Table 4. LOOCV results for 165 polygenic diseases, based on seed genes and different disease phenotype networks processed with the logistic regression function.
| Disease Phenotype Networks | Best C valuea | MRR, % | Top-ranking genesb | TPR in the top 5, % | TPR in the top 10, % | TPR in the top 30, % |
|---|---|---|---|---|---|---|
| Lin | -12 | 7.89 | 80 | 39.34 | 47.78 | 62.06 |
| Sqrt | -12 | 7.90 | 81 | 39.11 | 48.01 | 61.83 |
| Maxmin | -18 | 7.96 | 81 | 36.77 | 46.37 | 61.12 |
| Tanimoto | -18 | 7.91 | 83 | 38.88 | 48.48 | 61.59 |
| mimMiner | -14 | 7.96 | 82 | 42.39 | 50.59 | 64.17 |
MRR, mean rank ratio; TPR, true positive rate
a the best C value will be obtained when maximum number of top-ranking genes is reached.
b it signifies the maximum number of target genes ranked on top of the candidate list. Totally, there are 427 target genes in LOOCV for polygenic diseases.