SLE case–control pathway based aggregate association analysis
| Pathway | Genes in pathway | Genes in test | SNVs in test | P value* | FDR† |
| Th1 and Th2 cell differentiation (hsa04658) | 92 | 78 | 14 362 | 6.3E-11 | 2.2E-09 |
| Antigen processing and presentation (hsa04612) | 77 | 40 | 8017 | 1.8E-10 | 3.1E-09 |
| Hematopoietic cell lineage (hsa04640) | 97 | 71 | 13 013 | 3.8E-10 | 4.5E-09 |
| Th17 cell differentiation (hsa04659) | 107 | 96 | 19 347 | 1.7E-09 | 1.5E-08 |
| Intestinal immune network for IgA production (hsa04672) | 49 | 39 | 7909 | 3.4E-08 | 2.4E-07 |
| Natural killer cell-mediated cytotoxicity (hsa04650) | 131 | 100 | 15 821 | 4.7E-06 | 2.8E-05 |
| TNF signalling pathway (hsa04668) | 112 | 88 | 12 639 | 1.9E-05 | 9.4E-05 |
| JAK-STAT signalling pathway (hsa04630) | 162 | 133 | 18 003 | 7.4E-05 | 0.00032 |
| RIG-I-like receptor signalling pathway (hsa04622) | 70 | 63 | 8459 | 0.00021 | 0.00080 |
| NOD-like receptor signalling pathway (hsa04621) | 178 | 109 | 15 729 | 0.00031 | 0.0011 |
| Complement and coagulation cascades (hsa04610) | 79 | 50 | 7112 | 0.00041 | 0.0013 |
| Toll-like receptor signalling pathway (hsa04620) | 104 | 96 | 12 178 | 0.00080 | 0.0022 |
| Cytokine-cytokine receptor interaction (hsa04060) | 294 | 221 | 26 771 | 0.00083 | 0.0022 |
| C-type lectin receptor signalling pathway (hsa04625) | 104 | 75 | 12 986 | 0.0020 | 0.0050 |
| IL-17 signalling pathway (hsa04657) | 93 | 68 | 9358 | 0.0043 | 0.0100 |
| Fc epsilon RI signalling pathway (hsa04664) | 68 | 51 | 8514 | 0.0052 | 0.011 |
| Viral protein interaction with cytokine and receptor (hsa04061) | 100 | 75 | 8435 | 0.0062 | 0.013 |
| NF-kappa B signalling pathway (hsa04064) | 102 | 88 | 14 349 | 0.0078 | 0.015 |
| Osteoclast differentiation (hsa04380) | 128 | 101 | 18 602 | 0.013 | 0.023 |
| T cell receptor signalling pathway (hsa04660) | 103 | 85 | 14 268 | 0.014 | 0.025 |
| Cytosolic DNA-sensing pathway (hsa04623) | 63 | 40 | 4993 | 0.015 | 0.025 |
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.