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RegulonDB screenshot

A relational database that offers, in an organized and computable form, updated knowledge on transcriptional regulation in Escherichia coli K-12. Its electronic format enables researchers to compare their results with the legacy of previous knowledge and supports bioinformatics tools and model building. Major changes to the overall navigation and structure of the main pages have been made, offering more structured access to the data, based on the two dominant types of users: biologists, usually conducting individual search queries, and those interested in data collections.

Restrictions to use:
None
Data access:
File download, Web user interface
Version:
RegulonDB version 9.0
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Maintainer

  • Julio Collado-Vides <collado at ccg.unam.mx>

Institution(s)

Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Morelos, Mexico ; UMR_S 1090 TAGC, INSERM, Marseille, France; Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Santiago de Querétaro, QRO, Mexico; Departamento de Microbiologia Molecular, IBT, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico; Institute of Computational Linguistics, University of Zurich, Zurich, Switzerland

Funding source(s)

Universidad Nacional Autónoma de México; National Institute of General Medical Sciences of the National Institutes of Health [R01GM110597]; Department of Health and Human Services; National Institutes of Health; National Institute of General Medical Sciences, under Cooperative Agreement [2U24GM077678-24A1]

  • (Gama-Castro et al., 2016) RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond. Nucleic acids research.
    PMID: 26527724
  • (Weiss et al., 2013) Evidence classification of high-throughput protocols and confidence integration in RegulonDB. Database.
    PMID: 23327937
  • (Salgado et al., 2013) RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. Nucleic acids research.
    PMID: 23203884
  • (Salgado et al., 2012) Extracting regulatory networks of Escherichia coli from RegulonDB. Methods in molecular biology.
    PMID: 22144154
  • (Gama-Castro et al., 2011) RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units). Nucleic acids research.
    PMID: 21051347
  • (Gama-Castro et al., 2008) RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic acids research.
    PMID: 18158297
  • (Salgado et al., 2006) RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. Nucleic acids research.
    PMID: 16381895
  • (Salgado et al., 2004) RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. Nucleic acids research.
    PMID: 14681419
  • (Salgado et al., 2001) RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12. Nucleic acids research.
    PMID: 11125053
  • (Salgado et al., 2000) RegulonDB (version 3.0): transcriptional regulation and operon organization in Escherichia coli K-12. Nucleic acids research.
    PMID: 10592182
  • (Salgado et al., 1999) RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli. Nucleic acids research.
    PMID: 9847141
  • (Huerta et al., 1998) RegulonDB: a database on transcriptional regulation in Escherichia coli. Nucleic acids research.
    PMID: 9399800
  • Eubacteria
    • Escherichia coli

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