Table I.
Enriched pathways of modules 1–3.
| A, Module 1 | ||
|---|---|---|
| Pathway | FDR | Genes |
| Cytokine-cytokine receptor interaction | 2.80×10−9 | CCL20, CCL8, CSF1R, CXCL1, CXCL16, CXCL2, CXCL5, CXCL6, PPBP |
| Rheumatoid arthritis | 2.80×10−9 | CCL20, CXCL1, CXCL5, CXCL6, FOS, MMP1, MMP3 |
| Chemokine signaling pathway | 3.57×10−9 | CCL20, CCL8, CXCL1, CXCL16, CXCL2, CXCL5, CXCL6, PPBP |
| TNF signaling pathway | 3.57×10−9 | CCL20, CXCL1, CXCL2, CXCL5, FOS, MMP3, MMP9 |
| Pertussis | 1.35×10−6 | C1QB, CD14, CXCL5, CXCL6, FOS |
| Transcriptional misregulation in cancer | 8.55×10−5 | CD14, CSF1R, IGF1, MMP3, MMP9 |
| Salmonella infection | 0.000131 | CD14, CXCL1, CXCL2, FOS |
| Legionellosis | 0.00145 | CD14, CXCL1, CXCL2 |
| Pathways in cancer | 0.00145 | CSF1R, FOS, IGF1, MMP1, MMP9 |
| Complement and coagulation cascades | 0.00248 | BDKRB1, C1QB, SERPINE1 |
| Chagas disease (American trypanosomiasis) | 0.00628 | C1QB, FOS, SERPINE1 |
| Toll-like receptor signaling pathway | 0.00669 | CD14, FOS, SPP1 |
| Osteoclast differentiation | 0.011 | CSF1R, FOS, TYROBP |
| Bladder cancer | 0.0206 | MMP1, MMP9 |
| NOD-like receptor signaling pathway | 0.0439 | CXCL1, CXCL2 |
| B, Module 2 | ||
| Pathway | FDR | Genes |
| Cytokine-cytokine receptor interaction | 0.0431 | IL6, IL8, KIT |
| NOD-like receptor signaling pathway | 0.0431 | IL6, IL8 |
| Hematopoietic cell lineage | 0.0431 | IL6, KIT |
| Epithelial cell signaling in Helicobacter pylori infection | 0.0431 | HBEGF, IL8 |
| Salmonella infection | 0.0431 | IL6, IL8 |
| Pertussis | 0.0431 | IL6, IL8 |
| Legionellosis | 0.0431 | IL6, IL8 |
| Malaria | 0.0431 | IL6, IL8 |
| Pathways in cancer | 0.0431 | IL6, IL8, KIT |
| Rheumatoid arthritis | 0.0431 | IL6, IL8 |
| Toll-like receptor signaling pathway | 0.0494 | IL6, IL8 |
| Chagas disease (American trypanosomiasis) | 0.0494 | IL6, IL8 |
| Amoebiasis | 0.0494 | IL6, IL8 |
| C, Module 3 | ||
| Pathway | FDR | Genes |
| Intestinal immune network for IgA production | 0.00149 | HLA-DPA1, HLA-DRA |
| Type I diabetes mellitus | 0.00149 | HLA-DPA1, HLA-DRA |
| Staphylococcus aureus infection | 0.00149 | HLA-DPA1, HLA-DRA |
| Asthma | 0.00149 | HLA-DPA1, HLA-DRA |
| Autoimmune thyroid disease | 0.00149 | HLA-DPA1, HLA-DRA |
| Allograft rejection | 0.00149 | HLA-DPA1, HLA-DRA |
| Graft-versus-host disease | 0.00149 | HLA-DPA1, HLA-DRA |
| Viral myocarditis | 0.00152 | HLA-DPA1, HLA-DRA |
| Inflammatory bowel disease | 0.00172 | HLA-DPA1, HLA-DRA |
| Antigen processing and presentation | 0.00175 | HLA-DPA1, HLA-DRA |
| Leishmaniasis | 0.00175 | HLA-DPA1, HLA-DRA |
| Rheumatoid arthritis | 0.00244 | HLA-DPA1, HLA-DRA |
| Systemic lupus erythematosus | 0.00275 | HLA-DPA1, HLA-DRA |
| Toxoplasmosis | 0.00363 | HLA-DPA1, HLA-DRA |
| Cell adhesion molecules | 0.00499 | HLA-DPA1, HLA-DRA |
| Phagosome | 0.0051 | HLA-DPA1, HLA-DRA |
| Tuberculosis | 0.00645 | HLA-DPA1, HLA-DRA |
| Influenza A | 0.00645 | HLA-DPA1, HLA-DRA |
| Herpes simplex infection | 0.00645 | HLA-DPA1, HLA-DRA |
| Epstein-Barr virus infection | 0.00722 | HLA-DPA1, HLA-DRA |
| HTLV-I infection | 0.012 | HLA-DPA1, HLA-DRA |
FDR, false discovery rate; TNF, tumor necrosis factor; NOD, nucleotide-binding oligomerization domain; IgA, immunoglobulin A; HTLV-I, human T-lymphotrophic like virus I; CCL, C-C motif chemokine ligand; CSF1R, colony stimulating factor 1 receptor; CXCL, C-X-C motif chemokine ligand; PPBP, pro-platelet basic protein; FOS, FOS proto-oncogene, AP-1 transcription factor subunit; MMP, matrix metallopeptidase; C1QB, complement C1q B chain; CD14, CD14 molecule; IGF1, insulin like growth factor 1; BDKRB1, bradykinin receptor 1; SERPINE1, serpin family E member 1; SPP1, secrete phosphoprotein 1; TYROBP, TYRO protein tyrosine kinase binding protein; IL, interleukin; KIT, KIT proto-oncogene receptor tyrosine kinase; HBEGF, heparin binding EGF like growth factor; HLA-DPA1, major histocompatibility complex, class II, DP α 1; HLA-DRA, major histocompatibility complex, class II, DR α.