The DOI matches its Crossref record; 25 of the 25 references it cites were found in a registry or an index.
RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions
Open accessAbstract
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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“A comparison between these tools and others, including WGCNA, showed that WGCNA and ARACNE perform best at defining the network structure of Escherichia coli [130], for which a well-defined regulatory network was used as a gold standard [131].”
From Gene co-expression analysis for functional classification and gene–disease predictions (2017) · cites this paper as [131]
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Metadata
- 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
- 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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