EcoCyc: a comprehensive database of Escherichia coli biology

Ingrid M. Keseler; Julio Collado-Vides; Alberto Santos-Zavaleta; Martin Peralta-Gil; Socorro Gama-Castro; Luis Muniz-Rascado; César Bonavides-Martinez; Suzanne Paley; Markus Krummenacker; Tomer Altman; Pallavi Kaipa; Aaron Spaulding; John Pacheco; Mario Latendresse; Carol Fulcher; Malabika Sarker; Alexander G. Shearer; Amanda Mackie; Ian Paulsen; Robert P. Gunsalus; Peter D. Karp

doi:10.1093/nar/gkq1143

EcoCyc: a comprehensive database of Escherichia coli biology

Ingrid M. Keseler, Julio Collado-Vides, Alberto Santos-Zavaleta, Martin Peralta-Gil, Socorro Gama-Castro, Luis Muniz-Rascado, César Bonavides-Martinez, Suzanne Paley, Markus Krummenacker, Tomer Altman, Pallavi Kaipa, Aaron Spaulding, John Pacheco, Mario Latendresse, Carol Fulcher, Malabika Sarker, Alexander G. Shearer, Amanda Mackie, Ian Paulsen, Robert P. GunsalusPeter D. Karp

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Abstract

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.

Original language	English
Pages (from-to)	D583–D590
Number of pages	8
Journal	Nucleic Acids Research
Volume	39
Issue number	SUPPL. 1
DOIs	https://doi.org/10.1093/nar/gkq1143
Publication status	Published - Jan 2011

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This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/
by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., ... Karp, P. D. (2011). EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Research, 39(SUPPL. 1), D583–D590. https://doi.org/10.1093/nar/gkq1143

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abstract = "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.",

author = "Keseler, \{Ingrid M.\} and Julio Collado-Vides and Alberto Santos-Zavaleta and Martin Peralta-Gil and Socorro Gama-Castro and Luis Muniz-Rascado and C{\'e}sar Bonavides-Martinez and Suzanne Paley and Markus Krummenacker and Tomer Altman and Pallavi Kaipa and Aaron Spaulding and John Pacheco and Mario Latendresse and Carol Fulcher and Malabika Sarker and Shearer, \{Alexander G.\} and Amanda Mackie and Ian Paulsen and Gunsalus, \{Robert P.\} and Karp, \{Peter D.\}",

note = "This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.",

year = "2011",

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doi = "10.1093/nar/gkq1143",

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Keseler, IM, Collado-Vides, J, Santos-Zavaleta, A, Peralta-Gil, M, Gama-Castro, S, Muniz-Rascado, L, Bonavides-Martinez, C, Paley, S, Krummenacker, M, Altman, T, Kaipa, P, Spaulding, A, Pacheco, J, Latendresse, M, Fulcher, C, Sarker, M, Shearer, AG, Mackie, A, Paulsen, I, Gunsalus, RP & Karp, PD 2011, 'EcoCyc: a comprehensive database of Escherichia coli biology', Nucleic Acids Research, vol. 39, no. SUPPL. 1, pp. D583–D590. https://doi.org/10.1093/nar/gkq1143

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AU - Gama-Castro, Socorro

AU - Muniz-Rascado, Luis

AU - Bonavides-Martinez, César

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AU - Altman, Tomer

AU - Kaipa, Pallavi

AU - Spaulding, Aaron

AU - Pacheco, John

AU - Latendresse, Mario

AU - Fulcher, Carol

AU - Sarker, Malabika

AU - Shearer, Alexander G.

AU - Mackie, Amanda

AU - Paulsen, Ian

AU - Gunsalus, Robert P.

AU - Karp, Peter D.

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PY - 2011/1

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N2 - 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.

AB - 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.

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JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - SUPPL. 1

ER -

EcoCyc: a comprehensive database of Escherichia coli biology

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