Table 1.
| cSCC (39) | TCGA HNSC HPV (−) (243) |
TCGA LSCC (178) |
TCGA SKCM (278) |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MutSig q-value |
IntOGen FM q-value |
Chi-square FDR |
Multinomial FDR |
patients | patients | patients | patients | |||||
| # | % | # | % | # | % | # | % | |||||
| TP53 | 0* | 0* | 5.28E-21* | <1.0E-05* | 37 | 94.9% | 203 | 83.5%* | 161 | 90.4%* | 46 | 16.5%* |
| CDKN2A | 9.34E-07* | 3.48E-13* | 2.81E-12* | 2.70E-04* | 17 | 43.6% | 63 | 25.9%* | 32 | 18.0%* | 42 | 15.1%* |
| PEG10 | 3.66E-06* | ND | 9.69E-01 | 1 | 9 | 23.1% | 2 | 0.8% | 3 | 1.7% | 5 | 1.8% |
| NOTCH2 | 1.85E-03* | 2.79E-07* | 4.20E-08* | 1.00E-04* | 20 | 51.3% | 12 | 4.9% | 13 | 7.3% | 22 | 7.9% |
| NOTCH1 | 2.10E-02* | 0* | 1.04E-05* | 2.00E-05* | 23 | 59.0% | 49 | 20.2%* | 15 | 8.4% | 9 | 3.2% |
| HRAS | 2.10E-02* | 2.55E-02* | 9.69E-01 | 1 | 8 | 20.5% | 11 | 4.5%* | 5 | 2.8%* | 3 | 1.1% |
| BBS9 | 2.10E-02* | 6.61E-01 | 3.22E-01 | 6.22E-01 | 9 | 23.1% | 5 | 2.1% | 7 | 3.9% | 10 | 3.6% |
| CASP8 | 2.93E-02* | 1.47E-02* | 2.96E-01 | 2.30E-01 | 9 | 23.1% | 24 | 9.9%* | 2 | 1.1% | 9 | 3.2% |
| DCLK1 | 3.39E-02* | ND | 9.69E-01 | 1 | 17 | 43.6% | 3 | 1.2% | 4 | 2.2% | 10 | 3.6% |
| RBM46 | 3.67E-02* | ND | 1.03E-01 | 1.22E-01 | 13 | 33.3% | 0 | 0.0% | 1 | 0.6% | 15 | 5.4% |
| AJUBA | 9.99E-02* | 7.40E-12* | 6.82E-03* | 8.72E-02* | 7 | 17.9% | 17 | 7.0%* | 0 | 0.0% | 0 | 0.0% |
| SNX25 | 1 | 2.12E-02* | 3.95E-05* | 1.66E-02* | 7 | 17.9% | 4 | 1.6% | 3 | 1.7% | 2 | 0.7% |
| BF2D | 1 | 5.43E-02* | 3.35E-05* | 8.81E-02* | 2 | 5.1% | 0 | 0.0% | 1 | 0.6% | 0 | 0.0% |
| PARD3 | 1 | 6.04E-02* | 1.03E-02* | 4.00E-04* | 12 | 30.8% | 7 | 2.9% | 8 | 4.5% | 15 | 5.4% |
| OPN3 | 1 | 1.28E-02* | 2.26E-03* | 3.80E-01 | 4 | 10.3% | 0 | 0.0% | 2 | 1.1% | 4 | 1.4% |
| FBXO21 | 1 | 2.13E-02* | 2.44E-02* | 1.22E-01 | 5 | 12.8% | 2 | 0.8% | 2 | 1.1% | 6 | 2.2% |
| DCLRE1A | 1 | 4.49E-02* | 2.44E-02* | 1.61E-01 | 5 | 12.8% | 2 | 0.8% | 1 | 0.6% | 1 | 0.4% |
| COBLL1 | 1 | 5.43E-02* | 3.22E-01 | 6.90E-02* | 9 | 23.1% | 3 | 1.2% | 5 | 2.8% | 18 | 6.5% |
| RASA1 | 1 | 1.21E-01 | 8.93E-05* | 4.19E-03* | 5 | 12.8% | 13 | 5.3%* | 10 | 5.6% | 3 | 1.1% |
| SEC31A | 1 | 2.14E-01 | 6.28E02* | 8.76E-02* | 7 | 17.9% | 4 | 1.6% | 5 | 2.8% | 6 | 2.2% |
| ZNF644 | 1 | 2.42E-01 | 3.95E-05* | 8.72E-02* | 6 | 15.4% | 3 | 1.2% | 3 | 1.7% | 5 | 1.8% |
| KMT2C | 1 | 3.20E-01 | 1.14E-03* | 9.79E-03* | 15 | 38.5% | 21 | 8.6% | 29 | 16.3% | 45 | 16.2% |
| FAT1 | 1 | ND | 4.29E-10* | 1.00E-05* | 17 | 43.6% | 64 | 26.3%* | 26 | 14.6% | 27 | 9.7% |
| KMT2D | 1 | 7.80E-01 | 1.20E-01 | 1.50E-02* | 27 | 69.2% | 43 | 17.7%* | 36 | 20.2%* | 62 | 22.3% |
| NFE2L2 | 1 | ND | ND | ND | 0 | 0.0% | 17 | 7.0%* | 27 | 15.2%* | 3 | 1.1% |
| PIK3CA | 1 | 4.09E-01 | 3022E-01 | 4.03E-01 | 4 | 10.3% | 45 | 18.5%* | 28 | 15.7%* | 10 | 3.6% |
| RAC1 | 1 | 9.43E-01 | 6.95E-01 | ND | 2 | 5.1% | 8 | 3.3%* | 2 | 1.1% | 20 | 7.2%* |
| BRAF | 1 | 1 | 9.69E-01 | 1 | 7 | 17.9% | 3 | 1.2% | 8 | 4.5% | 140 | 50.4%* |
| NRAS | 1 | 1 | 6.95E-01 | ND | 2 | 5.1% | 1 | 0.4% | 0 | 0.0% | 86 | 30.9%* |
| STK19 | 1 | 4.02E-01 | 9.69E-01 | 1 | 8 | 20.5% | 3 | 1.2% | 4 | 2.2% | 4 | 3.4%* |
Statistically significant genes are indicated with an *.
TCGA data were collected from cBioPortal. TCGA significance was determined by MutSig in the pan-cancer analysis of Lawrence et.al. ND = not determined.