Research Paper

Figure 7. Relationships between WM_Score and genetic and epigenetic alterations. (A, B) Waterfall plot of tumor somatic mutations established by those with high WM_Score (A) and low WM_Score (B). Each column represents individual patients. Upper bar plots show TMB. The numbers on the right indicate mutation frequency in each gene. The right bar plot shows the proportion of each variant type. (C) Difference of TMB between WM_Score high and low groups (Wilcoxon test). (D) Correlation between WM_Score and TMB (R = -0.46, p < 2.2e-16, Pearson’s Correlation test). (E) Kaplan–Meier curves showing the overall survival status of WM_Score high and low patients with low or high TMB. H, high; L, low. P = 0.02 by Log-rank test. (F, G) Distribution of copy number amplification and deletion sites in the WM_Score high group (F) and WM_Score low group (G). The Abscissa axis represents the location of CNV on the chromosome. The ordinate axis represents the G-score. Amplifications are marked with red, and deletions with blue. (H) CNV frequency in WM_Score high and low groups (p = 0.006, Wilcoxon test). (I) Box plot showing the expression of genes with significant differences in CNVs between the two groups. (J) WM_Scores according to DNA methylation subtypes (Kruskal-Wallis test). (K) Kaplan–Meier curve showing the overall survival status of three methylation subtypes of patients in the TCGA-STAD cohort (p = 0.011, Log-rank test). (L) Box plot showing the methylation level of GC survival-related genes (*P < 0.05; **P < 0.01; ***P < 0.001).