Table 3 Performance comparison of the seven permutation models on breast and lung cancer
Method | Number of Significant genes | Overlap with CGC | Method consensus | CGC Rank | Consensus Rank | Average Rank |
|---|---|---|---|---|---|---|
Breast cancer | ||||||
 CADD | 263 | 0.041 | 0.45 | 1 | 4 | 2.5 |
 DANN | 158 | 0.011 | 0.57 | 6 | 2 | 4 |
 Fathmm-MKL coding | 178 | 0.022 | 0.58 | 2 | 2 | 2 |
 Fathmm-MKL noncoding | 184 | 0.021 | 0.49 | 3 | 3 | 3 |
 MetaLR | 174 | 0.013 | 0.5 | 5 | 3 | 4 |
 SPIDEX | 178 | 0.015 | 0.12 | 4 | 5 | 4.5 |
 VEST3 | 171 | 0.021 | 0.62 | 3 | 1 | 2 |
Lung cancer | ||||||
 CADD | 121 | 0.017 | 0.48 | 2 | 4 | 3 |
 DANN | 142 | 0.013 | 0.25 | 3 | 6 | 4.5 |
 Fathmm-MKL coding | 138 | 0.021 | 0.66 | 1 | 1 | 1 |
 Fathmm-MKL noncoding | 149 | 0.011 | 0.54 | 4 | 3 | 3.5 |
 MetaLR | 178 | 0.007 | 0.46 | 5 | 5 | 5 |
 SPIDEX | 171 | 0.002 | 0.11 | 6 | 7 | 6.5 |
 VEST3 | 164 | 0.011 | 0.57 | 4 | 2 | 3 |