Table 3.
Genotype-specific canonical pathways altered in progressive HCV liver injury.
| Ingenuity Canonical Pathways | Genes (n) | HCV G3 vs HCV G1 | HCV G1 vs NDL | HCV G3 vs NDL | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Rank | −log(p-value) | Ratio(%)* | Rank | −log(p-value) | Ratio(%)* | Rank | −log(p-value) | Ratio(%)* | ||
| Leukocyte Extravasation Signaling | 117 | 1 | 4.73 | 32.5 | — | — | — | 333 | 0.30 | 32.5 |
| Agranulocyte Adhesion and Diapedesis | 84 | 2 | 3.45 | 32.1 | — | — | — | 75 | 1.18 | 40.5 |
| Granulocyte Adhesion and Diapedesis | 91 | 3 | 3.21 | 30.8 | — | — | — | 33 | 1.69 | 42.9 |
| MSP-RON Signaling Pathway | 27 | 4 | 3.18 | 44.4 | — | — | — | — | — | — |
| B Cell Receptor Signaling | 113 | 5 | 2.89 | 28.3 | — | — | — | — | — | — |
| Role of Tissue Factor in Cancer | 70 | 6 | 2.77 | 31.4 | 255 | 0.33 | 40 | 45 | 1.41 | 42.9 |
| Role of Pattern Recognition Receptors in Recognition of Bacteria and Viruses | 76 | 7 | 2.63 | 30.3 | 270 | 0.30 | 39.5 | 240 | 0.52 | 35.5 |
| Glioma Invasiveness Signaling | 39 | 8 | 2.53 | 35.9 | 245 | 0.35 | 41 | 210 | 0.61 | 38.5 |
| Natural Killer Cell Signaling | 56 | 9 | 2.48 | 32.1 | — | — | — | 192 | 0.63 | 37.5 |
| FcƟ Receptor-mediated Phagocytosis in Macrophages and Monocytes | 57 | 10 | 2.39 | 31.6 | — | — | — | 36 | 1.64 | 45.6 |
| Bile Acid Biosynthesis, Neutral Pathway | 13 | — | — | — | 1 | 3.01 | 84.6 | 2 | 2.92 | 76.9 |
| Triacylglycerol Biosynthesis | 21 | 264 | 0.32 | 19 | 2 | 2.60 | 71.4 | 350 | 0.27 | 33.3 |
| Noradrenaline and Adrenaline Degradation | 21 | — | — | — | 3 | 2.60 | 71.4 | 58 | 1.36 | 52.4 |
| Serotonin Degradation | 37 | — | — | — | 4 | 2.06 | 59.5 | 9 | 2.33 | 54.1 |
| Coagulation System | 31 | 60 | 1.21 | 29 | 5 | 2.03 | 61.3 | 14 | 2.13 | 54.8 |
| LPS/IL-1 Mediated Inhibition of RXR Function | 158 | 265 | 0.32 | 17.1 | 6 | 1.99 | 48.1 | 5 | 2.61 | 43 |
| LXR/RXR Activation | 99 | 228 | 0.41 | 18.2 | 7 | 1.94 | 50.5 | 78 | 1.12 | 39.4 |
| PXR/RXR Activation | 56 | — | — | — | 8 | 1.76 | 53.6 | 15 | 2.06 | 48.2 |
| NAD biosynthesis II (from tryptophan) | 9 | 133 | 0.75 | 33.3 | 9 | 1.68 | 77.8 | 125 | 0.90 | 55.6 |
| Stearate Biosynthesis I (Animals) | 25 | — | — | — | 10 | 1.59 | 60 | 143 | 8.35 | 44 |
| Virus Entry via Endocytic Pathways | 54 | 90 | 0.98 | 24.1 | 294 | 0.26 | 38.9 | 1 | 3.51 | 55.6 |
| Endothelin-1 Signaling | 103 | 217 | 0.45 | 18.4 | 12 | 1.56 | 48.5 | 3 | 2.83 | 46.6 |
| Macropinocytosis Signaling | 42 | 115 | 0.82 | 23.8 | — | — | — | 4 | 2.70 | 54.8 |
| Prolactin Signaling | 53 | 292 | 0.27 | 17 | 103 | 0.69 | 45.3 | 6 | 2.47 | 50.9 |
| Thrombopoietin Signaling | 39 | 196 | 0.49 | 20.5 | 109 | 0.66 | 46.2 | 7 | 2.39 | 53.8 |
| Xenobiotic Metabolism Signaling | 183 | 236 | 0.38 | 17.5 | 121 | 0.61 | 41.5 | 8 | 2.35 | 41.5 |
| Hepatic Cholestasis | 116 | 86 | 0.99 | 21.6 | 100 | 0.71 | 43.1 | 10 | 2.31 | 44 |
*Ratio: The percentage of differentially expressed genes (up- or down-regulated), when compared with the total number of genes within a specified canonical pathway, as defined by Ingenuity Pathways Analysis, -log10(p-value) <1.30; -, not applicable.