Table 1.

List of the frequently altered genes by DNA methylation in HNSCC. N/A: not applicable.

Gene ID	HGNC ID	Function	Methylation Status	References
CDKN2A (p16; p14ARF)	HGNC:1787	cell cycle arrest/apoptosis/senescence	hypermethylated	[5,77,89,98,99,100,101,102,103,104]
MGMT	HGNC:7059	DNA damage repair	hypermethylated	[5,77,89,98,100,101,102,103,104]
DAPK	HGNC:2674	apoptosis	hypermethylated	[5,89,98,100,101,102,103,104]
APC	HGNC:583	cellular adhesion/migration	hypermethylated	[5,77,98,100,101,102]
RASSF1	HGNC:9882	cell cycle arrest/ cytoskeleton organization	hypermethylated	[5,77,89,101,103,104]
CDH1	HGNC:1748	cellular adhesion	hypermethylated	[77,100,102,103,104]
HOXA9	HGNC:5109	cell differentiation	hypermethylated	[91,98,105,106]
MLH1	HGNC:7127	DNA damage repair	hypermethylated	[5,77,101]
CDKN2B (p15)	HGNC:1788	cell cycle arrest	hypermethylated	[5,77,100,101]
TIMP3	HGNC:11822	extracellular matrix degradation	hypermethylated	[89,98,103,104]
ATM	HGNC:795	DNA damage repair	hypermethylated	[5,107]
MINT31	N/A	chromatin remodeling	hypermethylated	[89,98,100]
CALCA	HGNC:1437	cellular metabolism/ inflammatory response	hypermethylated	[99,103,106]
NPY	HGNC:7955	cell proliferation	hypermethylated	[105,106]
HS3ST2	HGNC:5195	circadian rhythm	hypermethylated	[105,106]
ADGRE3 (EMR3)	HGNC:23647	cellular surface receptor /inflammatory response	hypomethylated	[105]
PI3	HGNC:8947	inflammatory response	hypomethylated	[105]
AIM2	HGNC:357	apoptosis/ inflammatory response	hypomethylated	[105]
SPP1	HGNC:11255	cellular adhesion/ inflammatory response	hypomethylated	[105]