Table 3.
Enrichment of Ingenuity Pathway Analysis Pathways (P < 0.001) for the Differentially Expressed Genes between Subjects at Baseline and 1 Month
| Ingenuity Pathway Analysis Pathways | Number of DEGs (%) | −Log10 (P Values) | Genes |
|---|---|---|---|
| LXR/RXR activation | 8 | 4.5 | TLR4, LY96, CD14, SERPINA1, IRF3, HMGCR, MMP9, IL18RAP |
| Phagosome formation | 8 | 4.2 | FCAR, PIK3C2B, TLR4, CR1, ITGAM, RHOU, FCGR1A, FCGR1B |
| Osteoarthritis pathway | 10 | 4.2 | TLR4, TGFBR1, S100A9, RBPJ, NAMPT, TCF3, ALPL, MMP9, EP300, IL18RAP |
| Regulation of the epithelial–mesenchymal transition pathway | 9 | 3.9 | PIK3C2B, NOTCH2, TGFBR1, EGR1, RBPJ, TCF3, MAP2K1, MMP9, PSEN1 |
| Erythropoietin signaling | 6 | 3.8 | SOCS1, PIK3C2B, FOS, CBL, EPOR, MAP2K1 |
| Prolactin signaling | 6 | 3.7 | SOCS1, PIK3C2B, FOS, SOCS2, MAP2K1, EP300 |
| Acute phase response signaling | 8 | 3.5 | SOCS1, FOS, HP, RBP7, SOCS2, SERPINA1, TCF3, MAP2K1 |
| Role of macrophages, fibroblasts, and endothelial cells in rheumatoid arthritis | 11 | 3.4 | SOCS1, PIK3C2B, TLR4, FOS, TRAF4, TCF3, IL17RA, MAP2K1, FCGR1A, EP300, IL18RAP |
| Role of JAK2 in hormone-like cytokine signaling | 4 | 3.4 | SOCS1, EPOR, SOCS2, SIRPA |
| Pentose phosphate pathway (oxidative branch) | 2 | 3.2 | PGD, H6PD |
| Hepatic fibrosis/hepatic stellate cell activation | 8 | 3.2 | TLR4, LY96, TGFBR1, KLF6, CD14, MMP9, TIMP2, IL18RAP |
| Molecular mechanisms of cancer | 12 | 3.2 | PIK3C2B, FOS, CBL, TGFBR1, RHOU, ABL1, RBPJ, TCF3, MAP2K1, PSEN1, PRKAR1A, EP300 |
| IGF-1 signaling | 6 | 3.1 | SOCS1, PIK3C2B, FOS, SOCS2, MAP2K1, PRKAR1A |
| Production of nitric oxide and reactive oxygen species in macrophages | 8 | 3.1 | PIK3C2B, TLR4, FOS, CYBA, RHOU, SERPINA1, MAP2K1, SIRPA |
| IL-8 signaling | 8 | 3.0 | PIK3C2B, FOS, ITGAM, RHOU, IQGAP1, MAP2K1, CSTB, MMP9 |
| MIF regulation of innate immunity | 4 | 3.0 | TLR4, FOS, LY96, CD14 |
| Colorectal cancer metastasis signaling | 9 | 3.0 | PIK3C2B, TLR4, FOS, TGFBR1, RHOU, TCF3, MAP2K1, MMP9, PRKAR1A |
| Granzyme A signaling | 3 | 3.0 | ANP32A, HMGB2, EP300 |
| Toll-like receptor signaling | 5 | 3.0 | TLR4, FOS, LY96, TRAF4, CD14 |
Definition of abbreviations: DEGs = differentially expressed genes; IGF-1 = insulin-growth factor; JAK2 = Janus kinase 2; LXR/RXR = liver X receptor/retinoid X receptor; MIF = macrophage migration inhibitor factor.
The number and percentage of DEGs in each pathway, as well as the symbols of the DEGs, are listed in the table. The percentages of the DEGs are calculated from the number of DEGs in the specific pathway and the total number (239) of DEGs found between subjects at baseline and Month 1.