Cited by 368Bacterial Genetics and BiotechnologyGene Regulatory Network AnalysisMicrobial Metabolic Engineering and Bioproduction

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

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Salgado, H.·2006·Nucleic Acids Research

DOI 10.1093/nar/gkj156PMC PMC1347518

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Abstract

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.

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Self-citation

Authors: Salgado, H.
Affiliations: Universidad Nacional Autónoma de México (MX)
Corresponding author: Salgado, H.
ORCID: Salgado, H.
Venue: Nucleic Acids Research
Publisher: Oxford University Press (OUP)
Published: 2006-01-01
Volume: 34
Issue: 90001
Pages: D394-D397
ISSN: 0305-1048 (ISSN-L)
1362-4962
DOI: 10.1093/nar/gkj156
PMC: PMC1347518
OpenAlex: W2146856779
Cited by: 368
References: 25
Citations by year: 2026: 3 · 2025: 8 · 2024: 7 · 2023: 2 · 2022: 1 · 2021: 7 · 2020: 4 · 2019: 9 · 2018: 3 · 2017: 3 · 2016: 14 · 2015: 11 · 2014: 14 · 2013: 11 · 2012: 16
FWCI: 28.22
Type: journal article
Language: en
Open access: gold
doi.org
Licence: other-oa
Locations: Nucleic Acids Research (publishedVersion, other-oa)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Figshare (submittedVersion, cc-by)
Figshare (cc-by)
Funders: National Institutes of Health
National Institute of General Medical Sciences (R01GM062205, GM62205-02)
National Center for Research Resources (1-R01-RR07861, R01RR007861)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
Keywords: RegulonDB, Escherichia coli K-12, transcriptional regulatory networks, operon organization, regulon, gene expression regulation, literature curation, EcoCyc, microarray comparison, functional gene networks
MeSH terms: Operon, Software, Transcription, Genetic, User-Computer Interface, Gene Expression Regulation, Bacterial, Genome, Bacterial, Regulon, Internet, Databases, Genetic, Escherichia coli K12

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

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