TABLE 2.
Top differentially expressed pathways at 2 dpi
| Gene regulation comparison for indicated strainsa | Canonical pathwayb | No. of genes | Scorec |
|---|---|---|---|
| 129 more regulated than IFNAR1−/− | Acute-phase response signaling | 15 | 4.3 |
| LXR/RXR activation | 9 | 4.1 | |
| FXR/RXR activation | 10 | 4.0 | |
| TREM1 signaling | 8 | 4.0 | |
| Hepatic cholestasis | 11 | 3.1 | |
| 129 more regulated than STAT1−/− | Pattern recognition receptors in recognition of bacteria and viruses | 21 | 7.6 |
| Interferon signaling | 11 | 5.9 | |
| Allograft rejection signaling | 12 | 5.3 | |
| Antigen presentation pathway | 11 | 5.3 | |
| Graft-vs-host disease signaling | 12 | 5.2 | |
| IFNAR1−/− more regulated than 129 | Valine, leucine, and isoleucine degradation | 25 | 7.4 |
| Propanoate metabolism | 21 | 5.9 | |
| LPS/IL-1-mediated inhibition of RXR function | 43 | 4.9 | |
| β-alanine metabolism | 18 | 4.8 | |
| Pyruvate metabolism | 22 | 4.8 | |
| IFNAR1−/− more regulated than STAT1−/− | Valine, leucine, and isoleucine degradation | 28 | 8.9 |
| Propanoate metabolism | 23 | 6.1 | |
| Pyruvate metabolism | 23 | 5.5 | |
| β-alanine metabolism | 18 | 4.4 | |
| Interferon signaling | 12 | 4.1 | |
| STAT1−/− more regulated than 129 | Arginine and proline metabolism | 9 | 4.3 |
| Urea cycle and metabolism of amino groups | 6 | 4.2 | |
| Bile acid biosynthesis | 7 | 4.0 | |
| IL-10 signaling | 7 | 3.2 | |
| Complement system | 5 | 2.9 | |
| STAT1−/− more regulated than IFNAR1−/− | LXR/RXR activation | 9 | 6.2 |
| Acute-phase response signaling | 12 | 5.2 | |
| IL-10 signaling | 7 | 4.6 | |
| Cytokine mediation of communication between immune cells | 6 | 3.9 | |
| Hepatic cholestasis | 9 | 3.8 |
a
Lists of differentially expressed genes were determined as described in Materials and Methods and were investigated using IPA. The 5 top-scoring canonical pathways are shown.
b
LXR, liver X receptor; RXR, retinoid X receptor; FXR, farsenoid X receptor; LPS, lipopolysaccharide.
c
Enrichment scores are calculated as −log(P value). The P value is derived from Fisher's exact test as described in Materials and Methods.