We used published8 results on a massively parallel reporter assay measuring the activity of ENCODE-predicted enhancers in HepG2 and K562 cells. All results on non-scrambled sequences were considered, regardless of the level of conservation. 198 out of 738 tested K562 enhancers and 307 out of 1136 tested HepG2 enhancers had significant enhancer reporter activity (as determined by the original publication). We determined the expression in 401bp windows centered on mid points of ENCODE-predicted enhancers using FANTOM5 CAGE from the same cell lines. We further calculated the false discovery rate after a minimum expression threshold in the interval [0,0.5] TPM, as the fraction of non-significant enhancers among those fulfilling the expression cutoff.
