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ARS Home » Pacific West Area » Parlier, California » San Joaquin Valley Agricultural Sciences Center » Crop Diseases, Pests and Genetics Research » Research » Publications at this Location » Publication #216167
Title: VitisExpDB: A Database Resource for Grape Functional Genomics

Author
item DODDAPANENI,, HARSHAVARDHAN - UCD
item Lin, Hong
item WALKER, M. ANDREW - UCD
item YAO, JIQIANG - UCD
item Civerolo, Edwin

Submitted to: BMC Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/24/2008
Publication Date: 2/28/2008
Citation: Doddapaneni,, H., Lin, H., Walker, M., Yao, J., Civerolo, E.L. 2008. vitisExpDB: A database resource for grape functional genomics. Biomed Central (BMC) Plant Biology.8:23doi:10.1186/1471-2229-8-23

Interpretive Summary: VitisExpDB is an online database that carries gene expression data for Vitis vinifera (European Wine grape) and non-vinifera grape varieties such as V. shuttleworthii and V. aestivalis. Currently, the database stores ~320,000 expression gene sequences (ESTs) derived from 8 species/hybrids, their annotation and homologous details. Information such as percent identities, phylogenetic relationships and primers to amplify sets of homologous sequence sets can be retrieved. The database contains probe and expression details for over a dozen microarray experiments. A user-friendly web interface with multiple search indices and result features for efficient data retrieval along with online computational sequence analysis tools have been added. The developed database will be useful in grape genome annotation and gene function identification. VitisExpDB database is available at http://cropdisease.ars.usda.gov/vitis_at/main-page.htm

Technical Abstract: VitisExpDB is an online MySQL-PHP driven relational database that houses annotated EST and gene expression data for Vitis vinifera and non-vinifera grape varieties. Currently, the database stores ~320,000 EST sequences derived from 8 species/hybrids, their annotation details and gene ontology based structured vocabulary. Homologues for each EST in other species and varieties along with information on percent identities, phylogenetic relationships and common primers can be retrieved. The database also hosts information on probe sequence and annotation features of the high density 60-mer gene expression chip consisting of a ~20,000 non-redundant set of ESTs. The database includes 14 processed global microarray expression profile sets. Data from 12 of these expression profile sets have been mapped onto metabolic pathways. A user-friendly web interface with multiple search indices and extensively hyperlinked result features that permit efficient data retrieval has been developed. Several online bioinformatics tools that interact with the database along with other sequence analysis tools have been added. In addition, users can submit their ESTs to the database. The developed database will provide genomic resource to the grape research community for functional analysis of genes and their sequence variation in the collection. VitisExpDB database is available at http://cropdisease.ars.usda.gov/vitis_at/main-page.htm