Extended Data Fig. 3: Investigating components of the ABC score.
From: Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations
a, Precision-recall curves for classifying regulatory DE-G pairs, comparing each of the components of the ABC score. b, Scatterplot of Activity and Contact frequency for each tested DE-G pair. KR-normalized Hi-C contact frequencies are scaled for each gene so that the maximum score of an off-diagonal bin is 100 (see Methods). c, Precision-recall curves comparing different measures of Activity. ActivityFeature1,Feature2 = sqrt(Feature1 RPM x Feature2 RPM). (ABC score corresponds to ActivityDHS,H3K27ac x Contact). d, Precision-recall curves for the ABC model using H3K27ac HiChIP. ABCDHS x H3K27ac Hi-ChIP corresponds to a predictive model whose score is proportional to the DHS signal at the candidate element multiplied by the H3K27ac Hi-ChIP signal between the element and gene promoter (see Supplementary Methods). ABCH3K27ac Hi-ChIP is the same as above but only uses the existence of the DHS peak as opposed to the quantitative signal in the DHS peak. H3K27ac HiChIP HiCCUPS Loops is the HiCCUPS loop calls derived from the H3K27ac HiChIP experiment (see Supplementary Methods). ABC corresponds to ABCsqrt(DHS x H3K27ac) x Hi-C. These results suggest that the ABC score computed using H3K27ac HiChIP data is an effective predictor of regulatory enhancer-gene connections.
