Abstract:
:RegulonDB, first published 20 years ago, is a comprehensive electronic resource about regulation of transcription initiation of Escherichia coli K-12 with decades of knowledge from classic molecular biology experiments, and recently also from high-throughput genomic methodologies. We curated the literature to keep RegulonDB up to date, and initiated curation of ChIP and gSELEX experiments. We estimate that current knowledge describes between 10% and 30% of the expected total number of transcription factor- gene regulatory interactions in E. coli. RegulonDB provides datasets for interactions for which there is no evidence that they affect expression, as well as expression datasets. We developed a proof of concept pipeline to merge binding and expression evidence to identify regulatory interactions. These datasets can be visualized in the RegulonDB JBrowse. We developed the Microbial Conditions Ontology with a controlled vocabulary for the minimal properties to reproduce an experiment, which contributes to integrate data from high throughput and classic literature. At a higher level of integration, we report Genetic Sensory-Response Units for 200 transcription factors, including their regulation at the metabolic level, and include summaries for 70 of them. Finally, we summarize our research with Natural language processing strategies to enhance our biocuration work.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Santos-Zavaleta A,Salgado H,Gama-Castro S,Sánchez-Pérez M,Gómez-Romero L,Ledezma-Tejeida D,García-Sotelo JS,Alquicira-Hernández K,Muñiz-Rascado LJ,Peña-Loredo P,Ishida-Gutiérrez C,Velázquez-Ramírez DA,Del Moral-Chávez V,Bonaviddoi
10.1093/nar/gky1077subject
Has Abstractpub_date
2019-01-08 00:00:00pages
D212-D220issue
D1eissn
0305-1048issn
1362-4962pii
5160972journal_volume
47pub_type
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