Authors
Alberto Santos-Zavaleta, Heladia Salgado, Socorro Gama-Castro, Mishael Sánchez-Pérez, Laura Gómez-Romero, Daniela Ledezma-Tejeida, Jair Santiago García-Sotelo, Kevin Alquicira-Hernández, Luis José Muñiz-Rascado, Pablo Peña-Loredo, Cecilia Ishida-Gutiérrez, David A Velázquez-Ramírez, Víctor Del Moral-Chávez, César Bonavides-Martínez, Carlos-Francisco Méndez-Cruz, James Galagan, Julio Collado-Vides
Publication date
2019/1/8
Journal
Nucleic acids research
Volume
47
Issue
D1
Pages
D212-D220
Publisher
Oxford University Press
Description
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 …
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