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. Author manuscript; available in PMC: 2020 Jan 13.
Published in final edited form as: Cell Rep. 2019 Dec 17;29(12):4069–4085.e6. doi: 10.1016/j.celrep.2019.11.077

Figure 5. Differential Promoter DNA Methylation versus Differential Gene Expression.

Figure 5.

(A and D–F) Promoter DNA methylation beta difference is plotted on the x axis, and Log2 fold change for the corresponding gene is plotted on the y axis for MED12mt (n = 7), HMGA2hi (n = 2), HMGA1hi (n = 2), and normal myometrial (n = 4) samples with both methylation and expression results. This analysis is done for all fibroids (A) and for HMGA1hi (D), HMGA2hi (E), and MED12mt (F) versus normal samples. Color represents local dot density. Green-highlighted genes are some of the most highly correlated between promoter hypermethylation and reduced expression. Pink-highlighted genes are some of the most highly correlated between promoter hypomethylation and induced expression. The text is sized to account for both probe methylation difference and corresponding gene fold change.

(B) KRT19, an example of a gene likely silenced by DNA methylation, is further visualized as a heatmap of MED12mt (n = 16), HMGA2hi (n = 4), and HMGA1hi (n = 4) fibroids and normal myometria (n = 10), with multiple probes called within the same gene.

(C) Dotplot (probe methylation is plotted as the x axis and related gene expression as the y axis) of KLF4, showing that downregulation of gene expression is observed in all fibroid subtypes compared with normal myometria.