Table 3 Summary of comparison of results from ToppGene with other gene prioritization applications
From: Improved human disease candidate gene prioritization using mouse phenotype
A. Random cross-validation | |||
|---|---|---|---|
| Â | ENDEAVOUR | ToppGene | |
AUC (area under curve) | 86.6 | Â | 91.6 |
True positive rate/false positive rate | 74/90 | Â | 77/90 |
B. Locus region cross-validation | |||
| Â | 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 | Â | Â | Â |
| Â | 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 | Â | Â | Â |
| Â | 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% |