FIGURE 3 from Whole-genome CpG-resolution DNA Methylation Profiling of HNSCC Reveals Distinct Mechanisms of Carcinogenesis for Fine-scale HPV+ Cancer Subtypes

DNA methylation-based gene set enrichment captures gene expression-based pathway-level differences. A, Dotplot for top 40 significant RNA enrichment terms, colored by −log₁₀(P-value) illustrating enrichment results from RNA, DMRs across the whole genome, <5 kb from TSS, exons, and introns. B, Scatter plot for directional RNA and DNA methylation enrichment test results. Right quadrants represent significantly hypermethylated GO terms in IMU; top quadrants represent overexpressed terms in IMU. Red: terms significant with FDR < 0.05 for both methylation and expression. C–F, Specific genes’ visualization from paradigmatic GO terms, top: DNA methylation profile across gene body with 30% gene length flank regions. Gray lines: IMU versus KRT significant DMRs. Orange lines: Significant cis-eQTMs overlapped with DMRs, middle: differential 5hmc peaks in IMU versus KRT, bottom: bar plot for subgroups’ log₂cpm expression value with edgeR FDR values. Color: subgroups.