EcoCyc: a comprehensive database of Escherichia coli biology

By I. Keseler, Julio Collado-Vides, Alberto Santos-Zavaleta, Martín Peralta-Gil, S. Gama-Castro, Luis Muñiz-Rascado, César Bonavides-Martínez, Suzanne M. Paley, Markus Krummenacker, Tomer Altman and 11 more. 2010

523 citations recorded by the source corpus.

EcoCyc (http://EcoCyc.org) is a comprehensive model organism database for Escherichia coli K-12 MG1655. From the scientific literature, EcoCyc captures the functions of individual E. coli gene products; their regulation at the transcriptional, post-transcriptional and protein level; and their organization into operons, complexes and pathways. EcoCyc users can search and browse the information in multiple ways. Recent improvements to the EcoCyc Web interface include combined gene/protein pages and a Regulation Summary Diagram displaying a graphical overview of all known regulatory inputs to gene expression and protein activity. The graphical representation of signal transduction pathways has been updated, and the cellular and regulatory overviews were enhanced with new functionality. A specialized undergraduate teaching resource using EcoCyc is being developed.

Subfields: Molecular Biology

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Citations in the corpus

CRISPR interference (CRISPRi) for sequence-specific control of gene expression (2013, background): “Determine the DNA sequence of genes to be targeted using available genome databases 46–48 .”
The UniProt-GO Annotation database in 2011 (2011, methodology): “The UniProt GO annotations are supplemented with those from 36 external groups [annotations from the PAMGO (6), EcoCyc (7), EcoWiki (8), JCVI (9) and CGD (10) have been added to the data set since 2009], ensuring that all manual annotations from GO Consortium members that can be mapped to a UniProtK”
RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more (2012, methodology): “Our work maintains up-to-date information in both the RegulonDB and EcoCyc databases [(1,2) and an update by Keseler et al.”