For example, frequently mutated HNSCC genes ERBB2, FGD1, NOTCH1, NR4A2, SEMA3E and ARAP3 had HPV(−) DhMRs in cell morphogenesis, and other head and neck-relevant genes such as CTGF, PKN2, TERT, TGFBR2 and TP63 in signal transduction had DhMRs. Here, SEMA3E is linked to head and neck squamous cell carcinoma.