Extended Data Fig. 4: Orientation dependence in the HiDRA dataset.
From: Transcription imparts architecture, function and logic to enhancer units
a, Comparison of forward vs reverse cloning orientation for HiDRA fragments overlapping GM12878 DHS peaks. Data points are shown as log2 fold-change of RNA vs DNA read counts. Elements with significantly elevated activity in both orientations are called orientation-independent enhancers (green). Elements with significantly elevated activity in one orientation are called orientation-dependent (black). Remaining fragments are called inactive (gray). b-c, Percent of orientation-dependent (b) or -independent (c) fragments within each GRO-cap and ChromHMM class. Raw fragment counts are shown above each bar. Gray line marks the percent activity of all fragments judged by the same criteria. P-values are from two-sided Fisher’s exact test between indicated ratio and total enhancer ratio (372/4,367 for b, 41/767 for c). Error bars indicate standard error calculated for a sample of binary trials, centered on the observed probability.
