Fig. 2

Global DNA methylation profiling of gastric cardiac IM. a Flow chart for filtering pipeline used to generate a set of high-confidence probes. A total of 733,015 finalized probes were generated. b Clustering dendrogram from unsupervised hierarchical clustering based on overall methylation status. This analysis separates samples into two clusters discriminated also by histology classification (Normal and IM). c DNA methylation levels for different genomic locations. Violin plots show DNA methylation on genome-scale (n = 733,015), gene promoters (n = 234,687), intergenic regions (n = 200,913), gene body regions (n = 279,199), and 3′UTRs (n = 18,216). Box plots within each violin plot indicate the interquartile range, and the red horizontal lines denote the median methylation. In all cases, the y-axis represents the methylation level on a 0 to 1 scale (i.e., 0 to 100%)