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Open Access Highly Accessed Research article

Berry skin development in Norton grape: Distinct patterns of transcriptional regulation and flavonoid biosynthesis

Mohammad B Ali14, Susanne Howard1, Shangwu Chen3, Yechun Wang2, Oliver Yu2, Laszlo G Kovacs1 and Wenping Qiu1*

Author Affiliations

1 Center for Grapevine Biotechnology, William H. Darr School of Agriculture, Missouri State University, Mountain Grove, MO 65711, USA

2 The Donald Danforth Plant Science Center, St. Louis, MO 63132, USA

3 College of Food Sciences and Nutritional Engineering, China Agricultural University, Beijing 100083, PR China

4 Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA

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BMC Plant Biology 2011, 11:7  doi:10.1186/1471-2229-11-7

Published: 10 January 2011

Additional files

Additional file 1:

Principal Component Analysis (PCA) of the eighteen set of microarray hybridization data. Six stages (Stage 33 to 38) are denoted by different colors. Filled rectangle, rectangle, and filled circle represent three biological replicates.

Format: PPTX Size: 130KB Download file

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Additional file 2:

Hierarchical cluster analyses of the eighteen sets of data for assessing the quality of the data.

Format: PPTX Size: 123KB Download file

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Additional file 3:

Pearson correlation coefficient analysis of the eighteen set of data in pair-wise.

Format: XLS Size: 28KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 4:

A list of 15,823 probe sets that exhibited significant variations along six stages (at p-value ≤ 0.001). This list of probe sets was generated by conducting ANOVA on error-weighted intensity experiment definitions (EDs). Sequence description: Brief narrative description of gene annotation; Grand average: the average value of each probe set intensity across all factor levels in the ANOVA, and this average was computed after error-weighting; The Pooled Variance: the within mean square for each gene-analysis level item across all factor levels; Group p-value: the probability that the null hypothesis--that expression levels or differential expression ratio levels are not significantly different across factor levels--is not true. A low p-value indicates high confidence that the gene's expression level or ratio level is significantly different across the groups defined in the ANOVA.

Format: XLSX Size: 1.2MB Download file

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Additional file 5:

A list of 3,352 probe sets that exhibited significant variations along six stages (at p-value ≤ 0.001) with a ratio of more than 2. The legends of each column are the same as in Additional file 4. This list of probe sets was determined by conducting error-weighted ANOVA.

Format: XLSX Size: 840KB Download file

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Additional file 6:

Cluster analysis of the transcript abundance of the differentially expressed 2,359 unigenes across six developmental berry skin stages.

Format: XLSX Size: 4MB Download file

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Additional file 7:

GenBank accession number, Genoscope number, TC number, GeneChip ID number, primer sequences, expected size and sequences of amplified DNA fragments of the genes that were analyzed in the berry skin of Norton and Cabernet Sauvignon by the quantitative real-time PCR (qPCR). The qPCR-amplified DNA fragments were sequenced to verify the identity of each amplicon. Correlation coefficient analysis of the transcript levels between qPCR and microarray was also included.

Format: XLSX Size: 44KB Download file

Open Data