Table 2. Table of top genes containing significant DMRs based on TCGA-HNSC matched tumor and normal tissue methylation profiles.

Rank methods	Top genes*
Genes contain top 100 DMRs (promoter regions)	MARCHF11, ZNF154, ELMO1, ADCYAP1, PIEZO2, CCDC181, KCNA3, OTX2-AS1, PCDHGC4, DPP10-AS1, MIR129–2, ZNF582, WT1, DRD5, CBLN4, DPP6, SORCS3, ZNF135, GALR1, BOLL, ZSCAN18, BARHL2, ZNF577, CLVS2, ABCC9, INSC, GRM6, ZNF781, ZNF529, TBXT, ITGA8, GCSAML, CDO1, ZNF132, IRF8, NKX2–6, ZC4H2, ZSCAN1, NKAPL, NPY, PENK, ZNF85, ADAMTS16, EVX2, NETO1, ZNF583, VAX1, HOXD9, KLHL34, CFTR, PCSK1, ZNF471, ZIK1, SHISA3, SIX6, ZNF665
Genes contain top 100 DMRs (1kb downstream of TSS)	HOXD9, TRH, GRIA4, ZNF542P, PAX6, GSC, NTM, PPFIA3, PABPC5, SFTA3, NID2, HOXA11-AS, ASCL1, MAGI2-AS3, LOC100289656
Genes contain top 100 DMRs (other regions)	EN1, SOX17, LHX1, PANTR1, NXPH1, ZNF136, LINC00461, PAX2, SEPTIN9, VAX1, ZIC4, HOTAIR, UBD, GBX2, ZNF559-ZNF177, NKX2–2, SOX1, SOX11, GSC, LINC01304, LINC01623, PITX2, PCDHA13, RMCX5-GPRASP2
Top genes ranked by number of DMRs (>3 DMRs; No. of DMRs indicated in parentheses; Genes containing top 100 DMRs are highlighted in bold)	ZIC4 (11), ZIC1 (9), EN1(8), SOX1(8), TBX5-AS1(8), SOX17(7), BARHL2(6), ZBED9(6), EVX2(5), HOXB3(5), HOXD10(5), LINC00461(5), OTX2(5), PAX2(5), SOX3(5), VAX1(5), HOTAIR(4), HOXA3(4), HOXC4(4), HOXC6(4), LHX8(4), MIR124–2HG(4), MKI67(4), NXPH1(4), ONECUT2(4), PAX6(6), PAX6-AS1(4), PDX1(4), PITX2(4), PTF1A(4), PTPRN2(4), TBX15(4), TLX1(4), TLX3(4), UBD(4)

^*Full list of DMRs and their locations are listed in Supplementary Table 1.