From: Benchmarking subcellular localization and variant tolerance predictors on membrane proteins
 | TP | FP | TN | FN | Sensitivity | Specificity | PPV | NPV | ACC | MCC | OPM |
---|---|---|---|---|---|---|---|---|---|---|---|
CADD | 725 | 670 | 641 | 18 | 0.98 | 0.49 | 0.66 | 0.95 | 0.73 | 0.53 | 0.44 |
DANN | 737 | 1006 | 305 | 6 | 0.99 | 0.23 | 0.56 | 0.97 | 0.61 | 0.35 | 0.30 |
Eigen | 582 | 253 | 1058 | 161 | 0.78 | 0.81 | 0.80 | 0.79 | 0.80 | 0.59 | 0.50 |
Eigen-PC | 580 | 266 | 1045 | 163 | 0.78 | 0.80 | 0.79 | 0.78 | 0.79 | 0.58 | 0.49 |
FATHMM | 556 | 230 | 1053 | 183 | 0.75 | 0.82 | 0.81 | 0.77 | 0.79 | 0.57 | 0.49 |
FATHMM-MKL | 705 | 434 | 877 | 38 | 0.95 | 0.67 | 0.74 | 0.93 | 0.81 | 0.64 | 0.55 |
FitCons | 423 | 571 | 740 | 320 | 0.57 | 0.56 | 0.57 | 0.57 | 0.57 | 0.13 | 0.18 |
GenoCanyon | 605 | 313 | 998 | 138 | 0.81 | 0.76 | 0.77 | 0.80 | 0.79 | 0.58 | 0.49 |
LRT | 625 | 205 | 904 | 91 | 0.87 | 0.82 | 0.83 | 0.87 | 0.84 | 0.69 | 0.60 |
M-CAP | 707 | 104 | 152 | 13 | 0.98 | 0.59 | 0.71 | 0.97 | 0.79 | 0.62 | 0.53 |
MetaLR | 615 | 76 | 1235 | 128 | 0.83 | 0.94 | 0.93 | 0.85 | 0.88 | 0.77 | 0.70 |
MetaSVM | 629 | 59 | 1252 | 114 | 0.85 | 0.95 | 0.95 | 0.86 | 0.90 | 0.81 | 0.74 |
MutationAssessor | 278 | 36 | 999 | 96 | 0.74 | 0.97 | 0.96 | 0.79 | 0.85 | 0.73 | 0.64 |
MutationTaster2 | 694 | 251 | 1060 | 49 | 0.93 | 0.81 | 0.83 | 0.92 | 0.87 | 0.75 | 0.67 |
MutPred | 624 | 62 | 1240 | 117 | 0.84 | 0.95 | 0.95 | 0.86 | 0.90 | 0.80 | 0.73 |
PolyPhen HDIV | 668 | 213 | 925 | 37 | 0.95 | 0.81 | 0.84 | 0.94 | 0.88 | 0.77 | 0.69 |
PolyPhen HVAR | 633 | 151 | 1046 | 53 | 0.92 | 0.87 | 0.88 | 0.92 | 0.90 | 0.80 | 0.73 |
PON-P2 | 699 | 76 | 1235 | 48 | 0.94 | 0.94 | 0.90 | 0.96 | 0.94 | 0.87 | 0.82 |
PROVEAN | 646 | 263 | 1040 | 92 | 0.88 | 0.80 | 0.71 | 0.92 | 0.83 | 0.65 | 0.56 |
REVEL | 650 | 56 | 1255 | 93 | 0.87 | 0.96 | 0.95 | 0.88 | 0.92 | 0.83 | 0.77 |
SIFT | 659 | 330 | 979 | 84 | 0.89 | 0.75 | 0.78 | 0.87 | 0.82 | 0.64 | 0.55 |
VEST3 | 641 | 79 | 1232 | 102 | 0.86 | 0.94 | 0.93 | 0.87 | 0.90 | 0.80 | 0.73 |