Please use this identifier to cite or link to this item: http://hdl.handle.net/2440/83121
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Type: Journal article
Title: VTCdb: a gene co-expression database for the crop species Vitis vinifera (grapevine)
Author: Wong, D.
Sweetman, C.
Drew, D.
Ford, C.
Citation: BMC Genomics, 2013; 14(1):1-17
Publisher: BioMed Central Ltd.
Issue Date: 2013
ISSN: 1471-2164
1471-2164
Statement of
Responsibility: 
Darren CJ Wong, Crystal Sweetman, Damian P Drew, and Christopher M Ford
Abstract: BACKGROUND Gene expression datasets in model plants such as Arabidopsis have contributed to our understanding of gene function and how a single underlying biological process can be governed by a diverse network of genes. The accumulation of publicly available microarray data encompassing a wide range of biological and environmental conditions has enabled the development of additional capabilities including gene co-expression analysis (GCA). GCA is based on the understanding that genes encoding proteins involved in similar and/or related biological processes may exhibit comparable expression patterns over a range of experimental conditions, developmental stages and tissues. We present an open access database for the investigation of gene co-expression networks within the cultivated grapevine, Vitis vinifera. DESCRIPTION The new gene co-expression database, VTCdb (http://vtcdb.adelaide.edu.au/Home.aspx webcite), offers an online platform for transcriptional regulatory inference in the cultivated grapevine. Using condition-independent and condition-dependent approaches, grapevine co-expression networks were constructed using the latest publicly available microarray datasets from diverse experimental series, utilising the Affymetrix Vitis vinifera GeneChip (16 K) and the NimbleGen Grape Whole-genome microarray chip (29 K), thus making it possible to profile approximately 29,000 genes (95% of the predicted grapevine transcriptome). Applications available with the online platform include the use of gene names, probesets, modules or biological processes to query the co-expression networks, with the option to choose between Affymetrix or Nimblegen datasets and between multiple co-expression measures. Alternatively, the user can browse existing network modules using interactive network visualisation and analysis via CytoscapeWeb. To demonstrate the utility of the database, we present examples from three fundamental biological processes (berry development, photosynthesis and flavonoid biosynthesis) whereby the recovered sub-networks reconfirm established plant gene functions and also identify novel associations. CONCLUSIONS Together, we present valuable insights into grapevine transcriptional regulation by developing network models applicable to researchers in their prioritisation of gene candidates, for on-going study of biological processes related to grapevine development, metabolism and stress responses.
Keywords: Vitis; Computational Biology; Genomics; Gene Expression Regulation, Plant; Internet; User-Computer Interface; Databases, Genetic; Gene Regulatory Networks; Molecular Sequence Annotation
Rights: © 2013 Wong et al.; licensee BioMed Central Ltd. 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.
RMID: 0020136404
DOI: 10.1186/1471-2164-14-882
Appears in Collections:Agriculture, Food and Wine publications

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