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 |