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Related Experiment Video

Updated: Jun 17, 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

VitisNet: "Omics" integration through grapevine molecular networks.

Jérôme Grimplet¹, Grant R Cramer, Julie A Dickerson

¹Horticulture, Forestry, Landscape, and Parks Department, South Dakota State University, Brookings, South Dakota, USA.

|December 23, 2009

Summary

This summary is machine-generated.

Grapevine molecular networks (VitisNet) were developed to provide biological meaning to vast genomic data. This system integrates gene annotation and omics data for improved systems biology understanding in Vitis vinifera.

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Area of Science:

Plant genomics
Systems biology
Bioinformatics

Background:

Exponential growth in grapevine genomic data necessitates methods for biological interpretation.
Development of Vitis EST, transcriptomic, proteomic, and metabolomic tools is ongoing.
Annotating genes and integrating data into biological context is a critical challenge.

Purpose of the Study:

To develop and validate Grapevine Molecular Networks (VitisNet).
To provide biological meaning to large-scale grapevine genomic data.
To integrate gene annotation with omics data for systems biology.

Main Methods:

Manual annotation of 39,424 unique sequences from Vitis vinifera genome and ESTs.
Assignment of 13,145 genes into 219 molecular networks.
Loading quantitative omics data onto molecular networks for simultaneous visualization.

Main Results:

VitisNet comprises 219 networks, including Metabolic, Genetic Information Processing, Environmental Information Processing, Cellular Processes, Transport, and Transcription Factors.
13,145 genes are assigned to these networks, facilitating functional analysis.
Simultaneous visualization of transcriptome, proteome, and metabolome changes is enabled.

Conclusions:

VitisNet facilitates integration of large datasets and streamlines functional analysis in grapevine systems biology.
The system is based on the Vitis vinifera genome and is updateable.
Molecular network files are accessible via the MetNet Pathway database and downloadable from a dedicated web portal.