Table 2.
The top 25 enriched Reactome pathways within the network at the acute stage of infection.
| Pathway | Total | Hits | P-value |
|---|---|---|---|
| Immune system | 1,140 | 114 | 1.62E−37 |
| Innate immune system | 521 | 69 | 1.00E−27 |
| Toll-like receptors cascades | 123 | 36 | 2.09E−26 |
| Toll-like receptor 4 (TLR4) cascade | 103 | 31 | 3.27E−23 |
| Activated TLR4 signaling | 100 | 29 | 3.03E−21 |
| TRIF-mediated TLR3/TLR4 signaling | 87 | 24 | 3.62E−17 |
| MyD88-independent cascade | 88 | 24 | 4.85E−17 |
| Toll-like receptor 3 (TLR3) cascade | 88 | 24 | 4.85E−17 |
| MyD88:Mal cascade initiated on plasma membrane | 81 | 23 | 8.42E−17 |
| Toll-like receptor TLR1:TLR2 cascade | 81 | 23 | 8.42E−17 |
| Toll-like receptor TLR6:TLR2 cascade | 81 | 23 | 8.42E−17 |
| Toll-like receptor 2 (TLR2) cascade | 81 | 23 | 8.42E−17 |
| Toll-like receptor 10 (TLR10) cascade | 74 | 20 | 2.74E−14 |
| Toll-like receptor 5 (TLR5) cascade | 74 | 20 | 2.74E−14 |
| MyD88 cascade initiated on plasma membrane | 74 | 20 | 2.74E−14 |
| Cytokine signaling in immune system | 286 | 37 | 2.78E−14 |
| Signaling by interleukins | 116 | 24 | 4.31E−14 |
| Toll-like receptor 7/8 (TLR7/8) cascade | 77 | 19 | 7.62E−13 |
| MyD88 dependent cascade initiated on endosome | 77 | 19 | 7.62E−13 |
| Toll-like receptor 9 (TLR9) cascade | 79 | 19 | 1.26E−12 |
| TRAF6-mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation | 76 | 18 | 6.71E−12 |
| Hemostasis | 511 | 46 | 1.02E−11 |
| Adaptive immune system | 654 | 53 | 1.15E−11 |
| TRAF6-mediated induction of proinflammatory cytokines | 62 | 16 | 2.54E−11 |
| Nucleotide-binding domain, leucine rich repeat containing receptor signaling pathways | 55 | 15 | 4.58E−11 |
The pathways are ranked by their raw P values from functional enrichment analysis based on hypergeometric tests. (Note that multiple testing adjustments such as FDR are inappropriate here owing to the overlap and interdependence of genes within the pathways.)