TY - JOUR
T1 - The EcoCyc database
AU - Karp, Peter D.
AU - Weaver, Daniel
AU - Paley, Suzanne
AU - Fulcher, Carol
AU - Kubo, Aya
AU - Kothari, Anamika
AU - Krummenacker, Markus
AU - Subhraveti, Pallavi
AU - Weerasinghe, Deepika
AU - Gama-Castro, Socorro
AU - Huerta, Araceli M.
AU - Muñiz-Rascado, Luis
AU - Bonavides-Martinez, César
AU - Weiss, Verena
AU - Peralta-Gil, Martin
AU - Santos-Zavaleta, Alberto
AU - Schröder, Imke
AU - Mackie, Amanda
AU - Gunsalus, Robert
AU - Collado-Vides, Julio
AU - Keseler, Ingrid M.
AU - Paulsen, Ian
PY - 2014
Y1 - 2014
N2 - EcoCyc is a bioinformatics database available at EcoCyc.org that describes the genome and the biochemical machinery of Escherichia coli K-12 MG1655. The longterm goal of the project is to describe the complete molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts, to facilitate a system-level understanding of E. coli. EcoCyc is an electronic reference source for E. coli biologists and for biologists who work with related microorganisms. The database includes information pages on each E. coli gene, metabolite, reaction, operon, and metabolic pathway. The database also includes information on E. coli gene essentiality and on nutrient conditions that do or do not support the growth of E. coli. The website and downloadable software contain tools for analysis of high-throughput data sets. In addition, a steady-state metabolic flux model is generated from each new version of EcoCyc. The model can predict metabolic flux rates, nutrient uptake rates, and growth rates for different gene knockouts and nutrient conditions. This review provides a detailed description of the data content of EcoCyc and of the procedures by which this content is generated.
AB - EcoCyc is a bioinformatics database available at EcoCyc.org that describes the genome and the biochemical machinery of Escherichia coli K-12 MG1655. The longterm goal of the project is to describe the complete molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts, to facilitate a system-level understanding of E. coli. EcoCyc is an electronic reference source for E. coli biologists and for biologists who work with related microorganisms. The database includes information pages on each E. coli gene, metabolite, reaction, operon, and metabolic pathway. The database also includes information on E. coli gene essentiality and on nutrient conditions that do or do not support the growth of E. coli. The website and downloadable software contain tools for analysis of high-throughput data sets. In addition, a steady-state metabolic flux model is generated from each new version of EcoCyc. The model can predict metabolic flux rates, nutrient uptake rates, and growth rates for different gene knockouts and nutrient conditions. This review provides a detailed description of the data content of EcoCyc and of the procedures by which this content is generated.
UR - http://www.scopus.com/inward/record.url?scp=84932633215&partnerID=8YFLogxK
U2 - 10.1128/ecosalplus.ESP-0009-2013
DO - 10.1128/ecosalplus.ESP-0009-2013
M3 - Article
C2 - 25431773
AN - SCOPUS:84932633215
VL - 6
SP - 1
EP - 13
JO - EcoSal Plus
JF - EcoSal Plus
SN - 2324-6200
IS - 1
ER -