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We identified gene coexpression networks in the transcriptome of developing Arabidopsis
(Arabidopsis thaliana) seeds from the globular to mature embryo stages by analyzing publicly accessible
microarray datasets. Genes encoding the known enzymes in the fatty acid biosynthesis
pathway were found in one coexpression subnetwork (or cluster), while genes encoding
oleosins and seed storage proteins were identified in another subnetwork with a distinct
expression profile. In the triacylglycerol assembly pathway, only the genes encoding
diacylglycerol acyltransferase 1 (DGAT1) and a putative cytosolic "type 3" DGAT exhibited
a similar expression pattern with genes encoding oleosins. We also detected a large
number of putative cis-acting regulatory elements in the promoter regions of these genes, and promoter motifs
for LEC1 (LEAFY COTYLEDON 1), DOF (DNA-binding-with-One-Finger), GATA, and MYB transcription
factors (TF), as well as SORLIP5 (Sequences Over-Represented in Light-Induced Promoters
5), are overrepresented in the promoter regions of fatty acid biosynthetic genes.
The conserved CCAAT motifs for B3-domain TFs and binding sites for bZIP (basic-leucine
zipper) TFs are enriched in the promoters of genes encoding oleosins and seed storage
proteins.
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