Table 2.
Comparison of cancer driver variant predictors on the EXPDRV+NEUT and EXPDRV+ALL benchmark data sets
| EXPDRV+ALL | EXPDRV+NEUT | EXPDRV+DEL | ||||
|---|---|---|---|---|---|---|
| Method | AUC | AUPRC | AUC | AUPRC | AUC | AUPRC |
| ParsSNP | 86.9 | 30.0 | 90.1 | 61.9 | 82.6 | 33.9 |
| CanDrA v+ | 87.1 | 47.2 | 87.2 | 57.6 | 86.9 | 58.8 |
| Chasm 3.1 | 91.1 | 54.5 | 94.0 | 73.7 | 87.3 | 58.8 |
| CHASMplus | 94.3 | 56.9 | 96.6 | 80.5 | 91.1 | 60.4 |
| FATHMM cancer | 91.0 | 39.1 | 93.2 | 67.3 | 87.7 | 43.6 |
| TransFIC | 68.0 | 6.0 | 80.6 | 22.0 | 51.0 | 7.9 |
| Condel | 64.3 | 4.5 | 83.9 | 24.3 | 38.5 | 5.6 |
| DEOGEN2 | 68.8 | 4.6 | 91.3 | 43.7 | 38.9 | 5.2 |
| CADD | 73.7 | 6.4 | 88.5 | 26.5 | 54.0 | 7.9 |
| M-CAP | 54.0 | 4.9 | 83.1 | 37.9 | 38.9 | 5.4 |
| MetaSVM | 66.8 | 4.5 | 89.4 | 34.0 | 36.8 | 5.2 |
| Dummy | 98.1 | 46.6 | 98.7 | 67.9 | 97.4 | 59.7 |