ArticleNucleic acids research2011
RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units).
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 189 papers.
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189 citing papers in PubMed.
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- Gene regulatory network inference based on causal discovery integrating with graph neural network.Quantitative biology (Beijing, China) · 2023Article
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- Gene Self-Expressive Networks as a Generalization-Aware Tool to Model Gene Regulatory Networks.Biomolecules · 2023Article
- Review and assessment of Boolean approaches for inference of gene regulatory networks.Heliyon · 2022Review
- Is energy excess the initial trigger of carbon overflow metabolism? Transcriptional network response of carbon-limited Escherichia coli to transient carbon excess.Microbial cell factories · 2022Article
- Advances and prospects in metabolic engineering of Escherichia coli for L-tryptophan production.World journal of microbiology & biotechnology · 2022Review
- Evaluating the performance of random forest and iterative random forest based methods when applied to gene expression data.Computational and structural biotechnology journal · 2022Article
- Independent Component Analysis Identifies the Modulons Expanding the Transcriptional Regulatory Networks of EnterohemorrhagicFrontiers in microbiology · 2022Article
- Uncovering Transcriptional Regulators and Targets of sRNAs Using an Integrative Data-Mining Approach: H-NS-Regulated RseX as a Case Study.Frontiers in cellular and infection microbiology · 2021Article
- FINET: Fast Inferring NETwork.BMC research notes · 2020Article
- Globally learning gene regulatory networks based on hidden atomic regulators from transcriptomic big data.BMC genomics · 2020Article
- Intrinsic limitations in mainstream methods of identifying network motifs in biology.BMC bioinformatics · 2020Article
- Homolog comparisons further reconcile in vitro and in vivo correlations of protein activities by revealing over-looked physiological factors.Protein science : a publication of the Protein Society · 2019Article
- From biophysics to 'omics and systems biology.European biophysics journal : EBJ · 2019Review
129 more citing papers are in PubMed but not listed here.
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28 authors.
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Abstract
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.
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