Figure 3

Boxplots of two SNPs, rs17150656 and rs2123615, showing significant association with methylation alterations. (A-B) Boxplots were used to demonstrate the difference of methylation level between specific SNPs (AA and AG versus GG for rs17150656 and TT and TG versus GG for rs2123615). Significance level was determined by a Wilcoxon rank sum test. The Y-axis represents methylation differences. (A) MAGI2, rs17150656, was correlated with hypermethylation. (B) HK2, rs2123615, was correlated with hypomethylation. (C-D) To evaluate whether the methylation alterations were able to drive downstream gene expression changes, a Wilcoxon rank sum test was performed on the expression difference between tumor and normal tissue for each SNP. (C) MAGI2 showed significantly differential expression (p-values < 0.05) but (D) HK2 did not. The Y-axis denotes relative expression ratios on a log scale. Dotted lines indicate the unchanging baseline.