RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions

• Published in: Nucleic acids research 2006-01, Vol.34 (1), p.D394-D397
• Main Authors: Salgado, Heladia, Gama-Castro, Socorro, Peralta-Gil, Martín, Díaz-Peredo, Edgar, Sánchez-Solano, Fabiola, Santos-Zavaleta, Alberto, Martínez-Flores, Irma, Jiménez-Jacinto, Verónica, Bonavides-Martínez, César, Segura-Salazar, Juan, Martínez-Antonio, Agustino, Collado-Vides, Julio
• Format: Article
• Language: English
• Subjects: Databases, Genetic; Escherichia coli; Escherichia coli K12 - genetics; Escherichia coli K12 - growth & development; Gene Expression Regulation, Bacterial; Genome, Bacterial; Internet; Operon; Regulon; Software; Transcription, Genetic; User-Computer Interface
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkj156

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.