Table 3.
Summary of comparison of results from ToppGene with other gene prioritization applications
| A. Random cross-validation | |||
| ENDEAVOUR | ToppGene | ||
| AUC (area under curve) | 86.6 | 91.6 | |
| True positive rate/false positive rate | 74/90 | 77/90 | |
| B. Locus region cross-validation | |||
| PROSPECTR | SUSPECTS | ToppGene | |
| Percentage of top 5% ranked target genes | 13% (20/155) | 56% (87/155) | 79% (118/150) |
| Average rank ratio of target gene | 31.23% | 12.93% | 7.39% |
| C. Congenital Heart Disease (CHD) test case | |||
| SUSPECTS | ENDEAVOUR | ToppGene | |
| Percentage of top 10% ranked target genes | 32% (9/28) | 50% (14/28) | 64% (18/28) |
| Percentage of top 5% ranked target genes | 18% (5/28) | 14%(4/28) | 25% (7/28) |
| Average rank ratio | 25.03% | 17.29% | 17.35% |
| D. Diabetic Retinopathy (DR) test case | |||
| SUSPECTS | ENDEAVOUR | ToppGene | |
| Percentage of top 10% ranked target genes | 63% (17/27) | 56% (15/27) | 70% (19/27) |
| Percentage of top 5% ranked target genes | 44% (12/27) | 44% (12/27) | 63% (17/27) |
| Average rank ratio | 17.04% | 13.31% | 8.60% |