Table 3.
Enriched Kegg pathways during acute HCV infection. Differentially expressed genes (DEGs) at each time point were analyzed with software that utilizes a Fisher’s exact test (p < 0.05 considered significant) to determine enriched pathways. The background gene list included only genes that were expressed (EGs), while genes that were not expressed were excluded from statistical analysis.
| KEGG Pathway name | Genes in Pathway | 6 h | 48 h | 72 h | |||
|---|---|---|---|---|---|---|---|
| DEGs (EGs) | p value | DEGs (EGs) | p value | DEGs (EGs) | p value | ||
| MAPK signaling | 268 | 5 (168) | 0.003 | 13 (173) | 0.01 | 33 (177) | 0.0005 |
| Cytokine-cytokine receptor interaction | 265 | 9 (90) | 0.005 | 19 (92) | 0.002 | ||
| Antigen processing and presentation | 78 | 2 (36) | 0.02 | ||||
| RIG-I-like receptor signaling | 71 | 12 (44) | 0.001 | ||||
| Toll-like receptor signaling | 102 | 11 (58) | 0.03 | ||||
| NOD-like receptor signaling | 59 | 9 (40) | 0.02 | ||||
| Cytosolic DNA-sensing pathway | 56 | 7 (28) | 0.02 | ||||
| Epithelial cell signaling in H. pylori infection | 68 | 11 (53) | 0.01 | ||||
| Adipocytokine signaling | 68 | 7 (50) | 0.002 | 13 (48) | 0.0008 | ||
| TGF-beta signaling | 85 | 6 (68) | 0.03 | 13 (55) | 0.02 | ||
| Regulation of autophagy | 34 | 5 (18) | 0.03 | ||||
| Apoptosis | 89 | 12 (68) | 0.04 | ||||
| ECM-receptor interaction | 85 | 4 (37) | 0.04 | ||||
| Jak-STAT signaling | 155 | 15 (77) | 0.01 | ||||
| Hepatitis C | 135 | 20 (98) | 0.002 | ||||
| mTOR signaling | 52 | 2 (41) | 0.02 | ||||
| Hedgehog signaling | 56 | 5 (30) | 0.004 | ||||
| Notch signaling | 47 | 9 (37) | 0.01 | ||||
| Renal cell carcinoma | 70 | 2 (58) | 0.04 | ||||
| Basal cell carcinoma | 55 | 4 (31) | 0.02 | ||||
| Hematopoietic cell lineage | 88 | 4 (29) | 0.02 | ||||
| Osteoclast differentiation | 128 | 7 (76) | 0.02 | 19 (76) | 0.0001 | ||
| Insulin signaling | 138 | 19 (110) | 0.01 | ||||
| Type II diabetes mellitus | 48 | 4 (27) | 0.01 | ||||
| Aminoacyl tRNA biosynthesis | 63 | 13 (41) | 0.0001 | ||||
| Ribosome biogenesis in eukaryotes | 81 | 12 (44) | 0.001 | ||||
| Sphingolipid metabolism | 40 | 9 (33) | 0.005 | ||||
| Glutathione metabolism | 50 | 2 (39) | 0.03 | ||||
| Cyanoamino acid metabolism | 7 | 1 (4) | 0.02 | ||||
| Ubiquinone and other terpenoid-quinone biosynthesis | 7 | 1 (5) | 0.03 | ||||
| Taurine and hypotaurine metabolism | 10 | 1 (5) | 0.03 | ||||
| Neurotophin signaling | 127 | 18 (94) | 0.006 | ||||
| One carbon pool by folate | 18 | 5 (17) | 0.03 | ||||
| Prion diseases | 36 | 2 (21) | 0.006 | ||||