Table 2

Over-represented (p<0.05) canonical pathways in which RA and SLE overlapping loci, RA only loci and SLE only loci are involved

Canonical pathwayType of pathwayp ValueGenes in pathway
SLE/RA overlap
Dendritic cell maturationCellular immune response, cytokine signalling, pathogen-influenced signalling1.4×10−4STAT4, FCGR2A, HLA-DRB1
T helper cell differentiationCellular immune response, cytokine signalling9.8×10−4STAT4, HLA-DRB1
CTLA4 signalling in cytotoxic T lymphocytesCellular immune response1.8×10−3HLA-DRB1, PTPN22
Role of NFAT in regulation of the immune responseCellular immune response, humoral immune response, intracellular and second messenger signalling6.2×10−3FCGR2A, HLA-DRB1
TNFR2 signallingApoptosis, cytokine signalling0.02TNFAIP3
B-cell developmentCellular growth, proliferation and development, humoral immune response0.02HLA-DRB1
Antigen presentation pathwayCellular immune response, humoral immune response0.03HLA-DRB1
Allograft rejection signallingCellular immune response, disease specific pathway0.03HLA-DRB1
Autoimmune thyroid disease signallingCellular immune response, disease specific pathway, humoral immune response0.03HLA-DRB1
Graft-versus-host disease signallingCellular immune response, disease specific pathway0.03HLA-DRB1
TNFR1 signallingApoptosis, cytokine signalling0.03TNFAIP3
Nur77 signalling in T lymphocytesApoptosis, cellular immune response, Nuclear receptor signalling0.04HLA-DRB1
Calcium-induced T lymphocyte apoptosisApoptosis, cellular immune response0.04HLA-DRB1
CD40 signallingCellular immune response, humoral immune response0.04TNFAIP3
IL-10 signallingCellular immune response, cytokine signalling0.04FCGR2A
JAK/Stat signallingApoptosis, cellular growth, proliferation and development, intracellular and second messenger signalling0.04STAT4
RA only
iCOS-iCOSL signalling in T helper cellsCellular immune response9.8×10−9PTPRC, CD28, PRKCQ, CD40, IL2RA, IL2RB
T helper cell differentiationCellular immune response, cytokine signalling5.2×10−8IL21, IL6ST, CD28, CD40, IL2RA
Altered T-cell and B-cell signalling in RACellular immune response, disease-specific pathways6.6×10−6IL21, CD28, CD40, CCL21
T-cell receptor signallingCellular immune response1.3×10−5PTPRC, CD28, PRKCQ, CTLA4
IL-12 signalling and production in macrophagesCellular immune response, cytokine signalling2.0×10−5TRAF6, PRKCQ, CD40, REL
CD28 signalling in T helper cellsCellular immune response2.7×10−5PTPRC, CD28, PRKCQ, CTLA4
CD40 signallingCellular immune response, humoral immune response1.0×10−4TRAF6, CD40, TRAF1
Cross-talk between dendritic cells and natural killer cellsCellular immune response3.7×10−4CD28, CD40, IL2RB
B cell developmentCellular growth, proliferation and development, humoral immune response9.3×10−4PTPRC, CD40
Systemic lupus erythematosus signallingDisease-specific pathways1.0×10−3PTPRC, CD28, CD40
Role of macrophages, fibroblasts and endothelial cells in rheumatoid arthritisDisease-specific pathways1.2×10−3TRAF6, IL6ST, PRKCQ, TRAF1
NF-κB signallingCellular immune response, cytokine signalling, humoral immune response, organismal growth and development1.3×10−3TRAF6, PRKCQ, CD40
April -mediated signallingApoptosis1.5×10−3TRAF6, TRAF1
Dendritic cell maturationCellular immune response, cytokine signalling, pathogen-influenced signalling1.6×10−3TRAF6, CD40, CD58
B-cell activating factor signallingCellular growth, proliferation and development, humoral immune response1.7×10−3TRAF6, TRAF1
Allograft rejection signallingCellular immune response, disease-specific pathways1.8×10−3CD28, CD40
Autoimmune thyroid disease signallingCellular immune response, disease-specific pathways, humoral immune response1.9×10−3CD28, CD40
Primary immunodeficiency signallingCellular immune response, disease-specific pathways, humoral immune response2.3×10−3PTPRC, CD40
IL-2 signallingCellular immune response, cytokine signalling3.1×10−3IL2RA, IL2RB
Lymphotoxin β receptor signallingApoptosis3.2×10−3TRAF6, TRAF1
Activation of IRF by cytosolic pattern recognition receptorsCellular immune response4.1×10−3TRAF6, CD40
Small cell lung cancer signallingCancer, disease-specific pathways5.5×10−3TRAF6, TRAF1
Communication between innate and adaptive immune cellsCellular immune response5.8×10−3CD28, CD40
IL-6 signallingCellular immune response, cytokine signalling8.1×10−3TRAF6, IL6ST
CTLA4 aignalling in cytotoxic T lymphocytesCellular immune response8.7×10−3CD28, CTLA4
Type I diabetes mellitus signallingApoptosis, disease-specific pathways,0.01TRAF6, CD28
PKC signalling in T lymphocytesCellular immune response0.01CD28, PRKCQ
Hepatic fibrosis/hepatic stellate cell activationDisease-specific pathways0.02CD40, CCL21
Hepatic cholestasisDisease-specific pathways0.02TRAF6, PRKCQ
B cell receptor signallingHumoral immune response0.02PTPRC, PRKCQ
IL-8 signallingCellular immune response, cytokine signalling0.03TRAF6, PRKCQ
Acute phase response signallingCytokine signalling0.03TRAF6, IL6ST
Role of NFAT in regulation of the immune responseCellular immune response, humoral immune response, intracellular and second messenger signalling0.03CD28, PRKCQ
Role of NFAT in cardiac hypertrophyCardiovascular signalling, disease-specific pathways0.03IL6ST, PRKCQ
TNFR2 signallingApoptosis, cytokine signalling0.04TRAF1
4-1BB signalling in T lymphocytesCellular immune response0.04TRAF1
SLE only
Mitotic roles of polo-like kinaseCell cycle regulation0.035PTTG1
Angiopoietin signallingCardiovascular signalling, cellular growth, proliferation and development, growth factor signalling0.041TNIP1
Ubiquinone biosynthesisMetabolism of cofactors and vitamins0.045UHRF1BP1
Caveolar-mediated endocytosis signallingCellular immune response, organismal growth and development, pathogen-influenced signalling0.046ITGAM

  • NFAT, nuclear factor of activated T cells; RA, rheumatoid arthritis; SLE, systemic lupus erythematosus.