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

Fei, Zhangjun, Tang, Xuemei, Alba, Rob, Giovannoni, James
Nucleic acids research 2006 v.34 pp. D766
Arabidopsis, Internet, complementary DNA, compliance, data collection, databases, experimental design, expressed sequence tags, fruiting, gene expression, genes, guidelines, microarray technology, mutants, ripening, tomatoes
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