Fig. 3
Immune cell markers involved in normal proliferation and activation of B-cells, T-cells, and NK cells are hypermethylated in tumor PBMCs. A Text clouds intuitively show the frequency of words enriched in immune-related terms. The color of the text indicates which group is hypermethylated (‘N-hyper’ is expressed as blue, ‘T-hyper’ as purple, ‘B-hyper’ as orange, and ‘C-hyper’ as red). The meaning of the four colors (blue, purple, orange, and red) was applied equally to the following graphs in this figure. B The number of hypermethylated genes included in immune cell type markers is expressed as a percentage (%) of total genes in the corresponding cell type. The number of matched genes is displayed on the top of each bar. The list of marker genes for 11 types of immune cells was downloaded from Panglao DB. C Among genes enriched in significant immune-associated terms, hypermethylated DMGs that reversely correlate with expression are shown. The y-axis of the bar graph on top means log2 fold change of methylation values, and that of the middle one means log2 fold change calculated using TPM values derived from RNA-seq. The y-axis of the bottom one shows the degree of inverse correlation between methylation and expression by Pearson’s correlation. Hypermethylated genes included in Panglao DB and its genomic features are listed in Table S8. D The scatter plots with linear regression (red line) in 4 representative genes among 49 genes listed in (C). The Pearson correlation coefficient, expression (fold-change), and methylation (fold-change) for every immune-related DMGs are also described in Table S9