Table 1. Power comparison for the 15 gold standard categories for type 2 diabetes.
| Category | GSASNP2 | GS2VEGAS (best P) | GSASNP1 | iGSEA 4GWAS | MAGMA-multi | MAGENTA (75%) | GOWINDA (P = 0.01) | sARTP | MAGMA-mean-sc* |
|---|---|---|---|---|---|---|---|---|---|
| Diabetes | 3/4 | 1/4 | 3/4 | 2/4 | 0/4 | 1/4 | 2/4 | 3/4 | 3/4 |
| Regulation of beta cell | 3/3 | 3/3 | 1/3 | 3/3 | 0/3 | 2/3 | 3/3 | 3/3 | 3/3 |
| Insulin/blood glucose level | 10/25 | 0/25 | 8/25 | 2/25 | 0/25 | 0/25 | 1/25 | 4/25 | 7/25 |
| Adipocytokine signaling | 1/6 | 0/6 | 0/6 | 0/6 | 0/6 | 0/6 | 0/6 | 2/6 | 1/6 |
| Cell cycle | 4/22 | 1/22 | 1/22 | 5/22 | 2/22 | 0/22 | 1/22 | 4/22 | 6/22 |
| Circadian rhythm | 0/6 | 0/6 | 0/6 | 0/6 | 0/6 | 0/6 | 0/6 | 0/6 | 0/6 |
| Unfolded protein response | 0/2 | 0/2 | 0/2 | 2/2 | 2/2 | 0/2 | 0/2 | 2/2 | 2/2 |
| Branched-chain a.a.** metabolism | 1/2 | 0/2 | 1/2 | 0/2 | 0/2 | 0/2 | 1/2 | 0/2 | 0/2 |
| Fatty acid metabolism | 2/10 | 0/10 | 3/10 | 1/10 | 0/10 | 1/10 | 0/10 | 5/10 | 3/10 |
| Glycolysis and Gluconeogenesis | 0/3 | 0/3 | 0/3 | 2/3 | 0/3 | 0/3 | 1/3 | 0/3 | 0/3 |
| Inflammation | 8/22 | 0/22 | 2/22 | 3/22 | 0/22 | 0/22 | 0/22 | 4/22 | 0/22 |
| NOTCH signaling | 6/14 | 0/14 | 3/14 | 5/14 | 0/14 | 0/14 | 4/14 | 5/14 | 5/14 |
| PPARG signaling | 0/1 | 0/1 | 0/1 | 0/1 | 0/1 | 0/1 | 0/1 | 1/1 | 0/1 |
| WNT signaling | 0/11 | 0/11 | 2/11 | 1/11 | 0/11 | 0/11 | 0/11 | 2/11 | 0/11 |
| Mitochondrial dysfunction | 0/5 | 0/5 | 0/5 | 0/5 | 0/5 | 0/5 | 0/5 | 0/5 | 1/5 |
| Total GS pathways | 38/100 | 5/7 | 24/100 | 26/100 | 4/11 | 4/9 | 13/23 | 35/100 | 31/100 |
Gold standard pathways detected within the top 100 pathways were counted for each category. Insignificant pathways (FDR > 0.25) were excluded. Total counts are shown in the bottom. The best counts in each category were marked in bold. *sc: self-contained method, **a.a.: amino acid.