title: RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more.
abstract: This article summarizes our progress with RegulonDB (http://regulondb.ccg.unam.mx/) during the past 2 years. We have kept up-to-date the knowledge from the published literature regarding transcriptional regulation in Escherichia coli K-12. We have maintained and expanded our curation efforts to improve the breadth and quality of the encoded experimental knowledge, and we have implemented criteria for the quality of our computational predictions. Regulatory phrases now provide high-level descriptions of regulatory regions. We expanded the assignment of quality to various sources of evidence, particularly for knowledge generated through high-throughput (HT) technology. Based on our analysis of most relevant methods, we defined rules for determining the quality of evidence when multiple independent sources support an entry. With this latest release of RegulonDB, we present a new highly reliable larger collection of transcription start sites, a result of our experimental HT genome-wide efforts. These improvements, together with several novel enhancements (the tracks display, uploading format and curational guidelines), address the challenges of incorporating HT-generated knowledge into RegulonDB. Information on the evolutionary conservation of regulatory elements is also available now. Altogether, RegulonDB version 8.0 is a much better home for integrating knowledge on gene regulation from the sources of information currently available.
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100.
authors.forename: Heladia
authors.initials: H
authors.lastname: Salgado
authors.forename: Martin
authors.initials: M
authors.lastname: Peralta-Gil
authors.forename: Socorro
authors.initials: S
authors.lastname: Gama-Castro
authors.forename: Alberto
authors.initials: A
authors.lastname: Santos-Zavaleta
authors.forename: Luis
authors.initials: L
authors.lastname: Muñiz-Rascado
authors.forename: Jair S
authors.initials: JS
authors.lastname: García-Sotelo
authors.forename: Verena
authors.initials: V
authors.lastname: Weiss
authors.forename: Hilda
authors.initials: H
authors.lastname: Solano-Lira
authors.forename: Irma
authors.initials: I
authors.lastname: Martínez-Flores
authors.forename: Alejandra
authors.initials: A
authors.lastname: Medina-Rivera
authors.forename: Gerardo
authors.initials: G
authors.lastname: Salgado-Osorio
authors.forename: Shirley
authors.initials: S
authors.lastname: Alquicira-Hernández
authors.forename: Kevin
authors.initials: K
authors.lastname: Alquicira-Hernández
authors.forename: Alejandra
authors.initials: A
authors.lastname: López-Fuentes
authors.forename: Liliana
authors.initials: L
authors.lastname: Porrón-Sotelo
authors.forename: Araceli M
authors.initials: AM
authors.lastname: Huerta
authors.forename: César
authors.initials: C
authors.lastname: Bonavides-Martínez
authors.forename: Yalbi I
authors.initials: YI
authors.lastname: Balderas-Martínez
authors.forename: Lucia
authors.initials: L
authors.lastname: Pannier
authors.forename: Maricela
authors.initials: M
authors.lastname: Olvera
authors.forename: Aurora
authors.initials: A
authors.lastname: Labastida
authors.forename: Verónica
authors.initials: V
authors.lastname: Jiménez-Jacinto
authors.forename: Leticia
authors.initials: L
authors.lastname: Vega-Alvarado
authors.forename: Victor
authors.initials: V
authors.lastname: Del Moral-Chávez
authors.forename: Alfredo
authors.initials: A
authors.lastname: Hernández-Alvarez
authors.forename: Enrique
authors.initials: E
authors.lastname: Morett
authors.forename: Julio
authors.initials: J
authors.lastname: Collado-Vides
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism; D030541:Databases, Genetic / Q000592:standards; D048168:Escherichia coli K12 / Q000235:genetics*; D019143:Evolution, Molecular; D015964:Gene Expression Regulation, Bacterial; D023281:Genomics; D020407:Internet; D011401:Promoter Regions, Genetic; D050436:Regulatory Elements, Transcriptional; D018085:Regulon; D012097:Repressor Proteins / Q000378:metabolism; D017423:Sequence Analysis, RNA; D014157:Transcription Factors / Q000378:metabolism; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D012097:Repressor Proteins; D014157:Transcription Factors; C068477:ferric uptake regulating proteins, bacterial