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Nucleic Acids Research 2006 34(Database Issue):D766-D770; doi:10.1093/nar/gkj110
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Nucleic Acids Research, 2006, Vol. 34, Database issue D766-D770
© 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{at}oxfordjournals.org

Article

Tomato Expression Database (TED): a suite of data presentation and analysis tools

Zhangjun Fei1,2,*, Xuemei Tang1, Rob Alba1 and James Giovannoni1,3

1Boyce Thompson Institute for Plant Research, Cornell University Ithaca, NY 14853, USA 2Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University VA 24061, USA 3USDA Plant, Soil, and Nutrition Laboratory Tower Rd, Ithaca, NY 14853, USA

*To whom correspondence should be addressed at Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, VA 24061, USA. Tel: 1 +540 231 3295; Fax: 1 +540 231 2606; Email: zfei{at}vt.edu

Received July 27, 2005. Revised October 17, 2005. Accepted October 17, 2005.

The Tomato Expression Database (TED) includes three integrated components. The Tomato Microarray Data Warehouse serves as a central repository for raw gene expression data derived from the public tomato cDNA microarray. In addition to expression data, TED stores experimental design and array information in compliance with the MIAME guidelines and provides web interfaces for researchers to retrieve data for their own analysis and use. The Tomato Microarray Expression Database contains normalized and processed microarray data for ten time points with nine pair-wise comparisons during fruit development and ripening in a normal tomato variety and nearly isogenic single gene mutants impacting fruit development and ripening. Finally, the Tomato Digital Expression Database contains raw and normalized digital expression (EST abundance) data derived from analysis of the complete public tomato EST collection containing >150 000 ESTs derived from 27 different non-normalized EST libraries. This last component also includes tools for the comparison of tomato and Arabidopsis digital expression data. A set of query interfaces and analysis, and visualization tools have been developed and incorporated into TED, which aid users in identifying and deciphering biologically important information from our datasets. TED can be accessed at http://ted.bti.cornell.edu.

Correspondence may also be addressed to James Giovannoni, USDA Plant, Soil, and Nutrition Laboratory, Tower Road, Cornell University campus, Ithaca, NY 14853, USA. Tel: 1 +607 255 1414; Fax: 1 +607 254 2958; Email: jjg33{at}cornell.edu


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