EcoCyc: a comprehensive database of Escherichia coli biology

被引：346

作者：

Keseler, Ingrid M. ^{[1
]}

Collado-Vides, Julio ^{[2
]}

Santos-Zavaleta, Alberto ^{[2
]}

Peralta-Gil, Martin ^{[2
]}

Gama-Castro, Socorro ^{[2
]}

Muniz-Rascado, Luis ^{[2
]}

Bonavides-Martinez, Cesar ^{[2
]}

Paley, Suzanne ^{[1
]}

Krummenacker, Markus ^{[1
]}

Altman, Tomer ^{[1
]}

Kaipa, Pallavi ^{[1
]}

Spaulding, Aaron ^{[1
]}

Pacheco, John ^{[1
]}

Latendresse, Mario ^{[1
]}

Fulcher, Carol ^{[1
]}

Sarker, Malabika ^{[1
]}

Shearer, Alexander G. ^{[1
]}

Mackie, Amanda ^{[3
]}

Paulsen, Ian ^{[3
]}

Gunsalus, Robert P. ^{[4
,5
]}

Karp, Peter D. ^{[1
]}

机构：

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

[2] Univ Nacl Autonoma Mexico, Ctr Ciencias Genom, Programa Genom Computac, Cuernavaca 62100, Morelos, Mexico

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

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

[5] Univ Calif Los Angeles, UCLA Inst Genom & Prote, Los Angeles, CA 90095 USA

来源：

NUCLEIC ACIDS RESEARCH | 2011年 / 39卷

基金：

美国国家卫生研究院;

关键词：

D O I：

10.1093/nar/gkq1143

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

EcoCyc (http://EcoCyc.org) is a comprehensive model organism database for Escherichia coli K-12 MG1655. From the scientific literature, EcoCyc captures the functions of individual E. coli gene products; their regulation at the transcriptional, post-transcriptional and protein level; and their organization into operons, complexes and pathways. EcoCyc users can search and browse the information in multiple ways. Recent improvements to the EcoCyc Web interface include combined gene/protein pages and a Regulation Summary Diagram displaying a graphical overview of all known regulatory inputs to gene expression and protein activity. The graphical representation of signal transduction pathways has been updated, and the cellular and regulatory overviews were enhanced with new functionality. A specialized undergraduate teaching resource using EcoCyc is being developed.

引用

页码：D583 / D590

页数：8

共 13 条

[1] Signal transduction via the multi-step phosphorelay: Not necessarily a road less traveled [J].

Appleby, JL ;

Parkinson, JS ;

Bourret, RB .

CELL, 1996, 86 (06) :845-848

[2] The Gene Ontology in 2010: extensions and refinements The Gene Ontology Consortium [J].

Berardini, Tanya Z. ;

Li, Donghui ;

Huala, Eva ;

Bridges, Susan ;

Burgess, Shane ;

McCarthy, Fiona ;

Carbon, Seth ;

Lewis, Suzanna E. ;

Mungall, Christopher J. ;

Abdulla, Amina ;

Wood, Valerie ;

Feltrin, Erika ;

Valle, Giorgio ;

Chisholm, Rex L. ;

Fey, Petra ;

Gaudet, Pascale ;

Kibbe, Warren ;

Basu, Siddhartha ;

Bushmanova, Yulia ;

Eilbeck, Karen ;

Siegele, Deborah A. ;

McIntosh, Brenley ;

Renfro, Daniel ;

Zweifel, Adrienne ;

Hu, James C. ;

Ashburner, Michael ;

Tweedie, Susan ;

Alam-Faruque, Yasmin ;

Apweiler, Rolf ;

Auchinchloss, Andrea ;

Bairoch, Amos ;

Barrell, Daniel ;

Binns, David ;

Blatter, Marie-Claude ;

Bougueleret, Lydie ;

Boutet, Emmanuel ;

Breuza, Lionel ;

Bridge, Alan ;

Browne, Paul ;

Chan, Wei Mun ;

Coudert, Elizabeth ;

Daugherty, Louise ;

Dimmer, Emily ;

Eberhardt, Ruth ;

Estreicher, Anne ;

Famiglietti, Livia ;

Ferro-Rojas, Serenella ;

Feuermann, Marc ;

Foulger, Rebecca ;

Gruaz-Gumowski, Nadine .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D331-D335

[3] The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases [J].

