Fig. 3

Hypomethylated DMRs associated with HPV infection show CpG island shore loss of boundary and functional correlation with gene expression. a Heatmap showing the top 50 DMRs associated with HPV status (FDR <0.05). b CpG context of the identified DMRs in the different anatomic sites compared with their distribution in the Illumina HumanMethylation 450 K array (HM450). c Correlation between CpG methylation at the SYCP2 DMR and relative gene expression in the HNSCC cases of the TCGA cohort. HPV(+) cases are indicated by full pink dots, HPV(–) cases by empty blue dots. d Co-methylation plots showing the CpGs in SYCP2 DMR ranked by p value and visualized based on their chromosomal coordinates, relative position to CpG island (green bar) and CpG content (red peak). The average methylation values in the DMR in HPV(+) (pink) or HPV(–) (blue) cases are shown. The correlation plot shows Spearman correlation values among the CpGs in the region