Table 3.

Hypermethylated 5′-cytosine-phosphate-guanine-3′ (CpG) sites methylation in HNSCC tissue compared to control healthy tissue and potentially premalignant oral lesions, and in potentially premalignant oral lesions compared to control healthy tissue. The list is merged of top fifteen differentially methylated genes according to the extent of methylation difference value.

Gene Name	Function	cg Position	MMD *	p-Value **
HNSCC Tissue vs. Healthy Tissue
LMBR1L	Probable receptor	cg12348519	0.93	4.59 × 10−8
CDH1	Adhesions, mobility, and proliferation	cg08285862	0.92	3.49 × 10−8
EIF6	Initiation of translation	cg09957666	0.92	1.96 × 10−8
C16orf70	Not known	cg03664901	0.92	3.48 × 10−8
ETNK2	Transferase and kinase activity	cg12142497	0.92	5.33 × 10−8
C11orf73	Cellular response to heat stress	cg23450586	0.91	5.01 × 10−9
ADARB2	RNA editing	cg26569590	0.91	2.10 × 10−8
GAB1	Cellular growth, transformation, and apoptosis	cg23020414	0.91	2.83 × 10−8
ITPR3	Metabolism and growth	cg05876496	0.91	6.35 × 10−8
WDR61	Transcriptional regulation	cg12339790	0.90	4.35 × 10−8
PGAP2	Protein transport	cg01156876	0.90	1.24 × 10−8
DDX10	RNA helicase	cg18585558	0.90	6.14 × 10−9
DGKH	Kinase activity	cg22899750	0.90	1.09 × 10−7
RAB40C	Oncogene	cg01770948	0.89	2.00 × 10−8
BEAN1	Not known	cg19471156	0.89	5.59 × 10−8
HNSCC Tissue vs. Oral Lesions
EIF6	Eukaryotic Translation Initiation Factor 6	cg09957666	0.91	5.68 × 10−10
KANSL1	KAT8 Regulatory NSL Complex Subunit 1	cg07281649	0.91	1.43 × 10−9
DDX10	DEAD–Box Helicase 10	cg18585558	0.89	3.58 × 10−10
AP2A1	Adaptor Related Protein Complex 2 Alpha 1 Subunit	cg08969148	0.89	8.97 × 10−10
RAB40C	RAB40C, Member RAS Oncogene Family	cg01770948	0.89	1.84 × 10−9
GAB1	GRB2 Associated Binding Protein 1	cg23020414	0.88	5.30 × 10−9
ERGIC1	Endoplasmic Reticulum-Golgi Intermediate Compartment 1	cg07769006	0.88	1.25 × 10−9
SNX14	Sorting Nexin 14	cg03776905	0.88	3.20 × 10−9
PIGU	Phosphatidylinositol Glycan Anchor Biosynthesis Class U	cg09450087	0.88	1.22 × 10−10
ARAP1	ArfGAP with RhoGAP Domain, Ankyrin Repeat, and PH Domain 1	cg09010791	0.87	1.56 × 10−9
LMTK2	Lemur Tyrosine Kinase 2	cg05941925	0.87	2.59 × 10−9
BEAN1	Brain Expressed Associated with NEDD4 1	cg19471156	0.87	6.96 × 10−9
AP1S3	Adaptor Related Protein Complex 1 Sigma 3 Subunit	cg25666945	0.87	1.66 × 10−9
CDH1	Cadherin 1	cg08285862	0.87	2.28 × 10−8
RYBP	RING1 and YY1 Binding Protein	cg08086385	0.86	3.11 × 10−10
Oral Lesions vs. Healthy Tissue
GRIP1	Glutamate Receptor Interacting Protein 1	cg09414535	0.68	0.000679
MTMR10	Myotubularin Related Protein 10	cg25430175	0.66	0.000585
RBM47	RNA Binding Motif Protein 47	cg11268702	0.66	0.000636
MPHOSPH9	M–Phase Phosphoprotein 9	cg02132191	0.65	0.001055
FOXK1	Forkhead Box K1	cg16026475	0.64	0.000765
SNX3	Sorting Nexin 3	cg14452952	0.64	0.000825
CIT	Citron Rho-Interacting Serine/Threonine Kinase	cg03601895	0.63	0.000866
ZBTB38	Zinc Finger and BTB Domain Containing 38	cg13318410	0.63	0.001548
DRD3	Dopamine Receptor D3	cg22253817	0.63	0.001115
SPPL3	Signal Peptide Peptidase Like 3	cg11330512	0.63	0.001072
ZNF407	Zinc Finger Protein 407	cg23863184	0.63	0.000942
ADAMTSL1	ADAMTS Like 1	cg12699984	0.62	0.000767
GNAT3	G Protein Subunit Alpha Transducin 3	cg10168361	0.62	0.000936
L3MBTL3	L3MBTL3, Histone Methyl-Lysine Binding Protein	cg22162357	0.62	0.001083
EEPD1	Endonuclease/Exonuclease/Phosphatase Family Domain Containing 1	cg06387870	0.61	0.001083

* Mean difference (MD) across all sites in a region (mean.mean.diff); ** false discovery rate (FDR) adjustment combined p-value (comb.p.adj.fdr).