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VitisExpDB: A database resource for grape functional genomics

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...

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Autores principales: Doddapaneni, Harshavardhan, Lin, Hong, Walker, M Andrew, Yao, Jiqiang, Civerolo, Edwin L
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2359749/
https://www.ncbi.nlm.nih.gov/pubmed/18307813
http://dx.doi.org/10.1186/1471-2229-8-23
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author Doddapaneni, Harshavardhan
Lin, Hong
Walker, M Andrew
Yao, Jiqiang
Civerolo, Edwin L
author_facet Doddapaneni, Harshavardhan
Lin, Hong
Walker, M Andrew
Yao, Jiqiang
Civerolo, Edwin L
author_sort Doddapaneni, Harshavardhan
collection PubMed
description 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 ~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 ~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 .
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spelling pubmed-23597492008-04-30 VitisExpDB: A database resource for grape functional genomics Doddapaneni, Harshavardhan Lin, Hong Walker, M Andrew Yao, Jiqiang Civerolo, Edwin L BMC Plant Biol Database 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 ~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 ~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 . BioMed Central 2008-02-28 /pmc/articles/PMC2359749/ /pubmed/18307813 http://dx.doi.org/10.1186/1471-2229-8-23 Text en Copyright © 2008 Doddapaneni et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database
Doddapaneni, Harshavardhan
Lin, Hong
Walker, M Andrew
Yao, Jiqiang
Civerolo, Edwin L
VitisExpDB: A database resource for grape functional genomics
title VitisExpDB: A database resource for grape functional genomics
title_full VitisExpDB: A database resource for grape functional genomics
title_fullStr VitisExpDB: A database resource for grape functional genomics
title_full_unstemmed VitisExpDB: A database resource for grape functional genomics
title_short VitisExpDB: A database resource for grape functional genomics
title_sort vitisexpdb: a database resource for grape functional genomics
topic Database
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2359749/
https://www.ncbi.nlm.nih.gov/pubmed/18307813
http://dx.doi.org/10.1186/1471-2229-8-23
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AT yaojiqiang vitisexpdbadatabaseresourceforgrapefunctionalgenomics
AT civeroloedwinl vitisexpdbadatabaseresourceforgrapefunctionalgenomics