title: EcoCyc: a comprehensive view of Escherichia coli biology.
abstract: EcoCyc (http://EcoCyc.org) provides a comprehensive encyclopedia of Escherichia coli biology. EcoCyc integrates information about the genome, genes and gene products; the metabolic network; and the regulatory network of E. coli. Recent EcoCyc developments include a new initiative to represent and curate all types of E. coli regulatory processes such as attenuation and regulation by small RNAs. EcoCyc has started to curate Gene Ontology (GO) terms for E. coli and has made a dataset of E. coli GO terms available through the GO Web site. The curation and visualization of electron transfer processes has been significantly improved. Other software and Web site enhancements include the addition of tracks to the EcoCyc genome browser, in particular a type of track designed for the display of ChIP-chip datasets, and the development of a comparative genome browser. A new Genome Omics Viewer enables users to paint omics datasets onto the full E. coli genome for analysis. A new advanced query page guides users in interactively constructing complex database queries against EcoCyc. A Macintosh version of EcoCyc is now available. A series of Webinars is available to instruct users in the use of EcoCyc.
authors.affiliation: SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA.
authors.forename: Ingrid M
authors.initials: IM
authors.lastname: Keseler
authors.forename: César
authors.initials: C
authors.lastname: Bonavides-Martínez
authors.forename: Julio
authors.initials: J
authors.lastname: Collado-Vides
authors.forename: Socorro
authors.initials: S
authors.lastname: Gama-Castro
authors.forename: Robert P
authors.initials: RP
authors.lastname: Gunsalus
authors.forename: D Aaron
authors.initials: DA
authors.lastname: Johnson
authors.forename: Markus
authors.initials: M
authors.lastname: Krummenacker
authors.forename: Laura M
authors.initials: LM
authors.lastname: Nolan
authors.forename: Suzanne
authors.initials: S
authors.lastname: Paley
authors.forename: Ian T
authors.initials: IT
authors.lastname: Paulsen
authors.forename: Martin
authors.initials: M
authors.lastname: Peralta-Gil
authors.forename: Alberto
authors.initials: A
authors.lastname: Santos-Zavaleta
authors.forename: Alexander Glennon
authors.initials: AG
authors.lastname: Shearer
authors.forename: Peter D
authors.initials: PD
authors.lastname: Karp
mesh_terms: D002462:Cell Membrane / Q000201:enzymology; D030541:Databases, Genetic; D004579:Electron Transport; D004926:Escherichia coli / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D023281:Genomics; D020407:Internet; D012984:Software; D014158:Transcription, Genetic