Research Paper Volume 15, Issue 12 pp 5445—5481

Figure 6. Relevance between WM_Score, biological characteristics, and clinical features. (A) Relative enrichment of stromal-related, immune-related and tumor-related pathways of four RNA modification patterns. Pathway names are listed below. (B) Relative protein enrichment levels of biological pathways. In (A, B), the color of the WM_Score-low group is blue, WM_Score-high group is red. The upper and lower ends of the boxes represent interquartile ranges of values. Lines in the boxes represent median values. Blue and red dots are outliers. Asterisks above the boxes represent the p-value (*P < 0.05; **P < 0.01; ***P < 0.001). (C) Correlation between WM_Score and known biological pathway gene signatures using Spearman analysis. A negative correlation is shown in blue; a positive correlation is in red. (D) Spearman correlation analysis between WM_Score and stromal score (R = 0.77, p < 2.2e-16). (E) Spearman correlation analysis between each ratio of stemness index to tumor purity and each RNA modification writers. Negative correlation: blue; positive correlation: red. (F) Differences in stemness indices between WM_Score high and low groups (*P < 0.05; **P < 0.01; ***P < 0.001). (G) Gene dendrogram of the identified co-expressed genes in different modules. Branches of the dendrogram correspond to the different gene modules. Each leaf on the dendrogram represents a gene. Each block marked by a color represents a module that contains a group of highly correlated genes. A total of four dynamic modules and three merged modules were identified. (H) Correlation between gene modules and clinical traits. The correlation coefficient and corresponding p-value are annotated in the blocks of the module-trait relationships map. Positive correlation: red; negative correlation: blue. (I) Different WM_Scores between ACRG molecular subtypes. (J) Different WM_Scores between Lauren subtypes. (K) WM_Scores according to the clinical stages of patients in the meta-GEO cohort. (L) Different WM_Scores in different TCGA-STAD molecular subtypes. (M) Different WM_Scores amongst different MSI statuses of patients in the TCGA-STAD cohort. (N) Different WM_Scores amongst patients with or without EBV infection in the TCGA-STAD cohort. In (I–N) Upper and lower ends of the boxes represent interquartile ranges. Lines in the boxes represent median values. Kruskal-Wallis tests were used to compare significant differences between each group.