Table 1.
Hypermethylated gene promoter 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 | MMD * | p-Value ** |
|---|---|---|---|
| HNSCC Tissue vs. Healthy Tissue | |||
| GPRC5D | G protein-coupled receptor | 0.78 | 6.49 × 10−7 |
| TMPRSS11B | Transmembrane protease | 0.76 | 2.04 × 10−8 |
| PIAS2 | Sumoylation | 0.66 | 1.22 × 10−6 |
| ARG1 | Arginase activity | 0.64 | 2.50 × 10−7 |
| SRPK2 | Protein kinase | 0.62 | 1.30 × 10−6 |
| AADACL2 | Hydrolase activity | 0.59 | 7.38 × 10−7 |
| RGPD4 | RNA transport | 0.58 | 4.71 × 10−6 |
| SPRR3 | Structural molecule activity | 0.53 | 2.44 × 10−7 |
| DEGS1 | Desaturase activity | 0.49 | 2.04 × 10−8 |
| TXNDC8 | Oxidoreductase activity | 0.48 | 1.15 × 10−5 |
| SH3TC1 | Myelination | 0.47 | 2.05 × 10−6 |
| ZPLD1 | Cerebral malformations | 0.47 | 6.17 × 10−6 |
| FBXO2 | Ubiquitination | 0.46 | 0.000236 |
| ATG16L1 | Autophagy | 0.46 | 0.000306 |
| GRHL1 | Transcription factor | 0.44 | 5.12 × 10−7 |
| HNSCC Tissue vs. Oral Lesions | |||
| RAD51B | RAD51 Paralog B | 0.85 | 2.53 × 10−8 |
| BARX2 | BARX Homeobox 2 | 0.81 | 3.94 × 10−8 |
| SLC5A10;FAM83G | Solute Carrier Family 5 Member 10 | 0.78 | 2.58 × 10−8 |
| NINL | Ninein Like | 0.77 | 3.96 × 10−8 |
| NSMCE2 | NSE2/MMS21 Homolog, SMC5-SMC6 Complex SUMO Ligase | 0.76 | 6.36 × 10−7 |
| PGAP2 | Post-GPI Attachment to Proteins 2 | 0.75 | 9.48 × 10−8 |
| INO80C | INO80 Complex Subunit C | 0.74 | 1.96 × 10−9 |
| IL34 | Interleukin 34 | 0.74 | 2.20 × 10−9 |
| ZNF516 | Zinc Finger Protein 516 | 0.73 | 4.90 × 10−8 |
| GFOD2 | Glucose-Fructose Oxidoreductase Domain Containing 2 | 0.73 | 1.36 × 10−7 |
| PARD3 | Par-3 Family Cell Polarity Regulator | 0.73 | 1.36 × 10−7 |
| MCEE | Methylmalonyl-CoA Epimerase | 0.72 | 2.89 × 10−8 |
| POLM | DNA Polymerase Mu | 0.72 | 3.93 × 10−7 |
| ASPG | Asparaginase | 0.71 | 4.43 × 10−8 |
| TBC1D2 | TBC1 Domain Family Member 2 | 0.71 | 3.74 × 10−7 |
| Oral Lesions vs. Healthy Tissue | |||
| SLC5A10;FAM83G | Solute Carrier Family 5 Member 10 | 0.78 | 2.58 × 10−8 |
| TBC1D2 | TBC1 Domain Family Member 2 | 0.71 | 3.74 × 10−7 |
| SH3BP5L | SH3 Binding Domain Protein 5 Like | 0.70 | 2.68 × 10−7 |
| VANGL1 | VANGL Planar Cell Polarity Protein 1 | 0.69 | 6.49 × 10−7 |
| DLEC1 | Deleted in Lung And Esophageal Cancer 1 | 0.61 | 3.84 × 10−6 |
| TGOLN2 | Trans-Golgi Network Protein 2 | 0.61 | 3.79 × 10−7 |
| CTBP2 | C-Terminal Binding Protein 2 | 0.59 | 4.99 × 10−6 |
| PPP1CB | Protein Phosphatase 1 Catalytic Subunit Beta | 0.56 | 2.20 × 10−6 |
| VPS52 | VPS52, GARP Complex Subunit | 0.53 | 8.05 × 10−6 |
| MEPCE | Methylphosphate Capping Enzyme | 0.52 | 2.89 × 10−7 |
| HDAC4 | Histone Deacetylase 4 | 0.51 | 6.47 × 10−6 |
| ARAP1 | ArfGAP with RhoGAP Domain, Ankyrin Repeat, and PH Domain 1 | 0.50 | 4.77 × 10−7 |
| TCF20 | Transcription Factor 20 | 0.49 | 4.14 × 10−5 |
| NDUFS7 | NADH:Ubiquinone Oxidoreductase Core Subunit S7 | 0.49 | 0.00017 |
| GATAD2A | GATA Zinc Finger Domain Containing 2A | 0.47 | 3.58 × 10−8 |
* Mean difference (MD) across all sites in a region (mean.mean.diff); ** false discovery rate (FDR) adjustment combined p-value (comb.p.adj.fdr).