Figure 2

Binding site location mirrors TF activity profile. (a) Analysis of the general IRF matrix (V$IFR_Q6_01). Top panel shows profile for the over-respresentation analysis, with red dots indicating significance at 2, 4, and 6 hours post infection (FDR q < 0.05). Bottom panel shows Boxplots of the absolute locations of binding sites in promoter regions of genes first up-regulated at each time-point. The number of genes in each group is indicated above the box. The medians are indicated by horizontal bars. The box at time zero shows a control group of genes, and contains all RefSeq genes with binding sites for the same matrix that are not differentially-expressed. Red bars indicate that the median binding site position is significantly closer to the TSS as compared with the control group (P < 0.05, Mann-Whitney test). When multiple binding sites for a matrix are present for a single gene, the one closest to the TSS is selected. (b) Plots the cumulative distributions of the P-values, testing for differences in binding site locations as described in (a), at the time of minimum enrichment P-value (highest inferred TF activity, solid line) and maximum enrichment P-value (least inferred TF activity, dashed line). We observe a significant shift in the locations distribution (P < 0.0002, Mann-Whitney test) toward the TSS during times of TF activity.