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Table 3 Comparison of EFIN with PolyPhen-2 on a subset of Swiss-Prot variants

From: EFIN: predicting the functional impact of nonsynonymous single nucleotide polymorphisms in human genome

Tools (Training set)

AUC

Accuracy

Precision

Sensitivity

Specificity

Testing set: Swiss-Prot dataset with HumDiv mutations excluded (36998 neutral variants, 17643 damaging variants)*

EFIN (HumDiv)

86.96%

80.71%

85.96%

84.96%

72.16%

polyphen2 (HumDiv)

85.26%

78.35%

63.27%

78.59%

78.24%

Testing set: Swiss-Prot dataset with HumVar mutations excluded (15819 neutral variants, 2284 damaging variants)*

EFIN (Swiss-Prot ∩ HumVar)**

84.91%

71.37%

96.72%

69.60%

83.64%

polyphen2 (HumVar)

80.60%

78.09%

32.28%

67.12%

79.67%

  1. *This test is based on a subset of Swiss-Prot dataset of which mutations can be processed by both EFIN and PolyPhen-2.
  2. **EFIN is trained by intersection of HumVar and Swiss-Prot datasets.