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Table 2 Comparison of cancer driver variant predictors on the EXPDRV+NEUT and EXPDRV+ALL benchmark data sets

From: Current cancer driver variant predictors learn to recognize driver genes instead of functional variants

 

EXPDRV+ALL

 

EXPDRV+NEUT

 

EXPDRV+DEL

 

Method

AUC

AUPRC

AUC

AUPRC

AUC

AUPRC

ParsSNP

86.9

30.0

90.1

61.9

82.6

33.9

CanDrA v+

87.1

47.2

87.2

57.6

86.9

58.8

Chasm 3.1

91.1

54.5

94.0

73.7

87.3

58.8

CHASMplus

94.3

56.9

96.6

80.5

91.1

60.4

FATHMM cancer

91.0

39.1

93.2

67.3

87.7

43.6

TransFIC

68.0

6.0

80.6

22.0

51.0

7.9

Condel

64.3

4.5

83.9

24.3

38.5

5.6

DEOGEN2

68.8

4.6

91.3

43.7

38.9

5.2

CADD

73.7

6.4

88.5

26.5

54.0

7.9

M-CAP

54.0

4.9

83.1

37.9

38.9

5.4

MetaSVM

66.8

4.5

89.4

34.0

36.8

5.2

Dummy

98.1

46.6

98.7

67.9

97.4

59.7