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Nucleic Acids Research 2006 34(8):2438-2444; doi:10.1093/nar/gkl310
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Published online 8 May 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

Evidence supporting predicted metabolic pathways for Vibrio cholerae: gene expression data and clinical tests

Jing Shi1,*, Pedro R. Romero4, Gary K. Schoolnik2, Alfred M. Spormann3 and Peter D. Karp5

1 Biomedical Informatics Program, MC 5429, Stanford University Stanford, CA 94305, USA 2 Department of Microbiology and Immunology, MC 5107, Stanford University Stanford, CA 94305, USA 3 Department of Civil and Environmental Engineering, MC 5429, Stanford University Stanford, CA 94305, USA 4 School of Informatics, Indiana University-Purdue University Indianapolis Indianapolis, IN 46202, USA 5 Bioinformatics Research Group, Artificial Intelligence Center SRI International Menlo Park, CA 94025, USA

*To whom correspondence should be addressed. Tel: +1 650 724 5013; Fax: +1 650 725 1536; Email: js2400{at}stanford.edu

Received December 16, 2005. Revised January 8, 2006. Accepted April 11, 2006.

Vibrio cholerae, the etiological agent of the diarrheal illness cholera, can kill an infected adult in 24 h. V.cholerae lives as an autochthonous microbe in estuaries, rivers and coastal waters. A better understanding of its metabolic pathways will assist the development of more effective treatments and will provide a deeper understanding of how this bacterium persists in natural aquatic habitats. Using the completed V.cholerae genome sequence and PathoLogic software, we created VchoCyc, a pathway-genome database that predicted 171 likely metabolic pathways in the bacterium. We report here experimental evidence supporting the computationally predicted pathways. The evidence comes from microarray gene expression studies of V.cholerae in the stools of three cholera patients [D. S. Merrell, S. M. Butler, F. Qadri, N. A. Dolganov, A. Alam, M. B. Cohen, S. B. Calderwood, G. K. Schoolnik and A. Camilli (2002) Nature, 417, 642–645.], from gene expression studies in minimal growth conditions and LB rich medium, and from clinical tests that identify V.cholerae. Expression data provide evidence supporting 92 (53%) of the 171 pathways. The clinical tests provide evidence supporting seven pathways, with six pathways supported by both methods. VchoCyc provides biologists with a useful tool for analyzing this organism's metabolic and genomic information, which could lead to potential insights into new anti-bacterial agents. VchoCyc is available in the BioCyc database collection (http://BioCyc.org).


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