Signature based on molecular subtypes of deoxyribonucleic acid methylation predicts overall survival in gastric cancer

Figure 1 Flow chart of the study. GC: Gastric cancer; LASSO: Least absolute shrinkage and selector operation; GO: Gene ontology; KEGG: Kyoto encyclopedia of genes and genomes.

Figure 2 Cluster analysis for Deoxyribonucleic acid methylation classification and the corresponding heatmap. A: Delta area curve obtained from unsupervised clustering using 1061 Deoxyribonucleic acid methylation sites, which indicates the relative change in the area under the CDF curve for each category number k compared with k-1; B: Heatmap corresponding to the 1061 Deoxyribonucleic acid methylation sites in three clusters.

Figure 3 Survival curves of deoxyribonucleic acid methylation subtypes and comparison of TNM stage, grade, and age between clusters. A: Survival curves of deoxyribonucleic acid (DNA) methylation subtypes in the training set; B: The size and extent of the main tumor; C: Lymph nodes invasion; D: Metastasis; E: TNM stage score; F: Age distributions for each DNA methylation subtype in the training set. The horizontal axis indicates the DNA methylation clusters.

Figure 4 Gene annotations of 1061 methylated sites. A: Cluster analysis heatmap for annotated genes associated with the 1061 CpG sites; B: Gene ontology enrichment analysis of the annotated genes.

Figure 5 Differential analysis of CpG sites for each deoxyribonucleic acid methylation subtype. A: The red and blue bars represent hypermethylated CpG sites and hypomethylated CpG sites, respectively (FDR < 0.05 and |log2 (fold change [FC])| > 1). The vertical bar to the left of the heatmap indicates the significance of methylation sites in each cluster, with the red and blue bars representing significance and insignificance, respectively; B: Heatmap for the annotated genes of specific sites among three Deoxyribonucleic acid methylation clusters; C: Kyoto encyclopedia of genes and genomes pathway enrichment analysis of the specific methylation sites; D: Crosstalk analysis of the enriched Kyoto encyclopedia of genes and genomes pathways shown in the enrichment map.

Figure 6 Selection of the prognostic methylation sites for gastric cancer patients by least absolute shrinkage and selection operator analysis. A: The changing trajectory of each independent variable. The horizontal axis represents the log value of the independent variable lambda and the vertical axis represents the coefficient of the independent variable; B: Confidence intervals for each lambda. The optimal values of the penalty parameter lambda were determined by ten-fold cross-validation.

Figure 7 Survival analysis and risk score distribution of the prognostic model for the training and test sets. A and E: K-M curves of the prognostic model in the training set and test set, respectively; B-D: The risk score distribution and heatmap of the methylation site profiles in the training set; F-H: The risk score distribution and heatmap of the methylation site profiles in the test set.