title: RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation.
abstract: RegulonDB (http://regulondb.ccg.unam.mx/) is the primary reference database offering curated knowledge of the transcriptional regulatory network of Escherichia coli K12, currently the best-known electronically encoded database of the genetic regulatory network of any free-living organism. This paper summarizes the improvements, new biology and new features available in version 6.0. Curation of original literature is, from now on, up to date for every new release. All the objects are supported by their corresponding evidences, now classified as strong or weak. Transcription factors are classified by origin of their effectors and by gene ontology class. We have now computational predictions for sigma(54) and five different promoter types of the sigma(70) family, as well as their corresponding -10 and -35 boxes. In addition to those curated from the literature, we added about 300 experimentally mapped promoters coming from our own high-throughput mapping efforts. RegulonDB v.6.0 now expands beyond transcription initiation, including RNA regulatory elements, specifically riboswitches, attenuators and small RNAs, with their known associated targets. The data can be accessed through overviews of correlations about gene regulation. RegulonDB associated original literature, together with more than 4000 curation notes, can now be searched with the Textpresso text mining engine.
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: Socorro
authors.initials: S
authors.lastname: Gama-Castro
authors.forename: Verónica
authors.initials: V
authors.lastname: Jiménez-Jacinto
authors.forename: Martín
authors.initials: M
authors.lastname: Peralta-Gil
authors.forename: Alberto
authors.initials: A
authors.lastname: Santos-Zavaleta
authors.forename: Mónica I
authors.initials: MI
authors.lastname: Peñaloza-Spinola
authors.forename: Bruno
authors.initials: B
authors.lastname: Contreras-Moreira
authors.forename: Juan
authors.initials: J
authors.lastname: Segura-Salazar
authors.forename: Luis
authors.initials: L
authors.lastname: Muñiz-Rascado
authors.forename: Irma
authors.initials: I
authors.lastname: Martínez-Flores
authors.forename: Heladia
authors.initials: H
authors.lastname: Salgado
authors.forename: César
authors.initials: C
authors.lastname: Bonavides-Martínez
authors.forename: Cei
authors.initials: C
authors.lastname: Abreu-Goodger
authors.forename: Carlos
authors.initials: C
authors.lastname: Rodríguez-Penagos
authors.forename: Juan
authors.initials: J
authors.lastname: Miranda-Ríos
authors.forename: Enrique
authors.initials: E
authors.lastname: Morett
authors.forename: Enrique
authors.initials: E
authors.lastname: Merino
authors.forename: Araceli M
authors.initials: AM
authors.lastname: Huerta
authors.forename: Luis
authors.initials: L
authors.lastname: Treviño-Quintanilla
authors.forename: Julio
authors.initials: J
authors.lastname: Collado-Vides
mesh_terms: D019295:Computational Biology; D030541:Databases, Genetic; D048168:Escherichia coli K12 / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D020407:Internet; D008957:Models, Genetic; D011401:Promoter Regions, Genetic; D038621:Regulatory Sequences, Ribonucleic Acid; D018085:Regulon; D012808:Sigma Factor / Q000378:metabolism; D012984:Software; D014157:Transcription Factors / Q000378:metabolism; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
chemical_list: D038621:Regulatory Sequences, Ribonucleic Acid; D012808:Sigma Factor; D014157:Transcription Factors