Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/21/2005
Publication Date: 1/21/2006
Citation: Fei, Z., Tang, X., Alba, R., Giovannoni, J.J. 2006. Tomato expression database (ted): a suite of data presentation and analysis tools. Nucleic Acids Research. 34:D766-D770. Interpretive Summary: With the advent of large expression data sets resulting from emerging genomics technologies there is a parallel need for databases that can effectively store and transmit said data to the research community. We have developed a suite of data storage and presentation tools based on public tomato EST collections and microarrays developed by our group. These resources are being used by public and private laboratories the world over. The database set described in this manuscript serves to warehouse raw data derived from the public tomato array and to present gene expression data resulting from analysis of EST abundance (digital northerns) and analyzed microarray results. The database also includes tools and functions to allow users easy navigation through genome sequences to expression information to correlation of expression patterns among similarly expressed genes. These tools will assist users in identifying target tomato genes for further characterization and analysis.
Technical Abstract: 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 over 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.