Research Paper

Figure 1. The landscape of genetic, epigenetic, and transcriptional alterations of RNA modification “writers” in gastric cancer. (A) Mutational frequency of the 26 RNA modification “writers” in 433 GC patients from the TCGA-STAD cohort. Each column represents individual patients. Upper bar plots show TMB, and numbers on the right indicate the mutational frequency in each “writer”. Right bar plots show the proportion of each variant type. Stacked bar plots below show the fraction of conversions in each sample. (B) Kaplan–Meier curve showing the overall survival status of patients with mutations (red curve) in one or more of the 26 writers or without mutations (blue curve) in the TCGA-STAD cohort. The grouping status of the STAD patients is indicated at the bottom of the chart. P < 0.05 in the Log-rank test was considered statistically significant. (C) CNV variation frequency of the 26 writers in the TCGA-STAD cohort. The height of the column represents the alteration frequency. Red dots represent deletion frequency; blue dots represent amplification frequency. (D) Location of the CNV alterations of RNA modification writers on 23 chromosomes from the TCGA cohort. (E) The methylation level of some writers between normal and gastric cancer tissues. In the box plot, blue represents normal tissues, and red represents cancer tissue. The upper and lower ends of the boxes represent the interquartile ranges of values. Lines in the boxes represent median values. Blue or red dots show outliers. Asterisks above the boxes represent the p-value (*P < 0.05; **P < 0.01; ***P < 0.001). (F) Heatmap of the methylation level of some writers. Methylation levels of these writers increase gradually with the color changes from green to red. (G) Expression levels of the 26 writers were composed of four types of RNA modification between normal and gastric cancer tissues. The description of the box plots is as in (E).