Table 1

SLE case–control pathway based aggregate association analysis

PathwayGenes in pathwayGenes in testSNVs in testP value*FDR†
Th1 and Th2 cell differentiation (hsa04658)927814 3626.3E-112.2E-09
Antigen processing and presentation (hsa04612)774080171.8E-103.1E-09
Hematopoietic cell lineage (hsa04640)977113 0133.8E-104.5E-09
Th17 cell differentiation (hsa04659)1079619 3471.7E-091.5E-08
Intestinal immune network for IgA production (hsa04672)493979093.4E-082.4E-07
Natural killer cell-mediated cytotoxicity (hsa04650)13110015 8214.7E-062.8E-05
TNF signalling pathway (hsa04668)1128812 6391.9E-059.4E-05
JAK-STAT signalling pathway (hsa04630)16213318 0037.4E-050.00032
RIG-I-like receptor signalling pathway (hsa04622)706384590.000210.00080
NOD-like receptor signalling pathway (hsa04621)17810915 7290.000310.0011
Complement and coagulation cascades (hsa04610)795071120.000410.0013
Toll-like receptor signalling pathway (hsa04620)1049612 1780.000800.0022
Cytokine-cytokine receptor interaction (hsa04060)29422126 7710.000830.0022
C-type lectin receptor signalling pathway (hsa04625)1047512 9860.00200.0050
IL-17 signalling pathway (hsa04657)936893580.00430.0100
Fc epsilon RI signalling pathway (hsa04664)685185140.00520.011
Viral protein interaction with cytokine and receptor (hsa04061)1007584350.00620.013
NF-kappa B signalling pathway (hsa04064)1028814 3490.00780.015
Osteoclast differentiation (hsa04380)12810118 6020.0130.023
T cell receptor signalling pathway (hsa04660)1038514 2680.0140.025
Cytosolic DNA-sensing pathway (hsa04623)634049930.0150.025
  • Pathways with FDR <0.05 in the association analysis including all genes are presented.

  • *SKAT-O SLE case-control association p value.

  • †SKAT-O SLE case–control association FDR.

  • FDR, false discovery rate; IL-17, interleukin 17; NF, nuclear factor; NOD, nucleotide-binding oligomerisation domain; RIG, retinoic acid-inducible gene; SKAT-O, sequence kernel association optimal test; SLE, systemic lupus erythematosus; SNV, single-nucleotide polymorphism; TNF, tumour necrosis factor.