EcoCyc: A comprehensive view of Escherichia coli biology

被引：266

作者：

Keseler, Ingrid M. ^{[1
]}

Bonavides-Martinez, Cesar ^{[2
]}

Collado-Vides, Julio ^{[2
]}

Gama-Castro, Socorro ^{[2
]}

Gunsalus, Robert P. ^{[3
,4
]}

Johnson, D. Aaron ^{[5
]}

Krummenacker, Markus ^{[1
]}

Nolan, Laura M. ^{[6
]}

Paley, Suzanne ^{[1
]}

Paulsen, Ian T. ^{[6
]}

Peralta-Gil, Martin ^{[2
]}

Santos-Zavaleta, Alberto ^{[2
]}

Glennon Shearer, Alexander ^{[1
]}

Karp, Peter D. ^{[1
]}

机构：

[1] SRI Int, Menlo Pk, CA 94025 USA

[2] Univ Nacl Autonoma Mexico, Ctr Ciencias Genom, Program Computat Genom, Cuernavaca 62100, Morelos, Mexico

[3] Univ Calif Los Angeles, Inst Mol Biol, Los Angeles, CA 90095 USA

[4] Univ Calif Los Angeles, Dept Microbiol Mol Genet & Immunol, Los Angeles, CA 90095 USA

[5] J Craig Venter Inst, Rockville, MD 20850 USA

[6] Macquarie Univ, Dept Chem & Biomol Sci, Sydney, NSW 2109, Australia

来源：

NUCLEIC ACIDS RESEARCH | 2009年 / 37卷

基金：

美国国家卫生研究院;

关键词：

REGULATORY NETWORK; K-12; TRANSCRIPTION; DATABASE; MOTIFS; ACTS;

D O I：

10.1093/nar/gkn751

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

070307 [化学生物学]; 071010 [生物化学与分子生物学];

摘要：

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.

引用

页码：D464 / D470

页数：7

共 14 条

[1]

Caspi R, 2008, NUCLEIC ACIDS RES, V36, pD623, DOI [10.1093/nar/gkt1103, 10.1093/nar/gkm900]

[2]

Discovery of Fur binding site clusters in Escherichia coli by information theory models [J].