Extended Data Fig. 7: DNA methylation displays distinct patterns in UL subclasses.
From: Deficient H2A.Z deposition is associated with genesis of uterine leiomyoma
a, Overall genome-wide DNA methylation in ULs and normal myometrium. Each dot represents a sample. b, Enrichment of hyper- and hypomethylated loci in different tumour subclasses on five chromatin states from normal myometrium. ORs and P values (log_pvalue stands for –log10(P value)) from one-sided Fisher’s exact test implemented in the LOLA R package. c–g, Overall DNA methylation on active (c) and bivalent (d) TSSs, other active chromatin (e), repressed/poised chromatin (f) and other, quiescent, chromatin regions (g). Significance of methylation difference against normals evaluated by ordinary least squares regression: ***P < 0.0001, **P < 0.001, *P < 0.01. Test controlled by global methylation levels. Sample sizes: normal 96, MED12 13, HMGA1 21, HMGA2 28, YEATS4 11, OM 9, FH 6, Unknown 14. Box covers the central two quartiles of the distribution. Median is highlighted. Whiskers extend to the minimum and maximum of the distribution or at most 1.5× IQR from the edge of the box, whichever is closer. Multiple testing correction was not performed. h, Mean sample-wise DNA methylation in ULs and normal myometrium at H2A.Z binding sites derived from pooled normal myometrium tissue samples. Asterisks, box-and-whiskers plots and sample sizes are as in c–g.
