Table 2. EMERGE-predicted human heart enhancers are located in interacting chromatin domains as identified by HiC.

HiC datasets (cell lines)	# of intergenic HiC peaks	Area Under the Curve
GM12878	11 803	0.70
HeLa	4003	0.76
HMEC	7211	0.74
HUVEC	5004	0.76
K562	7074	0.73
KBM7	3403	0.77
NHEK	5923	0.71

EMERGE predicted enhancers were overlapped with intergenic HiC peaks. Heart enhancer prediction was done using validated human heart enhancers as true positives (TPs) for training; enhancers active in other tissues than heart were used as TNs. We calculated overlap between the predicted enhancer track and high resolution HiC peaks (Rao et al. .) of various human cell lines. HICCUPS was used to call peaks on the HiC data (as detailed in Rao et al.). All HiC peaks located at transcription start sites (TSS) were removed (−3000 bp +1000 bp of all known UCSC gene promoters (hg19)). To construct ROC curves, the weights of the EMERGE predicted enhancer track were used. HiC peaks were then used as TPs and a matching number of random genomic regions were used as TNs. The Area Under the Curve (AUC) values of these ROC curves are given.