ArticleDatabase : the journal of biological databases and curation2013
Evidence classification of high-throughput protocols and confidence integration in RegulonDB.
Article in Database : the journal of biological databases and curation, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- RegulonDB v12.0: a comprehensive resource of transcriptional regulation in E. coli K-12.Nucleic acids research · 2024Article
- Flexible gold standards for transcription factor regulatory interactions inFrontiers in genetics · 2024Article
- Curation, inference, and assessment of a globally reconstructed gene regulatory network for Streptomyces coelicolor.Scientific reports · 2022Article
- Abasy Atlas v2.2: The most comprehensive and up-to-date inventory of meta-curated, historical, bacterial regulatory networks, their completeness and system-level characterization.Computational and structural biotechnology journal · 2020Article
- Limits to a classic paradigm: most transcription factors in E. coli regulate genes involved in multiple biological processes.Nucleic acids research · 2019Article
- Evolutionary constraints on the complexity of genetic regulatory networks allow predictions of the total number of genetic interactions.Scientific reports · 2019Article
- RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12.Nucleic acids research · 2019Article
- A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0.BMC biology · 2018Article
- Using RegulonDB, the Escherichia coli K-12 Gene Regulatory Transcriptional Network Database.Current protocols in bioinformatics · 2018Article
- Global transcriptional regulatory network forProceedings of the National Academy of Sciences of the United States of America · 2017Article
- RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond.Nucleic acids research · 2016Article
- Assisted curation of regulatory interactions and growth conditions of OxyR in E. coli K-12.Database : the journal of biological databases and curation · 2014Article
- RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more.Nucleic acids research · 2013Article
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Authors and funding
7 authors.
Funding
Abstract
RegulonDB provides curated information on the transcriptional regulatory network of Escherichia coli and contains both experimental data and computationally predicted objects. To account for the heterogeneity of these data, we introduced in version 6.0, a two-tier rating system for the strength of evidence, classifying evidence as either 'weak' or 'strong' (Gama-Castro,S., Jimenez-Jacinto,V., Peralta-Gil,M. et al. RegulonDB (Version 6.0): gene regulation model of Escherichia Coli K-12 beyond transcription, active (experimental) annotated promoters and textpresso navigation. Nucleic Acids Res., 2008;36:D120-D124.). We now add to our classification scheme the classification of high-throughput evidence, including chromatin immunoprecipitation (ChIP) and RNA-seq technologies. To integrate these data into RegulonDB, we present two strategies for the evaluation of confidence, statistical validation and independent cross-validation. Statistical validation involves verification of ChIP data for transcription factor-binding sites, using tools for motif discovery and quality assessment of the discovered matrices. Independent cross-validation combines independent evidence with the intention to mutually exclude false positives. Both statistical validation and cross-validation allow to upgrade subsets of data that are supported by weak evidence to a higher confidence level. Likewise, cross-validation of strong confidence data extends our two-tier rating system to a three-tier system by introducing a third confidence score 'confirmed'. Database URL: http://regulondb.ccg.unam.mx/
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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.