Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

Open Access Highly Accessed Research article

Gene coexpression clusters and putative regulatory elements underlying seed storage reserve accumulation in Arabidopsis

Fred Y Peng and Randall J Weselake*

Author Affiliations

Agricultural Lipid Biotechnology Program, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada

For all author emails, please log on.

BMC Genomics 2011, 12:286  doi:10.1186/1471-2164-12-286

Published: 2 June 2011

Additional files

Additional File 1:

A list of select genes identified in the subnetwork including the majority of fatty acid biosynthetic genes. Genes without informative annotation such as hypothetical proteins were excluded.

Format: XLS Size: 308KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional File 2:

A list of select genes identified in the subnetwork including those encoding oleosins and seed storage proteins. Genes without informative annotation such as hypothetical proteins were excluded.

Format: XLS Size: 221KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional File 3:

The log2 expression values of genes involved in storage reserve accumulation across the eight seed development stages. Genes involved in seed storage reserve accumulation were adopted from early surveys [17,59], and additional genes implicated in this process were identified through sequence analysis using BLAST [87].

Format: XLS Size: 26KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional File 4:

The 118 high-quality position weight matrices (PWMs) compiled for the analysis. In each matrix the definition line starts with a '>' sign and an identifier (ID), followed by the description including the transcription factor (TF) name. A row represents a position in the motif sequence, and the four columns represent nucleotides A, C, G, T respectively. Each matrix was standardized such that its frequency sum for the four nucleotides at each position (row) is 1.0000. A blank line was added between every two matrices. One matrix (MA17) was excluded from the file via a manual examination due to ambiguous TF description for the matrix existing in JASPAR [78].

Format: TXT Size: 43KB Download file

Open Data

Additional File 5:

Predicted cis-acting promoter motifs for genes involved in seed storage reserve accumulation. The start and end positions of an predicted transcription factor (TF) binding site are relative to the start of each promoter sequence, not to the transcription start site (TSS) of the gene. The numbers +1 and -1 indicate sense and antisense strand, respectively. The score was determined by the transcription factor binding site analysis tool TFBS [76].

Format: XLS Size: 252KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data