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Table 4 Performance of the evaluated methods on the training (TS270) and control (CS30) sets

From: MutaCYP: Classification of missense mutations in human cytochromes P450

Dataset Methoda Confusion scoresb Correlation,r
B-B B-D D-B D-D PolyPhen-2 HumVar PolyPhen-2 HumDiv SIFT
TS270 MutaCYP 55 18 13 184 0.69 0.67 0.58
PolyPhen-2 HumVar 56 17 26 171   0.96 0.66
PolyPhen-2 HumDiv 48 25 19 178    0.67
SIFT 50 18 31 108    
CS30 MutaCYP 1 0 0 29 0.38 0.19 0.12
PolyPhen-2 HumVar 1 0 3 26   0.94 0.58
PolyPhen-2 HumDiv 0 1 1 28    0.67
SIFT - - 5 16    
  1. aSIFT predictions miss 63 mutations in TS270 (58 deleterious and 5 benign) and 9 mutations in CS30 (8 deleterious and 1 benign).
  2. bConfusion scores notation: B-B – the number of benign mutations predicted as benign; B-D – benign as deleterious, D-D – deleterious as deleterious; D-B – deleterious as benign.
  3. Confusion scores are computed for binary classification. Pearson correlation coefficient is computed for real valued predictions.