Figure 8

Normalized affinity scores versus distances from the TSS. (Upper) This plot presents the normalized affinity scores returned from the p53 single-site model versus the distance from the Transcription Start Site (TSS) for 158 experimentally validated p53-binding sites. Low affinity sites exist in a tight band around the TSS (cyan vertical line). p53 activation-sites are plotted in green, repression-sites in red, and both activation and repression in black. All sites ≥ 11 Kb from the TSS have relative affinity scores above the average of ≈ 78 (purple horizontal line). (Lower) This plot presents the estimated normalized affinity scores versus the positive distance (absolute value) from the TSS. Three dynamic acceptance thresholds are shown for scoring for putative p53 binding sites. The blue linear threshold corresponds to the formula .00107·ΔX + 65.16 and has a false negative rate of 18 out of 158 validated p53 sites (11.4%). The orange logarithmic threshold corresponds to the formula 9.6854·log(ΔX + 593.31) - 15.308 and has a false negative rate of 5 out of 158 validated p53 sites (3.2%). Finally, the black square-root threshold corresponds to the formula .23186·sqrt(ΔX + 7.5231) + 45.6 and has a false negative rate of 1 out of 158 validated p53 sites (0.63%). (ΔX = distance from TSS)