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Table 1 Top shared pathways associated with psoriasis identified in GWAS and EWAS at FDR < 5%, and their corresponding network key drivers (KDs) in skin and blood networks

From: Multi-omics integration reveals molecular networks and regulators of psoriasis

Supersets Module Size Resources Pathways KDs in skin KDs in blood
S1: Antigen processing and presentation 149 KEGG Antigen processing and presentation HLA-B, GBP1, C3, HLA-A, PSMB9 HLA-C, WARS, BCL3, BIRC3, SAT1
KEGG Viral myocarditis
KEGG Autoimmune thyroid disease
KEGG Type-I Diabetes mellitus
KEGG Graft versus host disease
KEGG Allograft rejection
S2: Intestinal immune network for IGA production 45 KEGG Asthma N/A BIRC3, SELL, LAPTM5, IRF8, CD40
KEGG Intestinal immune network for IGA production
S3: Cytokine cytokine receptor interaction 327 KEGG Cytokine-cytokine receptor interaction GRB2, STAT1, TNFAIP3, TNFSF10, EGFR BIRC3, SLA, PLAUR, LAPTM5, CSF2RB
KEGG JAK-STAT signaling pathway
S4: TCR signaling 51 Reactome TCR signaling LCK, CHUK, NFKBIA, NFKB2, FYB LCK, ZAP70, CD247, CD3E, CD8A
Reactome Generation of second messenger molecules
Reactome PD1 signaling
Reactome Phosphorylation of CD3 and TCR zeta chains
Reactome Translocation of ZAP 70 to immunological synapse
S5: CTLA4 pathway 31 Biocarta CTL pathway LCK, FYB, IKZF1, GAB1 LCK, CD247, GZMA, CD3E, NKG7
Biocarta CTLA4 pathway
Biocarta TCRA pathway
S6: LAIR pathway 22 Biocarta Lair pathway TNFAIP3, ICAM1 ITGAL, IFITM2, BIRC3, HLA-DPB1, MSN
Biocarta Granulocytes pathway
S7: IL10 pathway 24 Biocarta IL10 pathway IL6ST, STAT1, ICAM1 STAT3, LAPTM5, BCL3, IFNGR1, ARPC1B
Biocarta IL22BP pathway
S8: Inflammatory pathway 43 Biocarta Inflammation pathway MYD88 LAPTM5, CSF1R
Biocarta Cytokine pathway
Biocarta DC pathway
ABC transporters 44 KEGG ABC transporters N/A N/A
Adaptive immune system 522 Reactome Adaptive immune system PSMD13, PSMD14, PSMC5, PSMA1, PSMD8 PSMD6, PSMC5, PSMD1, PSMC1, PSMD4
Cell adhesion molecules (CAMs) 114 KEGG Cell adhesion molecules (CAMs) LCK LCK, ITGAL, SLA, LAPTM5, LILRB2
Endocytosis 177 KEGG Endocytosis GRB2, EGFR, RAB5A, UBC, CBL FYN, CD58, ATP6V0D1, LHFPL2
Hematopoietic cell lineage 83 KEGG Hematopoietic cell lineage MCL1, TIMP1 CSF1R, LAPTM5, PLAUR, SERPINB1, IRF8
Heparan sulfate biosynthesis and metabolism 41 Coexpression Heparan sulfate biosynthesis and metabolism THYN1, BBS4, YBX1, HSDL1, GNL3 N/A
Immunoregulatory interactions between a lymphoid and a non-lymphoid cell 64 Reactome Immunoregulatory interactions between a lymphoid and a non-lymphoid cell LCK, ICAM1, HLA-F LCK, KLRK1, CD247, LY96, PRF1
Initial triggering of complement 16 Reactome Initial triggering of complement N/A IFITM2, C2, C1QB, CCL18, C1R
Leishmania infection 58 KEGG Leishmania infection MYD88, IER3, NFKB1, NFKBIA, TNFAIP3 PLAUR, BCL3, BIRC3, LAPTM5, CXCL2
Natural killer cell-mediated cytotoxicity 132 KEGG Natural killer cell mediated cytotoxicity GRB2, LCK, FYN, RAC2, ABL1 LCK, SLA, PTPN6, GZMA, PRF1
NO2IL12 pathway 17 Biocarta NO2IL12 pathway LCK CD3E, GZMK, GZMA, LCK, ZAP70
PPARA pathway 58 Biocarta PPARA pathway AR, FOS, IER2, TRIB1, PPP1R15A TRIB1, NFKBIA, ZFP36, BCL6, BTG2
Primary immunodeficiency 35 KEGG Primary immunodeficiency LCK, IL32 CD247, CD8A, LCK, CD3E, MS4A1
SODD pathway 10 Biocarta SODD pathway TNFSF10, CASP8, BIRC2, LYN TRAF1, IL4R, LTB, CEBPD, FAS
  1. Note: The detailed MSEA results in GWAS and EWAS are in Additional file 1: Tables S5 and S6. The detailed results and full list of key driver genes identified in skin and blood networks are in Additional file 1: Table S9