Supervised differential methylation analysis reveals human papillomavirus-positive (HPV+) signature, showing a skew towards hypermethylation. (A) Histogram of P-values from the supervised analysis a clear trend towards small significant P values. (B) Independence of HPV status and sex: scatter plot of t-statistics of individual CpGs reflecting HPV status (positive t-statistics indicate hypermethylation in HPV-infected samples). wiht P value computed using Wilcoxon rank sum test. (C) Methlyation status according to gene-feature annotation, showing a clear trend towards hypermethylation (P = 0.017). Gene features: TSS1500, TSS200, 5' untranslated region (UTR), first exon, gene body, 3' UTR.