Collado-Vides
mesh_terms: D030541:Databases, Genetic; D048168:Escherichia coli K12 / Q000235:genetics* / Q000254:growth & development; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D020407:Internet; D009876:Operon; D018085:Regulon; D012984:Software; D014158:Transcription, Genetic; D014584:User-Computer Interface