Fig. 4

Evaluation of supervised learning methods for predicting cCRE-gene pairs. a PR curves for three supervised methods evaluated using RNAPII ChIA-PET pairs in GM12878: PEP-motif (green) and two versions of TargetFinder (full model in darker blue and core model in lighter blue). For comparison, two unsupervised methods presented in Fig. 3 (the distance (gray) and average-rank (black) methods) are also shown along with the AUPR for a random method (dashed line at 0.15). The AUPRs for the methods are listed in the legend. b AUPRs for the three supervised methods, two unsupervised methods, and a random approach, colored as in a, for each of the six BENGI datasets from LCLs. c Scatter plot of AUPRs for TargetFinder (triangles) and PEP-motif (circles) across the BENGI datasets evaluated using 12-fold random CV (X-axis) vs. chromosome-based CV (Y-axis). The diagonal dashed line indicates X = Y. d Schematic diagram for the full and core4 TargetFinder models