Table 2. Immune-related biological pathways with over-represented genes of 1481 significantly up-regulated genes using a web tool (DAVID Bioinformatics Resources 6.8) during the first 18 hours of infection.
| Pathway # | Biological pathways | Hours PI | Count11 | FDR22 |
|---|---|---|---|---|
| GO:0006915 | apoptotic process | 6 | 30 | 0.03 |
| GO:0045824 | negative regulation of innate immune response | 6 | 6 | 0.00 |
| GO:0045071 | negative regulation of viral genome replication | 6, 9, 12, 15 | 16 | 0.00 |
| GO:0060333 | interferon-gamma-mediated signaling pathway | 6, 9, 12, 15 | 18 | 0.00 |
| GO:0006955 | immune response | 6, 9, 12, 15, 18 | 27 | 0.00 |
| GO:0009615 | response to virus | 6, 9, 12, 15, 18 | 22 | 0.00 |
| GO:0032480 | negative regulation of type I interferon production | 6, 9, 12, 15, 18 | 11 | 0.00 |
| GO:0045087 | innate immune response | 6, 9, 12, 15, 18 | 32 | 0.00 |
| GO:0051607 | defense response to virus | 6, 9, 12, 15, 18 | 38 | 0.00 |
| GO:0060337 | type I interferon signaling pathway | 6, 9, 12, 15, 18 | 25 | 0.00 |
| R-HSA-877300 | Interferon gamma signaling | 6, 9, 12, 15, 18 | 21 | 0.00 |
| R-HSA-909733 | Interferon alpha/beta signaling | 6, 9, 12, 15, 18 | 25 | 0.00 |
| R-HSA-936440 | Negative regulators of DDX58/IFIH1 signaling | 6, 9, 12, 15, 18 | 10 | 0.00 |
| GO:0006954 | inflammatory response | 6, 12, 18 | 27 | 0.00 |
| GO:0032689 | negative regulation of interferon-gamma production | 9 | 6 | 0.04 |
| GO:0032728 | positive regulation of interferon-beta production | 12 | 7 | 0.04 |
| hsa04620 | Toll-like receptor signaling pathway | 12 | 13 | 0.02 |
| hsa04622 | RIG-I-like receptor signaling pathway | 12 | 13 | 0.00 |
| hsa04623 | Cytosolic DNA-sensing pathway | 12 | 12 | 0.00 |
| R-HSA-918233 | TRAF3-dependent IRF activation pathway | 12 | 6 | 0.02 |
| R-HSA-933541 | TRAF6 mediated IRF7 activation | 12 | 8 | 0.02 |
| GO:0007165 | signal transduction | 12, 15, 18 | 52 | 0.00 |
| hsa04064 | NF-kappa B signaling pathway | 12, 15, 18 | 12 | 0.02 |
| GO:0002250 | adaptive immune response | 12, 18 | 16 | 0.00 |
| hsa04060 | Cytokine-cytokine receptor interaction | 12, 18 | 23 | 0.00 |
| R-HSA-380108 | Chemokine receptors bind chemokines | 12, 18 | 10 | 0.02 |
| GO:0031295 | T cell co-stimulation | 15 | 12 | 0.02 |
| GO:0050690 | regulation of defense response to virus by virus | 15 | 8 | 0.02 |
| GO:0050852 | T cell receptor signaling pathway | 15 | 18 | 0.00 |
| GO:0007166 | cell surface receptor signaling pathway | 15, 18 | 24 | 0.01 |
| hsa04660 | T cell receptor signaling pathway | 15, 18 | 16 | 0.00 |
| GO:0000184 | nonsense-mediated nuclear-transcribed mRNA decay | 18 | 23 | 0.00 |
| GO:0006614 | SRP-dependent co-translational protein targeting to membrane | 18 | 20 | 0.01 |
| GO:0006968 | cellular defense response | 18 | 15 | 0.03 |
| GO:0007169 | transmembrane receptor protein tyrosine kinase signaling pathway | 18 | 23 | 0.00 |
| GO:0019083 | viral transcription | 18 | 21 | 0.02 |
| GO:0042110 | T cell activation | 18 | 15 | 0.00 |
| GO:0070098 | chemokine-mediated signaling pathway | 18 | 17 | 0.01 |
| GO:0072678 | T cell migration | 18 | 6 | 0.03 |
| hsa04062 | Chemokine signaling pathway | 18 | 32 | 0.01 |
| R-HSA-192823 | Viral mRNA Translation | 18 | 21 | 0.00 |
| GO:0033209 | tumor necrosis factor-mediated signaling pathway | pooled3 | 24 | 0.05 |
| hsa04650 | Natural killer cell mediated cytotoxicity | pooled | 28 | 0.01 |
| hsa05340 | Primary immunodeficiency | pooled | 13 | 0.02 |
1: The number of differentially expressed genes in biological process or pathways.
2: False discovery rate
3: Differentially expressed genes were pooled from all tested time points