Nucleic Acids Research Advance Access originally published online on October 16, 2007
Nucleic Acids Research 2007 35(22):7577-7590; doi:10.1093/nar/gkm740
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Nucleic Acids Research, 2007, Vol. 35, No. 22 7577-7590
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Multidimensional annotation of the Escherichia coli K-12 genome
1SRI International, 333 Ravenswood Ave EK207, Menlo Park CA 94025, 2J. Craig Venter Institute, Rockville, MD 20850, USA, 3Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia, 2109, 4Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México and 5University of California, Davis, USA
*To whom correspondence should be addressed. Tel: +1 650 859 4358; Fax: +1 650 859 3735; Email: pkarp{at}ai.sri.com
Received June 8, 2007. Revised August 9, 2007. Accepted September 6, 2007.
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.
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