Fig. 2: Gained and lost enhancers contribute to aberrant gene expression.

a Normalized H3K27ac peak enrichment in (upper panel) and expression (lower panel) of differential enhancer (G1–G6)-associated genes in Nor (n = 10), EC (n = 10), and LNC (n = 8) samples. The P values for all comparisons were <0.001, as calculated by the Kruskal–Wallis rank-sum test. Boxes correspond to interquartile ranges (IQR), thick black lines indicate the median values, and the whiskers extend to the lowest or highest data point that are still within 0.5 IQR of the bottom or top quartile, respectively. b Numbers of upregulated and downregulated genes (EC vs. Nor or LNC vs. Nor) linked to differential enhancers (G1–G6). c The expression fold changes (EC/Nor or LNC/Nor) in differential enhancer (G1–G6)-associated genes. P value was calculated by the two-sided Wilcoxon test (no adjustments). d The expression fold change (EC/Nor, LNC/Nor, or LNC/EC) in all differential enhancer-associated genes (EC vs. Nor, LNC vs. Nor, or LNC vs. EC) from Nor (n = 10), EC (n = 10), and LNC (n = 8) samples. P value was calculated by the two-sided Wilcoxon test (no adjustments). *P < 10e-10, **P < 10e-20, ***P < 10e-30. e The expression fold changes in genes associated with the indicated number of gained (red) and lost enhancers (gray) are presented. P value was calculated by the two-sided Wilcoxon test (no adjustments). Upper panel: *P < 10e-8, **P < 10e-14, ***P < 10e-18. Lower panel: *P < 10e-3, **P < 10e-10, ***P < 10e-20. c–e, Data points represent means of Nor (n = 10), EC (n = 10), and LNC (n = 8) samples. Boxes correspond to interquartile ranges (IQR), thick black lines indicate the median values, and the whiskers extend to the lowest or highest data point that are still within 1.5 IQR of the bottom or top quartile, respectively. Source data are provided as a Source Data file.