Overlap between predicted TFBSs.

<p>(A) Venn diagrams showing the overlap between the ChIP predicted by the PWM model(blue) and PIM (red). (B) Difference (one minus the proportion of shared binding sites) between the best binding sites predicted by the PIM and PWM model on ChIPseq peaks (light red), and the same quantity when including the next best predicted binding sites on each peak (dark red). In several cases (<i>e.g.</i> Fosl1, Max, N-Myc, Srf, STAT3, Usf1), the difference between predicted binding sites is much smaller when the two best binding sites are considered, indicating that the PIM and the PWM model rank differently the two best binding sites in ChIP peaks with multiple bound sites.