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Related Experiment Video

Updated: Jul 7, 2026

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

VitisExpDB: a database resource for grape functional genomics.

Harshavardhan Doddapaneni¹, Hong Lin, M Andrew Walker

¹USDA-ARS, San Joaquin Valley Agricultural Science Center, 9611 So. Riverbend Ave, Parlier, CA 93648, USA. harsha@fresno.ars.usda.gov <harsha@fresno.ars.usda.gov>

BMC Plant Biology

|March 1, 2008

Summary

This summary is machine-generated.

VitisExpDB is a new online database offering genomic resources for Vitaceae family species. This comprehensive resource aids in grape gene functional analysis and genome annotation.

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Area of Science:

Genomics
Bioinformatics
Plant Science

Background:

The Vitaceae family encompasses diverse grape species adapted to various climates.
Recent advancements have yielded functional genomic data for multiple Vitis species, including Vitis vinifera.
A need exists for a centralized, comprehensive data source for Vitaceae genomics.

Purpose of the Study:

To develop a comprehensive web-based data resource for the Vitaceae family.
To integrate and provide access to expressed sequence tag (EST) and gene expression data for various grape species.

Main Methods:

Developed VitisExpDB, a MySQL-PHP relational database.
Housed approximately 320,000 annotated EST sequences from 8 Vitis species/hybrids.
Incorporated gene expression data, including 14 processed microarray profiles and a gene expression chip dataset.
Implemented a user-friendly web interface with bioinformatics tools for data retrieval and analysis.

Main Results:

The database contains annotated ESTs, gene expression profiles, and homology information across Vitis species.
Includes data on probe sequences, gene annotation, and phylogenetic relationships.
Features include metabolic pathway mapping for expression data and user submission capabilities.

Conclusions:

VitisExpDB serves as a valuable genomic resource for the grape research community.
Facilitates functional gene analysis, grape genome annotation, and gene function identification.
The database is accessible online at http://cropdisease.ars.usda.gov/vitis_at/main-page.htm.