Fig. 4: TF motif order affects enhancer activity.
From: Simultaneous epigenomic profiling and regulatory activity measurement using e2MPRA
a Representative example demonstrating how rearranging motif order (HNF1A, PPARA, REST, and XBP1) affects enhancer epigenetic activity. n = 2 templates × 3 replicates per box plot. b Statistical analysis (one-way ANOVA) with Benjamini–Hochberg correction evaluating whether changes in motif order within each set of four distinct motifs (24 permutations per set) significantly affects epigenetic activities. All 70 unique combinations (selecting 4 TF motifs from 8, 8C4 = 70) were tested. The x-axis represents the difference in activity between the permutation with the highest activity and lowest activity among the 24 permutations tested for each combination. The y-axis indicates the corresponding statistical significance (−log₁₀ adjusted P-value). c Positional enrichment analysis of TF motifs within the top and bottom 200 permutations ranked by transcriptional activity. Statistical significance of enrichment was determined by hypergeometric tests with Benjamini–Hochberg correction (*: adj-P < 5.0e−2; **; adj-P < 1.0e−2; ***:adj-P < 1.0e−3; ****:adj-P < 1.0e−4). Motif positions are numbered from distal (position 1) to proximal (position 4) relative to the minimal promoter. In the box plots, the median is indicated by the black line; the lower and upper bounds of the box represent the first (25th percentile) and third (75th percentile) quartiles, respectively; and the lower and upper whiskers indicate the minimum and maximum values within 1.5× the interquartile range (IQR). Source data are provided as a Source Data file.
