Table 3.
Biological pathway analyses
| DAVID GO functional annotation biological processes | KEGG pathways | Ingenuity pathways (fold change) | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| A. Pathways | # | Term | Count | % | P value | Term | Count | % | P value | Top canonical pathways | P value | Overlap |
| 220 Stress genes (n = 220 genes, 232 probesets) | 1 | Antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent | 8 | 3.7 | 9.30E-06 | Antigen processing and presentation | 8 | 3.7 | 9.80E-05 | Antigen presentation pathway | 1.71E-06 | 15.8% 6/38 |
| 2 | Proteasome-mediated ubiquitin-dependent protein catabolic process | 12 | 5.6 | 3.10E-05 | Viral myocarditis | 7 | 3.3 | 1.50E-04 | Natural killer cell signaling | 2.67E-05 | 6.6% 8/122 | |
| 3 | Negative regulation of T cell proliferation | 6 | 2.8 | 7.10E-05 | Lysosome | 9 | 4.2 | 3.60E-04 | Autoimmune thyroid disease signaling | 1.02E-04 | 10.4% 5/48 | |
| 4 | Protein K48-linked ubiquitination | 6 | 2.8 | 2.30E-04 | Epstein–Barr virus infection | 11 | 5.1 | 1.20E-03 | Graft-vs.-host disease signaling | 1.02E-04 | 10.4% 5/48 | |
| 5 | Antigen processing and presentation of peptide antigen via MHC class I | 5 | 2.3 | 4.10E-04 | Graft-vs.-host disease | 5 | 2.3 | 1.70E-03 | Phagosome maturation | 1.02E-04 | 5.4% 8/148 | |
| B. Diseases | David | Ingenuity pathways disease | ||||||
|---|---|---|---|---|---|---|---|---|
| # | Term | Count | % | P value | Diseases and disorders | P value | # Molecules | |
| 220 Stress genes (n = 220 genes, 232 probesets) | 1 | HIV | 10 | 4.7 | 1.10E-03 | Cancer | 9.75E-03–2.15E-07 | 202 |
| 2 | Drug-induced liver injury | 4 | 1.9 | 2.70E-03 | Organismal injury and abnormalities | 9.75E-03–2.15E-07 | 206 | |
| 3 | HIV infections|[X]human immunodeficiency virus disease | 12 | 5.6 | 3.00E-03 | Infectious diseases | 8.66E-03–2.33E-06 | 53 | |
| 4 | Malaria, cerebral|malaria, falciparum | 3 | 1.4 | 3.00E-03 | Inflammatory response | 9.75E-03–3.06E-05 | 61 | |
| 5 | Adrenal hyperplasia, congenital | 3 | 1.4 | 4.00E-03 | Metabolic disease | 9.75E-03–6.01E-05 | 50 | |
For validated biomarkers (n = 232 probesets, 220 genes)