Supplementary Material
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. Click here for file   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. Click here for file   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]. Click here for file   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]. Click here for file   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]. Click here for file