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VTCdb: a gene co-expression database for the crop species Vitis vinifera (grapevine)

Darren CJ Wong1, Crystal Sweetman1, Damian P Drew12 and Christopher M Ford1*

Author Affiliations

1 School of Agriculture, Food and Wine, University of Adelaide, Adelaide 5064, South Australia, Australia

2 Department of Plant and Environmental Sciences, Section for Plant Biochemistry, University of Copenhagen, Frederiksberg 1871, Denmark

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BMC Genomics 2013, 14:882  doi:10.1186/1471-2164-14-882

Published: 16 December 2013

Additional files

Additional file 1:

Microarray datasets and associated meta-data used in the construction of the grape co-expression network. A brief description pertaining to the unique accession, title, and number of assays, reference and conditions of microarray datasets from 16 K Affymetrix Genechip and 29 K Nimblegen whole-genome array are listed in Tables S1 and S2, respectively. Figure S1 contains screenshots of the fully expanded VTCdb web interface containing various forms to perform gene co-expression analysis.

Format: DOCX Size: 43KB Download file

Open Data

Additional file 2:

A detailed description of the microarray datasets and associated meta-data used in the construction of the grape co-expression network from 16 K Affymetrix Genechip and 29 K Nimblegen whole-genome array are listed in sheets according to the respective PlexDB ID (for 16 K Affymetrix Genechip array) and GEO/Arrayexpress ID (for 29 K Nimblegen whole-genome array). Experiments that were considered potential outliers were highlighted in red.

Format: XLSX Size: 153KB Download file

Open Data

Additional file 3:

Excel file containing twelve worksheets with a list of co-expressed genes (HRR ≤ 350, P-value < 0.01) for grapevine CEB1 (Table S1), a list of all GO terms enriched associated with CEB1 co-expressed genes (Table S2), a table containing the expression specificity of CEB1 (Table S3), a list of genes and associated information from module All_MCL_6 (Table S4), a list of all GO terms enriched in module All_MCL_6 (Table S5), a table containing the expression specificity of module All_MCL_6 (Table S6), a list containing the significantly connected clusters to module All_MCL_6 (Table S7), screenshots of the utility and output of keyword query using ‘GO:0009698’ as input (Figure S1), a list of genes and associated information from module All_HCCA_181 (Table S8), and a list of all GO terms enriched in module All_HCCA_181 (Table S9), a table containing the expression specificity of module All_HCCA_181 (Table S10), a list containing the significantly connected clusters to module All_HCCA_181 (Table S11).

Format: XLSX Size: 190KB Download file

Open Data