The active enhancer sets of HeLa-S3, GM12878 and K562 cells were then centered on proximal (within 200bp) P300 (Stanford, Snyder) ENCODE binding site peaks (joint P300 and GATA1 (Yale) peaks for K562) to derive center positions. FANTOM5 CAGE data from the same ENCODE cell lines (pooled triplicates) were then overlaid these centered enhancer regions and the absence (0) and presence (1) of (one or more) CAGE tag 5’ ends in 10bp non-overlapping windows were determined and an average profile was calculated to assess the average bidirectional pattern of transcription at chromatin-derived enhancers.
