Table 5.
Gene sets enriched in MAGMA analyses
| Phenotype | Gene set | Genes | β | Padj |
|---|---|---|---|---|
| CRS | MHC class II receptor activity | 9 | 1.6939 | 0.036904 |
| NP | MHC class II receptor activity | 9 | 2.5209 | 1.96E-07 |
| NP | MHC class II receptor complex | 14 | 1.7043 | 0.000367 |
| NP | Positive regulation of interleukin 13 production | 15 | 1.2187 | 0.000453 |
| NP | Regulation of interleukin-4 production | 28 | 0.90161 | 0.003912 |
| NP | Interleukin 13 production | 24 | 0.88367 | 0.004649 |
| NP | MHC protein complex | 22 | 1.0476 | 0.008563 |
| NP | Interleukin-4 production | 34 | 0.78389 | 0.011623 |
| CDTA | Cytokine-mediated signaling pathway | 748 | 0.16085 | 0.005677 |
| CDTA | TNFR2 pathway | 16 | 1.0288 | 0.00569 |
| CDTA | Reactome cytokine signaling in immune system | 835 | 0.14811 | 0.006434 |
| CDTA | Peptidyl serine autophosphorylation | 8 | 1.3374 | 0.027797 |
| PA | Negative regulation of morphogenesis of an epithelium | 16 | 1.12272 | 0.025657 |
Gene sets were identified based on genes identified as phenotype-associated in MAGMA analysis. β is the effect size in the MAGMA gene set enrichment analysis. The considered gene sets encompassed a set 4761 curated gene sets and 5917 Gene Ontology terms, as used in the FUMA pipeline. P values were calculated using upper tail chi-square testing (one degree of freedom) from a t-statistic under a normal approximation. P values have been adjusted for these sets (10,678 tests).