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VitisExpDB: A database resource for grape functional genomics

Harshavardhan Doddapaneni12, Hong Lin1*, M Andrew Walker2, Jiqiang Yao3 and Edwin L Civerolo1

Author Affiliations

1 USDA-ARS. San Joaquin Valley Agricultural Science Center, 9611 So. Riverbend Ave. Parlier, CA 93648, USA

2 University of California Davis, Department of Viticulture and Enology, Davis, CA 95616, USA

3 Citrus Research Board, 323 W. Oak, P.O. Box 230, Visalia, CA 93279, USA

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BMC Plant Biology 2008, 8:23  doi:10.1186/1471-2229-8-23

Published: 28 February 2008

Additional files

Additional file 1:

Genetic-background of the ESTs curated. Document with details of the genetic background of the grape vines from which ESTs were generated.

Format: DOC Size: 28KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 2:

Example result pages of a Microarray database query. (A) Screenshot of a truncated page displaying annotation (BLAST top match description) search results for query term "thaumatin". (B) View of a page displaying the FASTA sequences and cultivar details. Further information to an external link to the NCBI's GenBank is provided. (C) View of a page displaying the results of the expression profile in the form of a graph which is generated dynamically, displaying the stage, expression value and the percentage of expression across the 12 data points. Values in the while boxes are fold-change differences for treatment over controls. Percentages given at the top of the bars were calculated by dividing the fold change value for that stage over the fold change across all the 12 stages. (D) View of a page displaying the microarray probe information.

Format: JPEG Size: 1.2MB Download file

Open Data

Additional file 3:

Example result pages of an EST database query. (A) Screenshot of a truncated page displaying BLAST search results for query term "mitochondria". BLAST matches with a E-value of greater than 1e-6 have been described as "Weakly similar" and less than that as "similar to" (B) Hyperlinked Gene Ontology terms and Enzyme details (C) Description of the related GO terms with hyperlink to the Gen Ontology tree view page for that term at AmiGO database (D) Tree view image of the GO term "GO:0003954".

Format: JPEG Size: 992KB Download file

Open Data

Additional file 4:

Example of result pages of putative homologs. (A) View of a page showing the combinations of varieties in the first column and the number of genes for that combination in column two; (B) Putative homologs gene sets in that comparison type, with one set per row in the first column; (C) Percent identity for that putative homologs set; (D) Unrooted neighbor-joining phylogenetic tree constructed using Phylip program with default settings showing their relationship; (E) Truncated list of common primers for that set; and (F) Truncated DNA sequences in FASTA format.

Format: JPEG Size: 756KB Download file

Open Data

Additional file 5:

Description of the bioinformatics tools. File has brief description of the usage of bioinformatics tools available.

Format: DOC Size: 30KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 6:

Screen shot of the online tools and the subsequent result pages. (A) BLAST web interface (B) CLUSTALW web interface (C) results page of the CLUSTALW search with links to the subsequent data files. Users can save these files on to their local hard drives for further analysis and interpretation. (D) TRF web interface (E) summary result page of the tandem repeats search with links to the result pages.

Format: JPEG Size: 985KB Download file

Open Data