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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
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BMC Bioinformatics

ISSN: 1471-2105

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