Fig. 4

Comparison of the performance of different methods for predicting E–P links using ChIA-PET and eQTL data as external validation. The y-axis shows the total number of predicted E–P links. The x-axis shows the percentage supported by the external source. a Pol-II ChIA-PET. b YY1 HiChIP. c GTEX eQTLs. In c the y-axis shows the total number of predicted E–P links where the promoter is annotated with a known gene. FOCS (green triangle) makes more predictions and also manifests the highest support rate by all methods: RNPII ChIA-PET, 59%; YY1 HiChIP, 37%; and eQTL, 38%. For all methods, the empirical p value by random permutation test was < 0.01 (“Methods”)