Table 4.
SKAT-O on pathways results (top 5 pathways).
| Pathway | EP | PPMI | combined p-value | |||
|---|---|---|---|---|---|---|
| Name | Tested variants | p-value | Tested variants | p-value | ||
| R-HSA-446343 | Localization of the PINCH-ILK-PARVIN complex to focal adhesions | 8 (2) | 0.0015 | 32 (6) | 0.6072 | NA |
| R-HSA-170660 | Adenylate cyclase activating pathway | 29 (10) | 0.0016 | 29 (10) | 0.0210 | 3.3.10−5* |
| R-HSA-5467333 | APC truncation mutants are not K63 polyubiquitinated | 7 (4) | 0.0156 | 27 (4) | 0.925 | NA |
| R-HSA-1483152 | Hydrolysis of LPE | 5 (4) | 0.0231 | 29 (4) | 0.4554 | NA |
| R-HSA-4411364 | Binding of TCF/LEF:CTNNB1 to target gene promoters | 20 (9) | 0.0233 | 66 (12) | 0.4361 | NA |
Tested variants are reported as number of tested variants (number of unique variants). EP, Extreme phenotypes cohort. P-value from SKAT-O tests on pathways in EP and in PPMI cohorts are reported. Combined p-values obtained with a Fisher test are reported in the last column. Combined p-values with a Fisher test were only calculated when both p-values in EP and in PPMI cohorts were found nominally significant (i.e., <0.05).
*
Significant p-value after Bonferroni correction.