Table 1 Percent significant sets at α = 0.05 by number of causal and noncausal genes in the set using modified p values
From: Application of family-based tests of association for rare variants to pathways
Pathway testing approach | Number of causal and noncausal genes in the set (all sets contain 5 genes) | |||
|---|---|---|---|---|
| Â | 0 causal, 5 noncausal | 1 causal, 4 noncausal | 3 causal, 2 noncausal | 5 causal, 0 noncausal |
Single-stage approach | ||||
FPCA | 2.5% (5/200) | 6.5% (13/200) | 5.0% (10/200) | 9.0% (18/200) |
| 3.5% (7/200) | 6.5% (13/200) | 8.5% (17/200) | 16.5% (33/200) |
T 2 | 5.0% (10/200) | 3.0% (6/200) | 1.5% (3/200) | 2.5% (5/200) |
CMC5% | 1.5% (3/200) | 0.0% (0/200) | 2.5% (5/200) | 1.5% (3/200) |
CMC0.5% | 3.5% (7/200) | 5.5% (11/200) | 9.5% (19/200) | 8.0% (16/200) |
Two-stage approach | ||||
FPCA | 2.0% (4/200) | 1.5% (3/200) | 9.0% (18/200) | 5.0% (10/200) |
Fishers_ | 3.5% (7/200) | 4.0% (8/200) | 8.5% (17/200) | 11.0% (22/100) |
Fishers_ T2 | 1.5% (3/200) | 3.5% (7/200) | 2.0% (4/200) | 1.0% (2/200) |
Fishers_ CMC5% | 3.0% (6/200) | 2.0% (4/200) | 3.5% (7/200) | 1.0% (2/200) |
Fishers_ CMC0.5% | 2.0% (4/200) | 2.0% (4/200) | 3.5% (7/200) | 0.5% (1/200) |