Figure 3

Normalized fold-change between ChIP-seq peak heights and peak shape analysis by functional PCA techniques show differences in binding behaviour. (A) Left panels for SVP: heat map of 521 TF binding sites for SVP:GFP in FLC WT for regions ±750 bp around the peak summits (the binding regions were sorted according to their maximum median value), and heat map for SVP:GFP binding intensity in flc-3 mutant. Regions and ordering are the same in both heat maps. Right panels for FLC: heat map of the 315 TF binding sites for FLC binding in SVP WT for regions of ±750 bp around the peak summits and heat map for FLC binding in svp-41 mutant. Regions and ordering are the same in both heat maps. Summary images above the heat maps plot the median profiles for each experiment. Values below the heat map indicate significant differentially occurring binding events (adjusted P ≤ 0.05) detected by comparison between the paired panels. (B) FLC and SVP ChIP-seq datasets used for analysis. Labels: 1TF, peaks enriched exclusively when only one TF is present; 2TF, peaks enriched exclusively when both TFs are present; UB, (ubiquitous) peaks enriched in both conditions. (C) Scatter-plot of the normalized peak scores calculated as in Bardet et al. [52] for SVP and FLC ChIP-seq peaks. 2TF (379 and 132 peaks, respectively), UB (144 and 175 peaks, respectively) and 1TF (98 and 244 peaks, respectively). No change in fold-enrichment is represented by the black line.