ArticleNucleic acids research2013
RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 240 papers.
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Who cites it
240 citing papers in PubMed.
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- Increased resistance against tellurite is conferred by a mutation in the promoter region of uncommon tellurite resistance geneApplied and environmental microbiology · 2024Article
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- tRNA anticodon cleavage by target-activated CRISPR-Cas13a effector.Science advances · 2024Article
- Genome-wide annotation of transcript boundaries using bacterial Rend-seq datasets.Microbial genomics · 2024Article
- Transcription factor competition facilitates self-sustained oscillations in single gene genetic circuits.PLoS computational biology · 2023Article
- Expanded roles of lactate-sensing LldR in transcription regulation of theMicrobial genomics · 2023Article
- Genomic SELEX Reveals Pervasive Role of the Flagella Master Regulator FlhDC in Carbon Metabolism.International journal of molecular sciences · 2023Article
- Growth rate-associated transcriptome reorganization in response to genomic, environmental, and evolutionary interruptions.Frontiers in microbiology · 2023Article
- RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation inMicrobial genomics · 2022Article
- 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
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- Quantifying the regulatory role of individual transcription factors in Escherichia coli.Cell reports · 2021Article
- From Molecular Recognition to the "Vehicles" of Evolutionary Complexity: An Informational Approach.International journal of molecular sciences · 2021Review
- A novel constrained genetic algorithm-based Boolean network inference method from steady-state gene expression data.Bioinformatics (Oxford, England) · 2021Article
- Composition of Transcription Machinery and Its Crosstalk with Nucleoid-Associated Proteins and Global Transcription Factors.Biomolecules · 2021Review
- Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems.Nature communications · 2021Article
- Regulation ofFrontiers in microbiology · 2021Article
180 more citing papers are in PubMed but not listed here.
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Authors and funding
27 authors.
Funding
Abstract
This article summarizes our progress with RegulonDB (http://regulondb.ccg.unam.mx/) during the past 2 years. We have kept up-to-date the knowledge from the published literature regarding transcriptional regulation in Escherichia coli K-12. We have maintained and expanded our curation efforts to improve the breadth and quality of the encoded experimental knowledge, and we have implemented criteria for the quality of our computational predictions. Regulatory phrases now provide high-level descriptions of regulatory regions. We expanded the assignment of quality to various sources of evidence, particularly for knowledge generated through high-throughput (HT) technology. Based on our analysis of most relevant methods, we defined rules for determining the quality of evidence when multiple independent sources support an entry. With this latest release of RegulonDB, we present a new highly reliable larger collection of transcription start sites, a result of our experimental HT genome-wide efforts. These improvements, together with several novel enhancements (the tracks display, uploading format and curational guidelines), address the challenges of incorporating HT-generated knowledge into RegulonDB. Information on the evolutionary conservation of regulatory elements is also available now. Altogether, RegulonDB version 8.0 is a much better home for integrating knowledge on gene regulation from the sources of information currently available.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.