VitisExpDB: a database resource for grape functional genomics.

TitleVitisExpDB: a database resource for grape functional genomics.
Publication TypeJournal Article
Year of Publication2008
AuthorsDoddapaneni, HV, Lin, H, M Walker, A, Yao, J, Civerolo, EL
JournalBMC Plant Biol
Volume8
Pagination23
Date Published2008 Feb 28
ISSN1471-2229
KeywordsComputational Biology, Databases, Genetic, Expressed Sequence Tags, Genomics, Internet, Vitis
Abstract

BACKGROUND: The family Vitaceae consists of many different grape species that grow in a range of climatic conditions. In the past few years, several studies have generated functional genomic information on different Vitis species and cultivars, including the European grape vine, Vitis vinifera. Our goal is to develop a comprehensive web data source for Vitaceae.DESCRIPTION: VitisExpDB is an online MySQL-PHP driven relational database that houses annotated EST and gene expression data for V. vinifera and non-vinifera grape species and varieties. Currently, the database stores approximately 320,000 EST sequences derived from 8 species/hybrids, their annotation (BLAST top match) details and Gene Ontology based structured vocabulary. Putative homologs for each EST in other species and varieties along with information on their percent nucleotide identities, phylogenetic relationship and common primers can be retrieved. The database also includes information on probe sequence and annotation features of the high density 60-mer gene expression chip consisting of approximately 20,000 non-redundant set of ESTs. Finally, 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.CONCLUSION: The developed database provides genomic resource to grape community for functional analysis of genes in the collection and for the grape genome annotation and gene function identification. The VitisExpDB database is available through our website http://cropdisease.ars.usda.gov/vitis_at/main-page.htm.

DOI10.1186/1471-2229-8-23
Alternate JournalBMC Plant Biol.
PubMed ID18307813
PubMed Central IDPMC2359749