EcoCyc: a comprehensive view of Escherichia coli biology.
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.
Keseler
Ingrid M
IM
SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA.
Bonavides-Martínez
César
C
Collado-Vides
Julio
J
Gama-Castro
Socorro
S
Gunsalus
Robert P
RP
Johnson
D Aaron
DA
Krummenacker
Markus
M
Nolan
Laura M
LM
Paley
Suzanne
S
Paulsen
Ian T
IT
Peralta-Gil
Martin
M
Santos-Zavaleta
Alberto
A
Shearer
Alexander Glennon
AG
Karp
Peter D
PD
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