Table 5 Gene sets enriched in MAGMA analyses

From: Inflammatory and infectious upper respiratory diseases associate with 41 genomic loci and type 2 inflammation

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

  1. 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).
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