Fig. 5: Epipolymorphism, methylation and gene expression.
From: Evidence of DNA methylation heterogeneity and epipolymorphism in kidney cancer tissue samples
Adjusted R2 for a linear model to predict gene expression based on methylation alone versus methylation and epipolymorphism for genes which had a statistically significant improvement in the R2. Results are shown separately for e-loci with significantly higher epipolymorphism in ccRCC (A) and e-loci with significantly higher epipolymorphism in normal kidney (B). SLC16A3 is the gene with the highest adjusted R2 and is an outlier, therefore it was explored more in detail in (C–E). Methylation levels along the promoter region of the SLC16A3 gene (C). Heatmap demonstrating epipolymorphism in each e-locus in the promoter region of SLC16A3, in ccRCC and normal kidney tissue (D). Scatterplot of gene expression versus epipolymorphism and average methylation in a 3D scale (E). Epipolymorphism and average methylation are higher for normal kidney than ccRCC, and there is associated reduced expression in normal kidney. In ccRCC, there is global hypomethylation, whereas in normal kidney there is evidence of disordered methylation (hypermethylation and hypomethylation of adjacent CpGs).
