RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units).
RegulonDB (http://regulondb.ccg.unam.mx/) is the primary reference database of the best-known regulatory network of any free-living organism, that of Escherichia coli K-12. The major conceptual change since 3 years ago is an expanded biological context so that transcriptional regulation is now part of a unit that initiates with the signal and continues with the signal transduction to the core of regulation, modifying expression of the affected target genes responsible for the response. We call these genetic sensory response units, or Gensor Units. We have initiated their high-level curation, with graphic maps and superreactions with links to other databases. Additional connectivity uses expandable submaps. RegulonDB has summaries for every transcription factor (TF) and TF-binding sites with internal symmetry. Several DNA-binding motifs and their sizes have been redefined and relocated. In addition to data from the literature, we have incorporated our own information on transcription start sites (TSSs) and transcriptional units (TUs), obtained by using high-throughput whole-genome sequencing technologies. A new portable drawing tool for genomic features is also now available, as well as new ways to download the data, including web services, files for several relational database manager systems and text files including BioPAX format.
Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, AP 565-A, Cuernavaca, Morelos 62100, México.
Socorro
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Gama-Castro
Heladia
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Salgado
Martin
M
Peralta-Gil
Alberto
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Santos-Zavaleta
Luis
L
Muñiz-Rascado
Hilda
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Solano-Lira
Verónica
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Jimenez-Jacinto
Verena
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Weiss
Jair S
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García-Sotelo
Alejandra
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López-Fuentes
Liliana
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Porrón-Sotelo
Shirley
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Alquicira-Hernández
Alejandra
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Medina-Rivera
Irma
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Martínez-Flores
Kevin
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Alquicira-Hernández
Ruth
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Martínez-Adame
César
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Bonavides-Martínez
Juan
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Miranda-Ríos
Araceli M
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Huerta
Alfredo
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Mendoza-Vargas
Leonardo
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Collado-Torres
Blanca
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Taboada
Leticia
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Vega-Alvarado
Maricela
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Olvera
Leticia
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Olvera
Ricardo
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Grande
Enrique
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Morett
Julio
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Collado-Vides
D001665:Binding Sites; D030541:Databases, Genetic; D048168:Escherichia coli K12 / Q000235:genetics* / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D015398:Signal Transduction; D018511:Systems Integration; D014157:Transcription Factors / Q000378:metabolism*; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
D014157:Transcription Factors