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Table 3 Analysis of features for false negative (FN) predictions of Provean, PolyPhen-2 and Mitoclass.1 in validation dataset

From: Machine learning classifier for identification of damaging missense mutations exclusive to human mitochondrial DNA-encoded polypeptides

AA substitution (polypeptide) FN CI F1 F2 F3
p.A132T (p.MT-ND1) PolyPhen-2 72.82 123.98 0.30 12.59
p.L289M (p.MT-ND1) Provean 29.72 78.64 1.99 16.07
p.S34P (p.MT-ND3) PolyPhen-2 and Provean 10.15 60.53 0.34 5.23
p.V65A (p.MT-ND4L) Mitoclass.1 24.72 103 35.06 6.78
  1. CI refers to conservation index for each position. F1, F2 and F3 refer to the numerical values of the three attributes considered for Mitoclass.1 classifier