Table 3.

Genetic pathways associated with the SLE phenotypes in the discovery stage

Pathway	Phenotype	#Genes	SNPs	P D	FDR D	P V	FDR V	P C
RIG-I/MDA5 negative regulation signaling	Antinuclear antibodies	31	464	2.00e-5	0.016	0.234	0.234	-
VEGFa	Oral ulcers	29	883	5.58e-5	0.044	0.013	0.026	2.08e-5

Two genetic pathways were significantly associated with systemic lupus erythematosus (SLE) phenotypes in the discovery stage

Abbreviations: SNP single-nucleotide polymorphism, P _D P value discovery cohort, FDR _D false discovery rate discovery cohort, P _V P value validation cohort, FDR _V false discovery rate validation cohort, P _C P value combined

^aThe association between the vascular endothelial growth factor (VEGF) pathway and oral ulcers was significantly replicated in the validation cohort