Figure 4

Boxplots of two SNPs, rs41799 and rs6558659, showing discordant changes between DNA modification and gene expression. (A-B) Boxplots were used to demonstrate the difference in copy number (A) or methylation level (B) between the specific SNPs (TT and TG versus GG for rs41799 and GG and GT versus TT for rs6558659). Significance level was determined by a Wilcoxon rank sum test. The Y-axes represent copy number (A) or methylation difference (B). (A) NAMPT, rs41799, was correlated with amplification. (B) MYOM2, rs6558659, was correlated with hypomethylation. (C-D) To evaluate whether the genetic modifications were able to drive downstream gene expression changes, a Wilcoxon ranksum test was performed on the expression difference between tumor and normal tissue for each SNP. (C) NAMPT and (D) MYOM2 both showed significantly differential expression (p-values < 0.05), but in the opposite direction with respect to the corresponding DNA modification. The Y-axis denotes relative expression ratios on a log scale. Dotted lines indicate the unchanging baseline.