Table 2.
Overall performance measures of four gene prioritization tools across 50 cases
| Tool | Evaluation criteria | Top 5% | Top 10% | Top 30% | Top 50% | Total gene list |
|---|---|---|---|---|---|---|
| VarElect | TPR (%) | 76 | 78 | 86 | 88 | 100 |
| MedRR (%) | 4.17 | 2.16 | 0.77 | 0.46 | 0.23 | |
| Median NDCG | 0.92 | 0.95 | 0.98 | 0.98 | 0.99 | |
| OMIMExplorer | TPR (%) | 76 | 76 | 86 | 86 | 86 |
| MedRR (%) | 22.01 | 11.01 | 4.02 | 2.41 | 1.2 | |
| Median NDCG | 0.82 | 0.88 | 0.94 | 0.96 | 0.98 | |
| Phenolyzer | TPR (%) | 60 | 64 | 78 | 84 | 96 |
| MedRR (%) | 7.53 | 3.9 | 2.59 | 2.69 | 1.72 | |
| Median NDCG | 0.88 | 0.92 | 0.96 | 0.98 | 0.99 |
NDCG-normalized discounted cumulative gain of the probe gene ranks, TPR-true positive rate, MedRR-median rank ratio. Above performance measures are a summary of all 50 cases used in this study across top 5%, Top 10%, Top 30%, and Top 50% of the prioritized list of genes. All (100%) HPO ID’s per case were used for all the above gene prioritization analysis