Fig. 5
Expression data are predictive of cell-type-specific regulatory interactions. a, b Performance curves for predicting bait–target interactions from CAGE-universal features, split according to CHICAGO score, testing negative-to-positive ratios and target feature type. c Features predictive of bait–target interactions, ordered by average mean decrease accuracy (MDA) across models from 10-fold cross-validation. d, e Loess curves representing feature separation over distance between high (top) and low (bottom) predicted probabilities, shown for features (d) XAD boundary insulation (nbounds, number of XAD boundaries between bins) and (e) enhancer expression at the target (eRNA_targ, mean tags per million across three replicates). f Overlaps of predicted bait–enhancer interactions between GM12878, HeLa-S3 and HepG2 cells. g An example of a loop predicted in HeLa-S3, but not in GM12878 cells, validated by HeLa-S3 RNAPII ChIA-PET interaction data
