Table 2 Results from pathway analysis in iGSEA4GWAS.

Gene set	Source	FDR (with HLA)	FDR (without HLA)
NO2-dependent IL-12 pathway in NK cells	Biocarta	6.7 × 10⁻⁴
JAK-STAT signalling pathway*^,^†	KEGG	0.001	0.013
IL-12 mediated signalling events	PID	0.001
IL-12- and Stat4-dependent signalling in Th1 development*^,^†	Biocarta		<0.001
Interferon signalling	REACTOME	0.001
PD-1 signalling	REACTOME	0.001
Phosphorylation of CD3 and TCR-ζ chains	REACTOME	0.001
IL-27-mediated signalling events*^,^†	PID	0.001	<0.001
Cytokine–cytokine receptor interaction^‡^,^§^,^\|\|^,^¶^,^#^,^**^,^†^,^††^,^‡‡	KEGG	0.002	0.010
IFN-γ signalling	REACTOME	0.002
MHC class II antigen presentation	REACTOME	0.003
Cytokine signalling in immune system	REACTOME	0.004
Antigen processing and presentation	KEGG	0.004
Intestinal immune network for IgA production	KEGG	0.004
Co-stimulation by the CD28 family	REACTOME	0.005
IL-2 mediated signalling events	PID	0.008
TCR signalling	REACTOME	0.008
Downstream TCR signalling	REACTOME	0.008
Cell adhesion molecules	KEGG	0.015
Th1, Th2 differentiation^†	Biocarta	0.019	0.012
IL-2 receptor beta chain in T-cell activation	Biocarta	0.021
Interferon α/β signalling	REACTOME	0.035
IL-23-mediated signalling events	PID	0.039

FDR, false discovery rate; IFN, interferon; IL, interleukin; PD, programmed cell death; TCR, T cell antigen receptor; NK, natural killer.
Gene sets with FDR <0.05 are listed. Results are shown with or without inclusion in the analysis of SNPs within the HLA region. The top 10 hits from our drug-positioning analysis using a combined pathway from the HLA excluded set are indicated by symbols for the associated pathways that they affect.
^*Tofacitinib.
^†Glatiramer acetate.
^‡Axitinib.
^§Pazopanib.
^||Vatalanib.
^¶Cediranib.
^#X-82.
^**Telatinib.
^††Linifanib.
^‡‡Tandutinib.

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