VTCdb

Overview

VTCdb offers an online platform for grapevine transcriptional regulatory inference for the cultivated grapevine. VTCdb provides users to query gene(s), modules or biological processes of interests in several ways.Querying a gene(s) gives a ranked list of co-expressed genes, functional annotations and its associated module. Alternatively, browsing of modules of interests retrieves hierarchical optimized Gene Ontology enrichment and tissue/condition specificity genes within the module along with interactive network visualisation and analysis via CytoscapeWeb.

Platform & updates

17.04.2014>> Empirical Bayes conditional independence grapevine gene network (condition-indepedent or "All") added (Beta). (Click to see example)
01.10.2013>> Major updates: Queries are now made with the VIT_ code of the V1 grapevine annotation. The Condition-independent (All datasets) and -
dependent (Berry and stress) co-expression analysis (guide gene and graph clustering) added. Co-expression stability of co-expressed genes in
various conditions can be examined (Click to see example)
01.09.2013>> 63 new 29K Nimblegen datasets, functional (GO) enrichment analysis and module identication using MCL added
01.07.2013>> Nimblegen Grape Whole-Genome Microarray 29K 090918-MD 418 arrays; 8 experiments
01.06.2013>> Affymetrix GeneChip 16K Vitis vinifera Genome Array 403 arrays; 20 experiments

Note: we are constantly updating and improving VTCdb for better grapevine transcriptional analysis as soon as new data is available. We appreciate any comments and suggestions for current and future releases (Email here).

Reference

For a detailed description on how to use VTCdb, please refer to the accompanying paper here [pdf] or the reference below. If you find this resource useful, please cite reference below.
Wong DCJ, Sweetman C, Drew DP and Ford CM. VTCdb: a gene co-expression database for the crop species Vitis vinifera (grapevine). BMC Genomics 2013, 14:882 (VTCdb tools)

Sweetman C, Wong DCJ, Ford CM and Drew DP. Transcriptome analysis at four developmental stages of grape berry (Vitis vinifera cv. Shiraz) provides insights into regulated and coordinated gene expression. BMC Genomics 2012, 13:691 (Additional tools: RNA-SeqQuery for grapevine berry development)

Bulk download

Compendium	Features
Compendium	Condition	No. of arrays/ experiments	No. of probesets*	Co-expression measure	Platform	Notes
2.1	All	480(451)/(9)	45000	HRR, MR, PCC, ELMM	GPL13936 GPL1320	Condition-independent (All datasets) co-expression analysis for both 29K Grape Whole-genome and 16K Affymetrix microarray.
	Berry	305	28811	HRR, MR, PCC	GPL13936	Condition-dependent (Berry datasets) co-expression analysis using berry-related samples.
	Stress	59	28811	HRR, MR, PCC	GPL13936	Condition-dependent (Stress datasets) co-expression analysis using stress-related/associated samples
1.0	16K Affymetrix	403(451)/(20)	16000	HRR, PCC	GPL1320	Greater variety of stress conditions (abiotic, biotic, chemical, hormone). Limited transcriptome coverage (~33%)

Searches may take up to 2-3 minutes, thanks for your patience...

CoexQuery
To search for genes co-expressed with your gene(s) of interests,
(i) input the unique gene identifiers for your gene [i.e. VIT_16s0100g00290, VIT_12s0028g03100(V1 grapevine annotation) or 1616094_at(Affymetrix)]

(ii) Select predefined datasets
All arrays (Condition-independent)
Berry (Various developmental series; condition-dependent)
Stress (Biotic, abiotic, etc; condition-dependent)

(iii) Select co-expression measure

Notes:
The 'HRR' method is the preferred co-expression measure.
Highest reciprocal rank (HRR): Highest reciproral PCC rank from gene A to gene B and that of gene B to gene A.
Mutual rank (MR): Geometric average of the PCC rank from gene A to gene B and that of gene B to gene A.
Empirical Light Mutual Min (ELMM): Empirical Bayes conditional dependence (with heurestic relaxation) between gene A to gene B and that of gene B to A. (See Mahdi et al. (2012))

Searches may take up to 2-3 minutes, thanks for your patience..

MultiQuery
To search for genes co-expressed with your genes of interests,
(i) input the unique probeset identifiers for your gene (i.e. CHR12_JGVV28_87_T01) individually into the box and
(ii) choose a preferred co-expression measure (MR or HRR)

Probeset ID Select cut-off Select preferred coexpression measure

Notes:
Examples given are probeIDs corresponding to Flavonone- 3-hydroxylase, Leucoanthocyanidin dioxgenase, MYBPA1 protein, Chalcone synthase and Chalcone-flavanone isomerase, in respective order (involved in Flavonoid biosynthesis and regulation).
Up to 5 probeset IDs can be searched at one time.
Please input NA in blank input boxes (Do not leave blank).
Highest reciprocal rank (HRR): Highest reciproral PCC rank from gene A to gene B and that of gene B to gene A.

Searches may take up to 2-3 minutes (or longer depending on the internet connection speed), thanks for your patience...

Keyword Query
(i) To search for your term or description(s) of interests,
Input the term of interests (e.g. VIT_02s0012g00570,APRR2,GO:0015979,Photosynthesis) for keyword query;
GO ID/description (e.g. GO:0009813 or flavonoid) for enriched term (guide-gene subnetwork & module) query.

(ii) Select query of interests
keyword
Enriched term (Guide-gene / module subnetwork)

Notes:

Keyword query performs a broad term (google-like) search across the entire fields of gene annotation (keyword radio-button) including gene identifiers, symbols, functional annotation an associated ontology/pathway terms and returns associated genes, information and links to proceed for further downstream analysis such as CoexQuery and ModuleQuery.
Choosing the 'Enriched term' searches enriched GO ID/descriptions (if present) within subnetworks of guide-genes and module.
Due to the heavy computational demand of these searches, queries can be time consuming when searching for general GO ID/descriptions of interests.
The form returns a list of query (guide) genes having the respective input terms (ID or description) enriched within the the guide' gene sub-network with a neighbourhood distance of 1.

Browse the inter-module co-expression network directly below. Nodes presents modules while edges represents inter-module connectivity between modules. Purple, Blue, Red, Yellow, Cyan, Green -colored modules represent meta-networks of Berry_HRR_MCL, All_HRR_MCL, Stress_HRR_MCL, All_HRR_HCCA, Stress_HRR_HCCA, Berry_HRR_HCCA, respectively.Right-click to select meta-network of interest (i.e. All_HRR_HCCA).
Upon selection, click selected node (module) or edges to preview enriched GO BP terms and connectivity score (P<0.01) between modules, respectively. Double-click node to go to module page for additional information (e.g. list of gene belonging in module, visualisation of intra-module network, detailed information on enriched terms and expression specificity inferred from the module.