Table 1. Significantly altered pathways in gingivo-buccal oral squamous cell carcinoma.
| KEGG ID: description of pathways (No. of genes comprising pathway) | No. of patients in whom altered | Total no. of variants | P-value* | No. of genes with somatic SNV and indels | No. of genes amplified | No. of genes deleted | % of genes altered in pathway |
|---|---|---|---|---|---|---|---|
| hsa04115: p53 signalling pathway (n=68) | 36 | 41 | 4.87 × 10−09 | 7 | 12 | 9 | 41.2 |
| hsa04210: apoptosis (n=88) | 37 | 49 | 5.21 × 10−09 | 13 | 16 | 8 | 42.0 |
| hsa05203: viral carcinogenesis (n=207) | 39 | 68 | 2.12 × 10−06 | 24 | 26 | 26 | 36.7 |
| hsa04722: neurotrophin signalling pathway (n=120) | 40 | 55 | 7.12 × 10−06 | 15 | 16 | 19 | 41.7 |
| hsa04310: Wnt signalling pathway (n=151) | 39 | 53 | 0.00095 | 21 | 16 | 20 | 37.7 |
| hsa04151: PI3K–Akt signalling pathway (n=338) | 46 | 104 | 0.00129 | 51 | 40 | 35 | 37.3 |
| hsa04320: dorso-ventral axis formation (n=24) | 15 | 18 | 0.0024 | 8 | 2 | 2 | 50.0 |
| hsa04360: axon guidance (n=129) | 28 | 51 | 0.00396 | 35 | 14 | 14 | 48.8 |
| hsa04010: MAPK signalling pathway (n=259) | 42 | 77 | 0.00706 | 35 | 37 | 31 | 39.8 |
| hsa04510: focal adhesion (n=204) | 33 | 74 | 0.02014 | 49 | 29 | 28 | 52.0 |
| hsa04514: cell adhesion molecules (CAMs) (n=133) | 19 | 34 | 0.02250 | 28 | 18 | 16 | 46.6 |
| hsa04080: neuroactive ligand-receptor interaction (n=273) | 30 | 55 | 0.02624 | 49 | 57 | 34 | 51.3 |
| hsa04330: Notch signalling pathway (n=47) | 17 | 20 | 0.04439 | 10 | 6 | 6 | 46.8 |
| hsa04726: serotonergic synapse (n=113) | 17 | 30 | 0.04671 | 18 | 21 | 12 | 45.1 |
* P-values correspond to likelihood-ratio tests used to assess enrichment.