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. 2013 Jan;41(Database issue):D605-12.
doi: 10.1093/nar/gks1027. Epub 2012 Nov 9.

EcoCyc: fusing model organism databases with systems biology

Ingrid M Keseler  1 , Amanda Mackie, Martin Peralta-Gil, Alberto Santos-Zavaleta, Socorro Gama-Castro, César Bonavides-Martínez, Carol Fulcher, Araceli M Huerta, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Luis Muñiz-Rascado, Quang Ong, Suzanne Paley, Imke Schröder, Alexander G Shearer, Pallavi Subhraveti, Mike Travers, Deepika Weerasinghe, Verena Weiss, Julio Collado-Vides, Robert P Gunsalus, Ian Paulsen, Peter D Karp
Affiliations

EcoCyc: fusing model organism databases with systems biology

Ingrid M Keseler et al. Nucleic Acids Res. 2013 Jan.

Abstract

EcoCyc (http://EcoCyc.org) is a model organism database built on the genome sequence of Escherichia coli K-12 MG1655. Expert manual curation of the functions of individual E. coli gene products in EcoCyc has been based on information found in the experimental literature for E. coli K-12-derived strains. Updates to EcoCyc content continue to improve the comprehensive picture of E. coli biology. The utility of EcoCyc is enhanced by new tools available on the EcoCyc web site, and the development of EcoCyc as a teaching tool is increasing the impact of the knowledge collected in EcoCyc.

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Figures

Figure 1.
Figure 1.
Biolog PM1 plate depicting E. coli carbon source utilization results from five different experiments under aerobic growth conditions.
Figure 2.
Figure 2.
The section of an EcoCyc gene page that provides gene essentiality information.
See this image and copyright information in PMC

References

    1. Latendresse M, Krummenacker M, Trupp M, Karp PD. Construction and completion of flux balance models from pathway databases. Bioinformatics. 2012;28:388–396. - PMC - PubMed
    1. Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 2012;40:D742–D753. - PMC - PubMed
    1. Paul BJ, Barker MM, Ross W, Schneider DA, Webb C, Foster JW, Gourse RL. DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. Cell. 2004;118:311–322. - PubMed
    1. Lemke JJ, Sanchez-Vazquez P, Burgos HL, Hedberg G, Ross W, Gourse RL. Direct regulation of Escherichia coli ribosomal protein promoters by the transcription factors ppGpp and DksA. Proc. Natl Acad. Sci. USA. 2011;108:5712–5717. - PMC - PubMed
    1. Barker MM, Gaal T, Josaitis CA, Gourse RL. Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro. J. Mol. Biol. 2001;305:673–688. - PubMed

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