VTCdb: A transcriptomics & co-expression database for the crop species Vitis vinifera (grapevine)

TL;DR

VTCdb is an online database for grapevine gene co-expression, constructed from extensive microarray data, enabling functional inference and visualization to support research in grapevine biology.

Contribution

This work provides the first comprehensive co-expression database for grapevine, integrating diverse datasets and offering interactive tools for functional gene analysis.

Findings

Identified modules involved in photosynthesis, secondary metabolism, and stress responses.

Revealed higher-level organization of gene modules based on biological processes.

Enabled functional annotation and visualization of gene networks in grapevine.

Abstract

Gene co-expression databases in model plants such as Arabidopsis and rice have been extensively developed and utilised for predicting gene function and identifying functional modules for underlying biological processes. However, such tools are less available for non-model plants such as grapevine. We have constructed a gene co-expression database, VTCdb (http://vtcdb.adelaide.edu.au/Home.aspx) that offers an online platform for transcriptional regulatory inference in the cultivated grapevine. Using a condition-independent approach, the grapevine co-expression network was constructed using 352 publicly available microarray datasets from a diverse experimental series, profiling approximately 9000 genes (40% of the predicted grapevine transcriptome). Using correlation rank transformation and graph-clustering, we have identified modules putatively involved in several fundamental biological processes such as photosynthesis, secondary metabolism and stress responses. Inter-module network connections revealed a higher-level organization of function, in which densely connected modules often participated in related biological processes and had similar expression profiles in grapevine. The database enables users to query genes, modules or biological processes of interest. Querying a gene will give a ranked list of co-expressed genes, functional annotations and information on the associated module. Alternatively, browsing modules of interest will retrieve information regarding Gene Ontology and Mapman enriched terms, as well as tissue- and condition-specific patterns of gene expression within the module. Furthermore, the database features interactive network visualisation via CytoscapeWeb. VTCdb should aid researchers in their prioritization of gene candidates for further study towards the understanding of biological processes related to many aspects of grapevine development and metabolism.