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Table 3 Performance comparison of the seven permutation models on breast and lung cancer

From: Comparison of different functional prediction scores using a gene-based permutation model for identifying cancer driver genes

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