FIGURE 6 from Whole-genome CpG-resolution DNA Methylation Profiling of HNSCC Reveals Distinct Mechanisms of Carcinogenesis for Fine-scale HPV+ Cancer Subtypes

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Inferred regulatory activity for genomic regions of interest differ between HNSCC subtypes and correlate with pathway scores. A, MIRA profile of CTCF binding sites in the NHEK cell line. Samples are colored by HPV(−), IMU, or KRT. B, Box plot displaying MIRA scores separated by subtype for CTCF binding sites, strong enhancers, and weak enhancers each from the NHEK cell line. C, Correlation between CTCF MIRA scores and gene expression–based keratinization scores with subtype shown by color. D, Box plot of MIRA scores by subtype for JunD, NFκB, and STAT3 binding sites each taken from different cell lines as indicated in the parentheses. E, Correlation between CTCF MIRA scores and JunD MIRA scores denoting subtype by color. Both scatter plots display the Pearson correlation coefficient (R) and corresponding P value. All P values < 0.05 are shown and P values < 0.00625 are considered significant. F, Box plot displaying gene expression values separated by subtype for transcription factors of interest. FDRs < 0.05 are indicated (*, FDR < 0.05; **, FDR < 0.01).

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