Figure 4

Linear regression of various prediction methods and relative binding affinity. In each panel, the highest score obtained from the EMSA probe was compared to relative binding affinity (fraction bound) calculated from the EMSA in Figure 2. Probes with more than one predicted site (Spk3 -1044 and Nkx2.2 -1503) were excluded. Scores from probes that were not bound in the EMSA (Gcg -1080, Nkx6.2 +1669, and Ins2 -144) were plotted along the X-axis and not used for r-squared calculation. Scores used were (A) average e-score from 7 overlapping octamers from PBM-mapping, (B) log-odds from TRANSFAC-PWM, and (C) Seed and Wobble matrix score from PBM-PWM.