Fig. 6.

Variation and trends among DNA motifs enriched with respect to GM6-increased genes (6–48 h). (a) Motif cluster analysis. The 656 motifs significantly enriched in regions upstream of GM6-increased genes (6–48 h, FDR < 0.05) were clustered based upon scores assigned to each position weight matrix (PWM). Scores were calculated based upon the degree of correspondence between each PWM and a series of short k-mer sequences (yellow-black heatmap). The 656 motifs were divided into groups based upon the cluster analysis, and representative sequence logos for each group are shown below the heatmaps (see color scale). Black-red heatmaps show enrichment scores representing the degree to which each motif resembles those from various TF superfamilies and classes. For each motif, enrichment scores represent log10-transformed p-values derived from the test of whether motifs belonging to a given TF superfamily or class are overrepresented among the set of 300 similar “nearest neighbor” motifs (Fisher’s Exact Test). (b) TF superfamilies most enriched among the 656 motifs. (c) TF classes most enriched among the 656 motifs. (d) TF families most enriched among the 656 motifs