Table 2.

Significant pathways

Immune category	Database	Pathway	FDR	Pathway GS	Effective GS
Cell death	GOTERM	Negative regulation of caspase activity	2.98E–02	16	16
Cell death	PANTHER	Other apoptosis	1.54E–02	14	10
Cell death	REACTOME	P75ntr signals via NFKB	2.01E–02	13	12
Cell death	REACTOME	NRIF signals cell death from the nucleus	3.23E–02	13	13
Misc immune	PANTHER	B cell and antibody-mediated immunity	3.66E–02	97	65
Misc immune	GOTERM	Initiation of viral infection	3.74E–02	11	11
NFKB	BIOCARTA	EPONFKB pathway	5.20E–03	11	11
NFKB	Ingenuity	NFKB signaling	3.05E–02	43	39
NFKB	REACTOME	Human TAK1 activates NFKB by phosphorylation and activation of IKKS complex	4.00E–02	15	13
NFKB	BIOCARTA	NFKB pathway	3.90E–03	23	20
T-cell activation	BIOCARTA	CD40 pathway	2.21E–02	15	13
T-cell activation	Panther	T-cell activation	2.23E–02	31	22
TGFβ signaling	wiki pathway	P38 MAPK signaling pathway	4.56E–02	54	52
TGFβ signaling	KEGG	MAPK signaling pathway	2.19E–02	267	241
TGFβ signaling	wiki pathway	MAPK signaling pathway	4.80E–02	34	33
TGFβ signaling	wiki pathway	TGFβ signaling pathway	4.62E–02	162	154
TLR and innate immunity	REACTOME	Toll-like receptor 3 cascade	1.61E–02	59	55
TLR and innate immunity	Ingenuity	LPSIL-1 mediated inhibition of RXR function	1.80E–02	59	55
TLR and innate immunity	KEGG	NOD-like receptor signaling pathway	4.91E–02	62	52
TLR and innate immunity	Panther	Toll receptor signaling pathway	4.26E–02	30	26
TLR and innate immunity	REACTOME	Toll receptor cascades	2.03E–02	86	78

NOTE: The 21 significant immune pathways assigned to one of six immune categories. For each pathway, the table lists the immune category, the database the pathway was found in, the official name of the pathway, FDR, and the gene size (GS, the number of genes included in the pathway) and the effective gene size (EGS, the number of genes found in the GWAS dataset).