Table 4.

Hypomethylated 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
ATXN1	Not known	cg07713291	−0.96	2.97 × 10−9
PPP2R2C	Cell growth	cg05805165	−0.93	1.22 × 10−8
CCR6	Immune regulation	cg05094429	−0.92	1.08 × 10−7
RAB37	Oncogene	cg25267982	−0.92	1.29 × 10−8
DUSP27	Phosphatase activity	cg23713934	−0.91	1.94 × 10−7
ZNF521	Transcription factor	cg21830945	−0.91	7.58 × 10−8
SLC6A17	Transporter	cg12072789	−0.90	7.38 × 10−8
SPIN1	Methylated histone binding	cg13554018	−0.90	1.63 × 10−8
CXCR1	Receptor	cg13519373	−0.90	1.22 × 10−8
SPTBN1	Cell shape	cg06149826	−0.89	6.91 × 10−9
NBAS	Golgi to ER transport	cg27424261	−0.89	5.31 × 10−7
NRG3	Ligand	cg10656958	−0.89	9.45 × 10−8
COL5A1	Forming collagen	cg26087052	−0.89	3.96 × 10−8
CDX1	Transcriptional regulation	cg12473781	−0.89	5.77 × 10−8
BATF3	Transcriptional regulation	cg03219362	−0.89	2.10 × 10−8
HNSCC Tissue vs. Oral Lesions
FAM69A	Family with Sequence Similarity 69 Member A	cg22727960	−0.93	7.05 × 10−11
ATP6V0A1	ATPase H+ Transporting V0 Subunit A1	cg19022525	−0.92	9.01 × 10−11
LBP	Lipopolysaccharide Binding Protein	cg18979491	−0.92	3.02 × 10−10
WDR25	WD Repeat Domain 25	cg24211276	−0.91	6.22 × 10−11
SH3RF3	SH3 Domain Containing Ring Finger 3	cg27294813	−0.91	1.01 × 10−9
NINJ2	Ninjurin 2	cg05534515	−0.91	2.74 × 10−12
RAB37	RAB37, Member RAS Oncogene Family	cg25267982	−0.90	1.17 × 10−9
CXCR1	C-X-C Motif Chemokine Receptor 1	cg13519373	−0.90	1.76 × 10−10
SPTBN	Spectrin Beta, Non–Erythrocytic 1	cg06149826	−0.90	1.54 × 10−10
RHOH	Ras Homolog Family Member H	cg15729055	−0.90	1.90 × 10−9
GRIK5	Glutamate Ionotropic Receptor Kainate Type Subunit 5	cg03100024	−0.90	2.47 × 10−9
KLRD1	Killer Cell Lectin Like Receptor D1	cg05377120	−0.90	6.88 × 10−9
TENM2	Teneurin Transmembrane Protein 2	cg26758826	−0.89	3.56 × 10−11
FAM69A	Family with Sequence Similarity 69 Member A	cg05172999	−0.89	3.14 × 10−10
ITK	IL2 Inducible T Cell Kinase	cg12250498	−0.89	3.46 × 10−10
Oral Lesions vs. Healthy Tissue
PHACTR1	Phosphatase and Actin Regulator 1	cg02381687	−0.80	0.000673
MARCH8	Membrane Associated Ring-CH-Type Finger 8	cg26841425	−0.80	0.000585
PPP1R1B	Protein Phosphatase 1 Regulatory Inhibitor Subunit 1B	cg03104421	−0.79	0.000585
HDAC4	Histone Deacetylase 4	cg21190228	−0.79	0.00057
IL22RA2	Interleukin 22 Receptor Subunit Alpha 2	cg23507945	−0.79	0.001772
CAMKK2	Calcium/Calmodulin Dependent Protein Kinase Kinase 2	cg03391567	−0.78	0.000679
INPP5D	Inositol Polyphosphate-5-Phosphatase D	cg22666015	−0.78	0.000709
CSGALNACT1	Chondroitin Sulfate N–Acetylgalactosaminyltransferase 1	cg24423468	−0.77	0.001266
GTDC1	Glycosyltransferase Like Domain Containing 1	cg19251811	−0.77	0.000676
IGSF3	Immunoglobulin Superfamily Member 3	cg13004173	−0.77	0.000585
HELZ	Helicase with Zinc Finger	cg15015109	−0.76	0.000772
DEFA4	Defensin Alpha 4	cg06617936	−0.76	0.000678
AK5	Adenylate Kinase 5	cg21487631	−0.76	0.000681
LHFPL2	LHFPL Tetraspan Subfamily Member 2	cg20879720	−0.76	0.000981
STK10	Serine/Threonine Kinase 10	cg22406187	−0.76	0.000765

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