EcoCyc: a comprehensive database resource for Escherichia coli

By I. Keseler, Julio Collado-Vides, S. Gama-Castro, J. Ingraham, Suzanne M. Paley, Ian T. Paulsen, Martín Peralta-Gil, Peter D. Karp. Nucleic Acids Res., 2004

781 citations recorded by the source corpus.

The EcoCyc database (http://EcoCyc.org/) is a comprehensive source of information on the biology of the prototypical model organism Escherichia coli K12. The mission for EcoCyc is to contain both computable descriptions of, and detailed comments describing, all genes, proteins, pathways and molecular interactions in E.coli. Through ongoing manual curation, extensive information such as summary comments, regulatory information, literature citations and evidence types has been extracted from 8862 publications and added to Version 8.5 of the EcoCyc database. The EcoCyc database can be accessed through a World Wide Web interface, while the downloadable Pathway Tools software and data files enable computational exploration of the data and provide enhanced querying capabilities that web interfaces cannot support. For example, EcoCyc contains carefully curated information that can be used as training sets for bioinformatics prediction of entities such as promoters, operons, genetic networks, transcription factor binding sites, metabolic pathways, functionally related genes, protein complexes and protein–ligand interactions.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/aa163167f51e580c3dcb1aaef00f60b08b6f64a8

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Citations in the corpus

RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions (2005, positive): “Curation in our team is coordinated with colleagues in EcoCyc so that literature on gene regulation as well as observations from users of both databases pertintent to gene regulation are unified and curated by our team.”
σE Regulates and Is Regulated by a Small RNA in Escherichia coli (2007, background): “a Description of genes from EcoCyc (27, 28) and results from this paper.”
Sub-lethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis (2010, background): “P acrAB is partially annotated to show the À10 and À35 regions (bold), the transcription start site (capitalized A), and the AcrR/EnvR binding site (underlined).”
Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles (2007, background): “The latest computational annotation for YnaE available in EcoCyc (http://ecocyc.org/) suggests that its function is also phage-related [36].”
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information (2007, methodology): “A reconstruction is easily accessible and transferable once developed and can be queried for content such as genes, proteins, reactions and metabolites.”
Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins (2009, methodology): “These include a genome-wide collection of single-gene deletion strains [2] along with extensive knowledge of regulatory circuits [3,5,7,9] and metabolic pathways [6,10,11].”
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes (2005, background): “Often called model organism databases, or organism-specific databases, examples include EcoCyc for Escherichia coli (1), PseudoCyc for Pseudomonas aeruginosa (2), PlasmoCyc for Plasmodium falciparum (3), SGD for Saccharomyces cerevisiae (4), TAIR for Arabidopsis thaliana (5), MGD for Mus musculus (m”
Hfq Modulates the σE-Mediated Envelope Stress Response and the σ32-Mediated Cytoplasmic Stress Response in Escherichia coli (2006, methodology): “Pathways from the EcoCyc database (21) with at least two members subject to Hfq regulation are listed in Table 4.”
PANTHER Pathway: an ontology-based pathway database coupled with data analysis tools (2009, methodology): “The first example of computation representation of pathway ontology was the EcoCyc database (Karp et al. 1996; Keseler et al. 2005).”
Introduction to systems biology. (2007, background): “For simple organisms, such as Escherichia coli or yeast, large parts of the metabolic network structure, the operon structure and their transcriptional regulators are now known [1–3].”
GO PaD: the Gene Ontology Partition Database (2006, background): “For instance, GO (10), MIPS (11), YPD (12) and EcoCyc (13) are all biological classification hierarchies, and thus contain overlapping information.”
The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases (2007, methodology): “The microbial portion of MetaCyc was initialized with the full complement of EcoCyc metabolic pathways (6) ensuring a comprehensive coverage of the basic pathways of central and intermediary metabolism typical of enteric bacteria.”
Escherichia coli K-12: a cooperatively developed annotation snapshot—2005 (2006, neutral): “13 http://www.ecoli-york.org (17). 14 http://www.ecocyc.org ( 18 ).”
Global transcriptional analysis of metabolic burden due to plasmid maintenance in Escherichia coli DH5α during batch fermentation (2006, background): “The lobal regulator CRP is known to positively control transcription f most of these genes [9].”
MetaCyc: a multiorganism database of metabolic pathways and enzymes (2005, methodology): “MetaCyc contains the full complement of EcoCyc metabolic pathways (6) and thus has most of the basic pathways of central and intermediary metabolism typical of enteric 25 bacteria.”