Table 3.
Top canonical pathways with p-value, FDR, ratio and molecules from the gene list associated with the respective pathways
| Gene list | Top canonical pathways | p-Value | FDR (%) | Ratio | Molecules associated with the pathway |
|---|---|---|---|---|---|
| A. Based on genes within PAM140 gene list (138 genes) | NF-kB signaling | 1.04E−03 | 8.6 | 6/172 | FCER1G, IL1B, IL1R2, PIK3CD, TANK, TNFRSF1B |
| Acute-phase response signaling | 1.07E−03 | 8.6 | 6/171 | FGG, IL1B, LPP, PIK3CD, SERPINA3, TNFRSF1B | |
| IL-10 signaling | 1.29E−03 | 8.6 | 4/72 | CCR1, IL1B, IL1R2, LBP | |
| IL-6 signaling | 1.3E−03 | 8.6 | 5/122 | IL1B, IL1R2, LBP, PIK3CD, TNFRSF1B | |
| Serotonin receptor signaling | 1.54E−03 | 8.6 | 3/33 | HTR2A, HTR3D, SLC18A1 | |
| B. Based on genes within PAM84 gene list (82 genes) | Hepatic cholestasis | 1.6E−03 | 12.3 | 4/143 | IL1A, IL1R2, LBP, SLCO1C1 |
| IL-10 signaling | 2.0E−03 | 12.3 | 3/72 | IL1A, IL1R2, LBP | |
| Acute-phase response signaling | 4.8E−03 | 12.6 | 4/172 | FGG, IL1A, LBP, RBP1 | |
| Retioate biosynthesis 1 | 6.3E−03 | 17.5 | 2/34 | ALDH1A3, RBP1 | |
| LPS/IL-1-mediated inhibition of RXR function | 8.7E−03 | 17.5 | 4/226 | ALDH1A3, IL1A, IL1R2, LBP | |
| C. Based on genes correlated to given dose (2,072 genes) | NF-kB signaling | 4.2E−05 | 2 | 37/169 | |
| Role of macrophages, fibroblasts and endothelial cells in rheumatoid arthritis | 8E−05 | 2 | 56/311 | ||
| LPS/IL-1-mediated inhibition of RXR function | 1.6E−04 | 2.6 | 43/222 | ||
| PPAR signaling | 5.40E−04 | 6 | 22/100 | ||
| Differential regulation of cytokine production in intestinal epithelial cells by IL-17A and IL17F | 7.00E−04 | 7 | 9/23 | ||
| D. Based on genes pos. correlated to given dose (1,069 genes) | Role of macrophages, fibroblasts and endothelial cells in rheumatoid arthritis | 6.2E−04 | 14 | 32/311 | |
| NF-kB signaling | 7.5E−04 | 14 | 21/169 | ||
| PPAR signaling | 9.5E−04 | 14 | 14/100 | ||
| E. Based on genes neg. correlated to given dose (1,035 genes) | VDR/RXR activation | 4.7E−04 | 18 | 13/78 | |
| Role of Oct4 in mammalian embryonic stem cell pluripotency | 8.4E−04 | 18 | 9/44 | ||
| Aryl hydrocarbon receptor signaling | 2.00E−03 | 25 | 17/141 | ||
| Top bio functions | p-Value | Molecules | |||
| F. Based on genes correlated to given dose (2,072 genes) | |||||
| Cancer | 8E−11/3E−04 | 1,120 | |||
| Organismal injury and abnormalities | 8E−10/2E−04 | 274 | |||
| Inflammatory response | 5E−09/3E−04 | 334 | |||
Results are shown for the different gene lists. A: PAM140 list, B: PAM84 list, C: pathway analysis based on genes correlated with given dose, D: genes positively correlated with given dose, E: top bio functions displayed with p-values and molecules involved for genes correlated with given dose, F: genes positively correlated with given dose.