Fig. 3: Enrichment of the predicted interactions in chromatin loops.

a, b Overlaps of the predicted PAIs with the chromatin loops identified by a Hi-C from Rao et al.²¹ and b POLR2A ChIA-PET from the ENCODE project²⁴. The red dash lines represent the observed number and histograms represent the distribution of control sets. c enrichment of the predicted interactions in the significant PCHi-C loops defined based on a range of P-value thresholds (P-values were obtained from Jung et al.²⁵). We used the PCHi-C loops identified from Jung et al. in GM12878 cell lines²⁵. PHM: the pairwise hierarchical model developed by Kumasaka et al.¹⁷. The fold enrichment value was computed by a 2 × 2 contingency table and the Fisher’s exact test was used to assess the statistical significance of the enrichment. The error bar around each estimate represents the 95% confidence interval. The horizontal red dashed line indicates no enrichment.