Table 2.
Common canonical pathways in PBMC at acute (W1 vs. W0) and chronic (W14 vs. W1, W14 vs. W0) stages of F. hepatica infection in cattle.
| Ingenuity canonical pathways | W1 vs. W0 | W14 vs. W1 | W14 vs. W0 | ||||||
|---|---|---|---|---|---|---|---|---|---|
| –log (p-value)a | Ratiob | z-scorec | –log (p-value)a | Ratiob | z-scorec | –log (p-value)a | Ratiob | z-scorec | |
| Sertoli cell-sertoli cell junction signaling | 3.91 | 0.030 | NA | 4.59 | 0.143 | NA | – | – | – |
| IL-6 signaling | 1.72 | 0.018 | 0 | 3.61 | 0.139 | −1.291 | 1.36 | 0.204 | 2.4 |
| Toll-like receptor signaling | 2.14 | 0.031 | 0 | 2.93 | 0.154 | −0.333 | – | – | – |
| Germ cell-sertoli cell junction signaling | 3.8 | 0.028 | NA | 2.38 | 0.106 | NA | – | – | – |
| PPAR signaling | 1.99 | 0.026 | 0 | 1.85 | 0.115 | 0.333 | – | – | – |
| IL-10 signaling | 2.23 | 0.034 | NA | 1.64 | 0.121 | NA | – | – | – |
| Osteoarthritis pathway | 1.64 | 0.017 | 0 | 1.49 | 0.094 | 2.111 | 2.76 | 0.244 | 2.2 |
| Breast cancer regulation by Stahmin 1 | 3.53 | 0.024 | NA | 1.45 | 0.084 | NA | – | – | – |
| B cell activating factor signaling | 2.55 | 0.05 | 0 | 1.35 | 0.125 | −0.447 | – | – | – |
| Axonal guidance signaling | 2.72 | 0.015 | NA | 1.3 | 0.073 | NA | – | – | – |
| 14-3-3-mediated signaling | 5.73 | 0.046 | 0 | – | – | – | – | – | – |
| Phagosome maturation | 4.18 | 0.035 | NA | – | – | – | – | – | – |
| TGF-β signaling | 2.04 | 0.027 | 0 | – | – | – | – | – | – |
| STAT3 pathway | 1.74 | 0.019 | 0 | – | – | – | 2.02 | 0.229 | 1.387 |
| Th2 pathway | 1.68 | 0.018 | 0 | – | – | – | – | – | – |
| Antigen presentation pathway | – | – | – | 3.72 | 0.235 | NA | 1.39 | 0.265 | NA |
| CD40 signaling | – | – | – | 3.19 | 0.155 | −2.111 | – | – | – |
| Apoptosis signaling | – | – | – | 2.92 | 0.136 | −1.265 | – | – | – |
| Hepatic cholestasis | – | – | – | 2.92 | 0.13 | NA | 2.29 | 0.24 | NA |
| TNFR1 signaling | – | – | – | 2.79 | 0.174 | −2.121 | – | – | – |
| TNFR2 signaling | – | – | – | 1.9 | 0.172 | 0.447 | – | – | – |
| Death receptor signaling | – | – | – | 1.63 | 0.106 | −1.667 | – | – | – |
| Dendritic cell maturation | – | – | – | 1.56 | 0.092 | 1.732 | 1.62 | 0.206 | 2.353 |
| Production of nitric oxide and reactive oxygen species in macrophages | – | – | – | 1.56 | 0.089 | −0.832 | – | – | – |
| HGF Signaling | – | – | – | 1.47 | 0.095 | −3.162 | – | – | – |
| Hepatic fibrosis/hepatic stellate cell activation | – | – | – | 1.41 | 0.097 | NA | 2.07 | 0.237 | NA |
| Complement system | – | – | – | – | – | – | 1.87 | 0.333 | 1.633 |
| IL-4 signaling | – | – | – | – | – | – | 1.35 | 0.215 | NA |
a
The probability of association of genes from our dataset with the canonical pathway by random chance alone using Fisher's exact test.
b
The number of genes in our dataset that meets the cut-off criteria (FDR <0.05 and detected only in the infected group), divided by the total number of genes involved in that pathway.
c
Overall activity status of the pathway. Z < -2 indicates a prediction of an overall decrease in activity while Z > 2 predicts an overall increase in the activity. NA indicates pathways that are currently ineligible for a prediction.