Table 1. Genes predicted with the highest flows in the optimal sub-network (p<0.05).
| Initial response genes (0.5–1 hour) | Intermediate regulators (2–4 hours) | Late effectors (6–8 hours) | Genes with no change in expression | ||||
| Gene | Flow | Gene | Flow | Gene | Flow | Gene | Flow |
| Jun | 13.68 | Socs3 | 85.85 | Cxcl10 | 10.91 | Stat1 | 8.74 |
| Fos | 10.34 | Nfκb1 | 76.87 | Ddx58 | 9.33 | Mapk8 | 8.72 |
| Il1b | 9.86 | Jak2 | 54.44 | Stat2 | 8.65 | Irf5 | 7.60 |
| Tnf | 9.36 | Src | 38.30 | Atf3 | 8.29 | Adcy5 | 7.43 |
| Cxcl2 | 7.59 | Pik3r5 | 27.86 | Isg15 | 8.15 | Mapk1 | 7.40 |
| Il1a | 7.40 | Rela | 23.35 | Irf7 | 7.30 | Sp1 | 7.37 |
| Akt1 | 6.43 | Stat5a | 20.40 | Nos2 | 6.91 | Stat6 | 7.17 |
| Atf4 | 5.49 | Met | 18.94 | Ifnar2 | 5.20 | Sp3 | 7.13 |
| Nfκbiz | 5.25 | Eif2ak2 | 17.77 | Stat3 | 5.01 | Creb1 | 6.88 |
| Egr1 | 5.20 | Irf1 | 17.53 | Rsad2 | 4.97 | Mapk12 | 6.80 |
| Sfpi1 | 4.99 | Ccl4 | 15.70 | Ccl5 | 4.93 | Il7r | 6.52 |
| Il1r2 | 4.79 | Ccl3 | 15.64 | Il15ra | 4.13 | Akt2 | 6.43 |
| Traf6 | 4.54 | Ripk2 | 14.43 | Ifngr1 | 4.09 | Mapk10 | 6.39 |
| Nfκbia | 4.39 | Nfκbib | 13.95 | Socs1 | 4.07 | Mapk9 | 6.39 |
| Hras1 | 4.39 | Hsp90aa1 | 13.94 | Rac2 | 4.03 | Rac1 | 6.27 |
| Tnfaip3 | 4.02 | Ccr2 | 12.58 | Zbp1 | 4.00 | Pik3r2 | 6.24 |
| Ereg | 4.00 | Traf1 | 11.48 | Gbp2 | 3.74 | Ppp2ca | 6.19 |
| Vegfa | 3.90 | Il6 | 10.94 | Casp1 | 3.31 | Trp53 | 6.08 |
| Areg | 3.87 | Ppp1cb | 10.86 | Cd40 | 3.31 | Mapk11 | 5.62 |
| Pgf | 3.60 | Icam1 | 10.46 | Il1r1 | 3.27 | Akt3 | 5.50 |