Figure 2.

DDM-MDS plot of the TFBS associations found in the E2F dataset. Every dot corresponds to a specific PWM from the TRANSFAC 8.4 Professional Motif library. The parameters for Match were set to 0.9 for core similarity and 0.75 for matrix similarity. Most of the PWMs were mapped around the origin, indicating that they are either common to either dataset or that they participate in random TFBS associations. The color of the dot indicates whether the TFBS participates more in associations found in promoters of up-regulated genes (red) or down-regulated genes (green). Associated with up-regulation (red), we find binding sites for E2F, ZF5, AP-2alpha and AP-2gamma. Associated with down-regulation, we find binding sites for several CEBPs, STATs and HNFs.