Table 2.
Hypomethylated 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 | |||
| TRBC2 | T cell receptor | −0.80 | 2.48 × 10−7 |
| DGAT2 | Acyltransferase activity | −0.70 | 2.48 × 10−7 |
| ALG1L | Transferase activity | −0.70 | 3.29 × 10−5 |
| PDE4D | Enzyme binding | −0.68 | 1.06 × 10−5 |
| TRDC | T cell receptor | −0.67 | 1.46 × 10−5 |
| DNAJC6 | Phosphatase activity | −0.67 | 1.63 × 10−6 |
| IGKV3-20 | Immunoglobulin receptor binding | −0.66 | 1.71 × 10−5 |
| TMEM150B | Transmembrane protein | −0.66 | 8.13 × 10−5 |
| LAIR2 | Innate immune response | −0.65 | 1.81 × 10−5 |
| UBQLN3 | Protein degradation | −0.64 | 2.57 × 10−6 |
| ANKFN1 | Not known | −0.64 | 1.71 × 10−7 |
| MS4A1 | Differentiation of B-cells | −0.63 | 3.80 × 10−5 |
| CCT8L2 | Channel activity | −0.62 | 3.59 × 10−6 |
| SPOCK1 | Not known | −0.61 | 5.06 × 10−5 |
| IGHV4-39 | Antigen recognition | −0.61 | 9.44 × 10−7 |
| HNSCC Tissue vs. Oral Lesions | |||
| ART4 | ADP-Ribosyltransferase 4 (Dombrock Blood Group) | −0.88 | 7.92 × 10−11 |
| EPB41L3 | Erythrocyte Membrane Protein Band 4.1 Like 3 | −0.87 | 6.18 × 10−11 |
| ESRRG | Estrogen Related Receptor Gamma | −0.86 | 8.51 × 10−9 |
| ENPP1 | Ectonucleotide Pyrophosphatase/Phosphodiesterase 1 | −0.86 | 1.26 × 10−9 |
| GNG7 | G Protein Subunit Gamma 7 | −0.86 | 4.75 × 10−9 |
| PAPSS2 | 3′-Phosphoadenosine 5′-Phosphosulfate Synthase 2 | −0.85 | 4.10 × 10−9 |
| NGEF | Neuronal Guanine Nucleotide Exchange Factor | −0.84 | 1.87 × 10−9 |
| HIPK4 | Homeodomain Interacting Protein Kinase 4 | −0.84 | 6.69 × 10−9 |
| GPR158 | G Protein-Coupled Receptor 158 | −0.83 | 9.82 × 10−10 |
| GSG1L | GSG1 Like | −0.83 | 1.04 × 10−8 |
| SMPD3 | Sphingomyelin Phosphodiesterase 3 | −0.83 | 1.64 × 10−8 |
| GDF2 | Growth Differentiation Factor 2 | −0.83 | 5.15 × 10−10 |
| RERE | Arginine-Glutamic Acid Dipeptide Repeats | −0.82 | 2.19 × 10−8 |
| CDH13 | Cadherin 13 | −0.82 | 1.81 × 10−10 |
| HS3ST4 | Heparan Sulfate-Glucosamine 3-Sulfotransferase 4 | −0.82 | 1.02 × 10−8 |
| Oral Lesions vs. Healthy Tissue | |||
| ART4 | ADP-Ribosyltransferase 4 (Dombrock Blood Group) | −0.88 | 7.92 × 10−11 |
| ENPP1 | Ectonucleotide Pyrophosphatase/Phosphodiesterase 1 | −0.86 | 1.26 × 10−9 |
| GNG7 | G Protein Subunit Gamma 7 | −0.86 | 4.75 × 10−9 |
| PKD1L3 | Polycystin 1 Like 3, Transient Receptor Potential Channel Interacting | −0.81 | 2.20 × 10−9 |
| PLXNC1 | Plexin C1 | −0.81 | 1.41 × 10−9 |
| CAMK2B | Calcium/Calmodulin Dependent Protein Kinase II Beta | −0.79 | 1.05 × 10−8 |
| CACNA1S | Calcium Voltage–Gated Channel Subunit Alpha1 S | −0.78 | 8.18 × 10−9 |
| SCGB1D1 | Secretoglobin Family 1D Member 1 | −0.78 | 2.34 × 10−7 |
| VPS13D | Vacuolar Protein Sorting 13 Homolog D | −0.76 | 6.12 × 10−8 |
| DLGAP4 | DLG Associated Protein 4 | −0.76 | 6.37 × 10−9 |
| LRP1B | LDL Receptor Related Protein 1B | −0.76 | 1.12 × 10−9 |
| COL2A1 | Collagen Type II Alpha 1 Chain | −0.75 | 1.30 × 10−8 |
| SLC24A3 | Solute Carrier Family 24 Member 3 | −0.74 | 3.07 × 10−9 |
| TBC1D8 | TBC1 Domain Family Member 8 | −0.74 | 1.84 × 10−8 |
| ABCC8 | ATP Binding Cassette Subfamily C Member 8 | −0.73 | 3.58 × 10−9 |
* Mean difference (MD) across all sites in a region (mean.mean.diff); ** false discovery rate (FDR) adjustment combined p-value (comb.p.adj.fdr).