ARS | Publication request: Tomato functional genomics database (TFGD): a comprehensive collection and analysis package for tomato functional genomics

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 5, 2010
Publication Date: October 21, 2010
Citation: Fei, Z., Joung, J., Tang, X., Zheng, Y., Huang, M., Lee, J., Mcquinn, R., Tieman, D., Klee, H., Giovannoni, J.J. 2010. Tomato functional genomics database (TFGD): a comprehensive collection and analysis package for tomato functional genomics. Nucleic Acids Research. 39:D1156-D1163.

Interpretive Summary: We previously described the Tomato Expression Database (TED), which serves as a central repository of tomato expression data and contains a suite of data presentation and analysis tools to assist in the development and testing of biological hypotheses. With the rapid accumulation of large-scale metabolite and small RNA data in tomato, we have expanded the database into what we now term the Tomato Functional Genomics Database (TFGD). TFGD is a comprehensive collection of tomato functional genomics data. Currently the database contains three major data components: gene expression, metabolite profiles and small RNAs. All the data were collected from the public domain or generated by our groups and collaborators.

Technical Abstract: Tomato Functional Genomics Database (TFGD; http://ted.bti.cornell.edu) provides a comprehensive systems biology resource to store, mine, analyze, visualize and integrate large-scale tomato functional genomics datasets. The database is expanded from the previously described Tomato Expression Database by including profiles of fruit flavor and nutrition-related metabolites generated from a number of well-defined tomato introgression lines as well as more than fifteen million small RNAs generated from tomato fruit, flower and leaf tissues. A set of computational pipelines has been developed to process microarray, metabolite and small RNA datasets archived in the database, respectively, and TFGD provides downloads of all the analyzed results. TFGD is also designed to enable users to easily retrieve biologically important information through a set of efficient query interfaces.