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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.