Table 3. The RA-related pathways identified by integrating GWAS and gene expression (FDR<0.05).
| Pathway ID | Pathway name | Combined_P-value | FDR | Function class |
|---|---|---|---|---|
| hsa04062 | *Chemokine signaling pathway | 0 | 0 | Organismal Systems; Immune system |
| hsa04145 | *Phagosome | 0 | 0 | Cellular Processes; Transport and catabolism |
| hsa04514 | *Cell adhesion molecules (CAMs) | 0 | 0 | Environmental Information Processing; Signaling molecules and interaction |
| hsa04612 | *Antigen processing and presentation | 0 | 0 | Organismal Systems; Immune system |
| hsa04650 | Natural killer cell mediated cytotoxicity | 0 | 0 | Organismal Systems; Immune system |
| hsa04672 | *Intestinal immune network for IgA production | 0 | 0 | Organismal Systems; Immune system |
| hsa04940 | *Type I diabetes mellitus | 0 | 0 | Human Diseases; Endocrine and metabolic diseases |
| hsa05140 | *Leishmaniasis | 0 | 0 | Human Diseases; Infectious diseases |
| hsa05145 | *Toxoplasmosis | 0 | 0 | Human Diseases; Infectious diseases |
| hsa05150 | *Staphylococcus aureus infection | 0 | 0 | Human Diseases; Infectious diseases |
| hsa05152 | *Tuberculosis | 0 | 0 | Human Diseases; Infectious diseases |
| hsa05162 | *Measles | 0 | 0 | Human Diseases; Infectious diseases |
| hsa05164 | *Influenza A | 0 | 0 | Human Diseases; Infectious diseases |
| hsa05168 | *Herpes simplex infection | 0 | 0 | Human Diseases; Infectious diseases |
| hsa05310 | *Asthma | 0 | 0 | Human Diseases; Immune diseases |
| hsa05320 | *Autoimmune thyroid disease | 0 | 0 | Human Diseases; Immune diseases |
| hsa05323 | *Rheumatoid arthritis | 0 | 0 | Human Diseases; Immune diseases |
| hsa05330 | *Allograft rejection | 0 | 0 | Human Diseases; Immune diseases |
| hsa05332 | *Graft-versus-host disease | 0 | 0 | Human Diseases; Immune diseases |
| hsa05340 | Primary immunodeficiency | 0 | 0 | Human Diseases; Immune diseases |
| hsa05416 | *Viral myocarditis | 0 | 0 | Human Diseases; Cardiovascular diseases |
| hsa04660 | *T cell receptor signaling pathway | 2.00E-05 | 0.000175 | Organismal Systems; Immune system |
| hsa04640 | Hematopoietic cell lineage | 3.00E-05 | 0.000251 | Organismal Systems; Immune system |
| hsa04666 | Fc gamma R-mediated phagocytosis | 0.00029 | 0.002325 | Organismal Systems; Immune system |
| hsa04662 | B cell receptor signaling pathway | 0.00042 | 0.003233 | Organismal Systems; Immune system |
| hsa04380 | Osteoclast differentiation | 0.00074 | 0.005477 | Organismal Systems; Development |
| hsa04620 | Toll-like receptor signaling pathway | 0.00111 | 0.007912 | Organismal Systems; Immune system |
| hsa04670 | *Leukocyte transendothelial migration | 0.00651 | 0.044744 | Organismal Systems; Immune system |
*
Pathways were reported as RA-related pathways in previous literatures.