Fig 1.
Conceptual description of a transcription factor network.
TFs are represented as green rounded squares, DNA motifs as pink diamonds, gene patterns as orange hexagons, and gene ontology (GO) terms as blue circles. Connections between TFs and motifs, and between motifs and patterns/GO terms are represented by a grey connecting line.
Fig 2.
Design and assembly of the SeqEnrich database.
Information on transcription factors, DNA binding site motifs, and gene functions were collected from publically available sources and integrated into the SeqEnrich program.
Table 1.
IUPAC codes used for representation of nucleotides in motifs and corresponding likelihood of each nucleotide at position.
Fig 3.
Predicted transcription factor networks from the chalazal endosperm of Arabidopsis.
A) Predicted transcriptional module developed from the ChipEnrich program; B) predicted transcriptional module using the SeqEnrich program; C) subset of the transcriptional module produced from the subanalysis function of the SeqEnrich program. A predicted bZIP, bHLH, MYB, and BES transcriptional module controlling biological processes within the mature endosperm of Arabidopsis.
Fig 4.
Predicted transcription factor networks from Brassica napus gene sets.
A) Subset of transcription factor network identified from funiculus vasculature dataset. MYB and MADS-box TFs are predicted to regulate genes associated with transport, metal ion homeostasis, and cell wall modification; B) subset of transcriptional module identified from the SeqEnrich subanalysis function predicted to be operative in seedlings infected with fungal pathogen Leptosphaeria maculans; C) transcriptional module depicted by arrow in (B), showing regulation of genes associated with defense bioprocesses by a family of calmodulin-binding transcriptional activators (CAMTAs).