Comparison of enhancer–promoter pairs with pairs predicted by the activity‐by‐contact model

Published predictions for E–P interactions in K562 cells Fulco et al, 2019) were downloaded from https://osf.io/uhnb4/. Putative enhancer annotations from K562.AllPredictions.txt and K562.PositivePredictions.txt were lifted from hg19 to hg38 genome build and then overlapped with K562 TT‐seq enhancer annotations. 68% of TT‐seq candidate enhancer regions were also tested by the ABC model. Since one of our pairing approaches pairs enhancers to the nearest active gene promoter (within 500 kbp), almost all of the putative enhancers reported in our study pair to at least one promoter. This resulted in a considerable fraction (59%) of putative enhancers which were paired in our study but not paired by the ABC model. Thus, we took only positive E–P pairs reported by the ABC model and compared them to E–P pairs described in our study for the same enhancers.