Multidimensional annotation of the Escherichia coli K-12 genome

Peter D. Karp*, Ingrid M. Keseler, Alexander Shearer, Mario Latendresse, Markus Krummenacker, Suzanne M. Paley, Ian Paulsen, Julio Collado-Vides, Socorro Gama-Castro, Martin Peralta-Gil, Alberto Santos-Zavaleta, Mónica I. Peñaloza-Spínola, César Bonavides-martinez, John Ingraham

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    148 Citations (Scopus)
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    The annotation of the Escherichia coli K-12 genome in the EcoCyc database is one of the most accurate, complete and multidimensional genome annotations. Of the 4460 E. coli genes, EcoCyc assigns biochemical functions to 76% and 66% of all genes had their functions determined experimentally. EcoCyc assigns E. coli genes to Gene Ontology and to MultiFun. Seventy-five percent of gene products contain reviews authored by the EcoCyc project that summarize the experimental literature about the gene product. EcoCyc information was derived from 15 000 publications. The database contains extensive descriptions of E. coli cellular networks, describing its metabolic, transport and transcriptional regulatory processes. A comparison to genome annotations for other model organisms shows that the E. coli genome contains the most experimentally determined gene functions in both relative and absolute terms: 2941 (66%) for E. coli, 2319 (37%) for Saccharomyces cerevisiae, 1816 (5%) for Arabidopsis thaliana, 1456 (4%) for Mus musculus and 614 (4%) for Drosophila melanogaster. Database queries to EcoCyc survey the global properties of E. coli cellular networks and illuminate the extent of information gaps for E. coli, such as dead-end metabolites. EcoCyc provides a genome browser with novel properties, and a novel interactive display of transcriptional regulatory networks.

    Original languageEnglish
    Pages (from-to)7577-7590
    Number of pages14
    JournalNucleic Acids Research
    Issue number22
    Publication statusPublished - Dec 2007

    Bibliographical note

    Copyright 2007 The Author(s). This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.


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