Table 8.
Performances of different prediction tools on the three filtered test sets
| Data Set | Tool | AUC | Balanced Accuracy | Sens | Spec | PPV | NPV | F-m | MCC |
|---|---|---|---|---|---|---|---|---|---|
| # 1 | PaPI | .9218 | .8575 | .8518 | .8631 | .8989 | .803 | .8747 | .7084 |
| Carol | .9120 | .8492 | .821 | .8774 | .9054 | .7742 | .8611 | .689 | |
| Provean | .8938 | .8264 | .7894 | .8634 | .892 | .7415 | .8375 | .643 | |
| SIFT | .883 | .8142 | .7633 | .8651 | .8899 | .7189 | .8218 | .6185 | |
| PolyPhen2 | .9144 | .8425 | .8503 | .8348 | .8803 | .796 | .865 | .6806 | |
| FATHMM | .8301 | .7517 | .6267 | .8766 | .8789 | .6217 | .7317 | .502 | |
| LRT | .8455 | .8249 | .8009 | .8488 | .8833 | .749 | .8401 | .6409 | |
| MutAssessor | .8899 | .812 | .7578 | .8662 | .89 | .7144 | .8186 | .6141 | |
| # 2 | PaPI | .9246 | .863 | .8623 | .8637 | .8989 | .8169 | .8802 | .7209 |
| Carol | .9121 | .8442 | .811 | .8774 | .9029 | .7675 | .8545 | .6794 | |
| Provean | .8984 | .8354 | .8074 | .8634 | .8926 | .7613 | .8479 | .6623 | |
| SIFT | .8836 | .8091 | .7532 | .8651 | .887 | .7137 | .8146 | .6094 | |
| PolyPhen2 | .9183 | .8491 | .8635 | .8348 | .8802 | .813 | .8717 | .6957 | |
| FATHMM | .8355 | .7603 | .6441 | .8766 | .8801 | .6366 | .7438 | .5187 | |
| LRT | .8506 | .8317 | .8147 | .8488 | .8834 | .7651 | .8477 | .656 | |
| MutAssessor | .8923 | .8134 | .7606 | .8662 | .8888 | .7202 | .8197 | .6178 | |
| # 3 | PaPI | .9332 | .8721 | .8751 | .8692 | .9046 | .8308 | .8896 | .7398 |
| Carol | .9239 | .8551 | .8187 | .8915 | .9145 | .7763 | .8639 | .7004 | |
| Provean | .9159 | .8444 | .8156 | .8731 | .9011 | .7697 | .8562 | .6797 | |
| SIFT | .8911 | .8166 | .759 | .8743 | .8953 | .7191 | .8215 | .6238 | |
| PolyPhen2 | .9303 | .8542 | .8729 | .8355 | .8826 | .8226 | .8777 | .7068 | |
| FATHMM | .8436 | .7643 | .6410 | .8876 | .8899 | .6356 | .7452 | .527 | |
| LRT | .8682 | .8408 | .8289 | .8527 | .8886 | .7786 | .8577 | .6744 | |
| MutAssessor | .8988 | .8273 | .7772 | .8774 | .8998 | .7354 | .8341 | .6449 |
Comparison of PaPI, PolyPhen2, SIFT, Carol, PROVEAN, FATHMM, LRT and MutationAssessor on the three test sets filtered for unpredictable variants by the other prediction tools. Area under the curve (AUC), balanced accuracy (sensitivity/2 + specificity/2), sensitivity (Sens), specificity (Spec), Positive Predictive Value (PPV), Negative Predictive Value (NPV), F-measure (F-m) and Matthews correlation coefficient (MCC) are reported for each method. Highest values for each set are marked in bold.