Fig. 2

Attention matrix of CREaTor implies cCRE-gene interactions. a, b auROC (a) and auPRC (b) of CREaTor outperform its counterparts on cCRE-gene pair classification. Attention (attn., yellow): normalized attention weights (genes to cCREs) in CREaTor. Adjusted attention (adj. attn., red): attention scores/log10 (distance). H3K27ac/dist (blue): approximate of the ABC score. Distance quantifies relative genomic distances between genes and cCREs. H3K27ac value of a cCRE is calculated as the sum of H3K27ac peak values of the element. Labels (positive/negative) of cCRE-gene pairs were collected from 3 independent CRISPR perturbation experiments [13,14,15]. c Attention scores derived from attention weights are significantly correlated with the effect of enhancer on gene expression quantified by Fulco et al. [13]. As the quantification measures the change of target gene expression upon enhancer knock-down using CRISPR perturbation, the quantitative effect values are inversely related to enhancer activities. d, e auPRC (d) and auROC (e) of CREaTor and its counterparts on the classification of cCRE-gene pairs collected from a Pol-II mediated ChIA-PET experiment. The performance is evaluated for each gene and each distance group separately. Groups with < 10 samples were filtered out. Center line, median; box limits, upper and lower quartiles; whiskers, 1.5 × interquartile range; points, outliers. f MYC locus showing predicted and previously reported regulators in K562 cells. For CREaTor (red) and H3K27ac/distance (gray), peaks on the tracks represent the scores of different cCRE regions. Enhancers track (red squares) denotes reported active regulators of MYC. Representative DNase, H3K4me3, H3K27ac, and CTCF tracks, as well as ChIA-PET interactions in K562, are also annotated