title: Multidimensional annotation of the Escherichia coli K-12 genome.
abstract: 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.
authors.affiliation: SRI International, 333 Ravenswood Ave EK207, Menlo Park, CA 94025, USA. pkarp@ai.sri.com
authors.forename: Peter D
authors.initials: PD
authors.lastname: Karp
authors.forename: Ingrid M
authors.initials: IM
authors.lastname: Keseler
authors.forename: Alexander
authors.initials: A
authors.lastname: Shearer
authors.forename: Mario
authors.initials: M
authors.lastname: Latendresse
authors.forename: Markus
authors.initials: M
authors.lastname: Krummenacker
authors.forename: Suzanne M
authors.initials: SM
authors.lastname: Paley
authors.forename: Ian
authors.initials: I
authors.lastname: Paulsen
authors.forename: Julio
authors.initials: J
authors.lastname: Collado-Vides
authors.forename: Socorro
authors.initials: S
authors.lastname: Gama-Castro
authors.forename: Martin
authors.initials: M
authors.lastname: Peralta-Gil
authors.forename: Alberto
authors.initials: A
authors.lastname: Santos-Zavaleta
authors.forename: Mónica I
authors.initials: MI
authors.lastname: Peñaloza-Spínola
authors.forename: César
authors.initials: C
authors.lastname: Bonavides-Martinez
authors.forename: John
authors.initials: J
authors.lastname: Ingraham
mesh_terms: D019295:Computational Biology; D030541:Databases, Genetic; D048168:Escherichia coli K12 / Q000235:genetics* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics / Q000502:physiology; D053263:Gene Regulatory Networks; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D012984:Software
chemical_list: D029968:Escherichia coli Proteins