Caspi, Ron ;

Altman, Tomer ;

Dale, Joseph M. ;

Dreher, Kate ;

Fulcher, Carol A. ;

Gilham, Fred ;

Kaipa, Pallavi ;

Karthikeyan, Athikkattuvalasu S. ;

Kothari, Anamika ;

Krummenacker, Markus ;

Latendresse, Mario ;

Mueller, Lukas A. ;

Paley, Suzanne ;

Popescu, Liviu ;

Pujar, Anuradha ;

Shearer, Alexander G. ;

Zhang, Peifen ;

Karp, Peter D. .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D473-D479

[4] The BioPAX community standard for pathway data sharing [J].

Demir, Emek ;

Cary, Michael P. ;

Paley, Suzanne ;

Fukuda, Ken ;

Lemer, Christian ;

Vastrik, Imre ;

Wu, Guanming ;

D'Eustachio, Peter ;

Schaefer, Carl ;

Luciano, Joanne ;

Schacherer, Frank ;

Martinez-Flores, Irma ;

Hu, Zhenjun ;

Jimenez-Jacinto, Veronica ;

Joshi-Tope, Geeta ;

Kandasamy, Kumaran ;

Lopez-Fuentes, Alejandra C. ;

Mi, Huaiyu ;

Pichler, Elgar ;

Rodchenkov, Igor ;

Splendiani, Andrea ;

Tkachev, Sasha ;

Zucker, Jeremy ;

Gopinath, Gopal ;

Rajasimha, Harsha ;

Ramakrishnan, Ranjani ;

Shah, Imran ;

Syed, Mustafa ;

Anwar, Nadia ;

Babur, Oezguen ;

Blinov, Michael ;

Brauner, Erik ;

Corwin, Dan ;

Donaldson, Sylva ;

Gibbons, Frank ;

Goldberg, Robert ;

Hornbeck, Peter ;

Luna, Augustin ;

Murray-Rust, Peter ;

Neumann, Eric ;

Reubenacker, Oliver ;

Samwald, Matthias ;

van Iersel, Martijn ;

Wimalaratne, Sarala ;

Allen, Keith ;

Braun, Burk ;

Whirl-Carrillo, Michelle ;

Cheung, Kei-Hoi ;

Dahlquist, Kam ;

Finney, Andrew .

NATURE BIOTECHNOLOGY, 2010, 28 (09) :935-942

[5] RegulonDB (version 6.0):: gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation [J].

Gama-Castro, Socorro ;

Jimenez-Jacinto, Veronica ;

Peralta-Gil, Martin ;

Santos-Zavaleta, Alberto ;

Penaloza-Spinola, Monica I. ;

Contreras-Moreira, Bruno ;

Segura-Salazar, Juan ;

Muniz-Rascado, Luis ;

Martinez-Flores, Irma ;

Salgado, Heladia ;

Bonavides-Martinez, Cesar ;

Abreu-Goodger, Cei ;

Rodriguez-Penagos, Carlos ;

Miranda-Rios, Juan ;

Morett, Enrique ;

Merino, Enrique ;

Huerta, Araceli M. ;

Trevino-Quintanilla, Luis ;

Collado-Vides, Julio .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D120-D124

[6] Biological Insights from Structures of Two-Component Proteins [J].

Gao, Rong ;

Stock, Ann M. .

ANNUAL REVIEW OF MICROBIOLOGY, 2009, 63 :133-154

[7] What we can learn about Escherichia coli through application of Gene Ontology [J].

Hu, James C. ;

Karp, Peter D. ;

Keseler, Ingrid M. ;

Krummenacker, Markus ;

Siegele, Deborah A. .

TRENDS IN MICROBIOLOGY, 2009, 17 (07) :269-278

[8] DNA-binding characteristics of the Escherichia coli CytR regulator:: a relaxed spacing requirement between operator half-sites is provided by a flexible, unstructured interdomain linker [J].

Jorgensen, CI ;

Kallipolitis, BH ;

Valentin-Hansen, P .

MOLECULAR MICROBIOLOGY, 1998, 27 (01) :41-50

[9] DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli [J].

Khodursky, AB ;

Peter, BJ ;

Cozzarelli, NR ;

Botstein, D ;

Brown, PO ;

Yanofsky, C .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2000, 97 (22) :12170-12175

[10] An advanced web query interface for biological databases [J].

Latendresse, Mario ;

Karp, Peter D. .

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2010, :baq006

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