Table 2.
True KO signaling pathways identified by SPIA from GSE22873.
| Order | Pathway ID | Pathway Name | Status | pSize | DEGs (%) | pGFdr | |
|---|---|---|---|---|---|---|---|
| Pathways identified from GSE22873_M (KO Myd88 vs. WT) | |||||||
| 1 | mmu04620 | Toll-like receptor signaling pathway | Inhibited | 87 | 36 (41.38) | 1.03E-33 | |
| 2 | mmu05161 | Hepatitis B | Inhibited | 149 | 36 (24.16) | 1.20E-24 | |
| 3 | mmu05140 | Leishmaniasis | Inhibited | 66 | 23 (34.85) | 9.51E-20 | |
| 4 | mmu05152 | Tuberculosis | Inhibited | 158 | 32 (20.25) | 2.20E-19 | |
| 5 | mmu04621 | NOD-like receptor signaling pathway | Inhibited | 148 | 30 (20.27) | 6.91E-18 | |
| 6 | mmu05162 | Measles | Inhibited | 131 | 28 (21.37) | 6.91E-18 | |
| 7 | mmu05142 | Chagas disease (American trypanosomiasis) | Inhibited | 99 | 23 (23.23) | 4.43E-15 | |
| 8 | mmu05169 | Epstein-Barr virus infection | Inhibited | 185 | 29 (15.68) | 1.16E-14 | |
| 9 | mmu05164 | Influenza A | Inhibited | 143 | 26 (18.18) | 1.40E-14 | |
| 10 | mmu05145 | Toxoplasmosis | Inhibited | 105 | 22 (20.95) | 2.62E-14 | |
| 11 | mmu05170 | Human immunodeficiency virus 1 infection | Inhibited | 194 | 28 (14.43) | 2.16E-13 | |
| 12 | mmu05135 | Yersinia infection | Inhibited | 116 | 22 (18.97) | 7.84E-13 | |
| 13 | mmu05133 | Pertussis | Inhibited | 67 | 17 (25.37) | 2.36E-12 | |
| 14 | mmu04064 | NF-kappa B signaling pathway | Inhibited | 92 | 18 (19.57) | 1.94E-10 | |
| 15 | mmu05168 | Herpes simplex virus 1 infection | Inhibited | 340 | 31 (9.12) | 3.64E-10 | |
| 16 | mmu05132 | Salmonella infection | Inhibited | 193 | 24 (12.44) | 5.73E-10 | |
| 17 | mmu05134 | Legionellosis | Inhibited | 51 | 13 (25.49) | 2.56E-09 | |
| 18 | mmu05235 | PD-L1/PD-1 checkpoint pathway in cancer | Inhibited | 84 | 15 (17.86) | 1.38E-08 | |
| 19 | mmu04010 | MAPK signaling pathway | Inhibited | 281 | 25 (8.90) | 3.65E-07 | |
| 20 | mmu05144 | Malaria | Inhibited | 48 | 9 (18.75) | 1.23E-05 | |
| 21 | mmu05143 | African trypanosomiasis | Inhibited | 31 | 7 (22.58) | 0.000126 | |
| Pathways identified from GSE22873_MA (KO Myd88_Ager vs. WT) | |||||||
| 1 | mmu05170 | Human immunodeficiency virus 1 infection | Inhibited | 194 | 61 (31.44) | 2.18E-50 | |
| 2 | mmu04620 | Toll-like receptor signaling pathway | Inhibited | 87 | 44 (50.57) | 1.24E-45 | |
| 3 | mmu05169 | Epstein-Barr virus infection | Activated | 185 | 53 (28.65) | 8.65E-41 | |
| 4 | mmu05142 | Chagas disease (American trypanosomiasis) | Inhibited | 99 | 35 (35.35) | 2.30E-29 | |
| 5 | mmu05162 | Measles | Inhibited | 131 | 38 (29.01) | 1.42E-28 | |
| 6 | mmu05161 | Hepatitis B | Inhibited | 149 | 40 (26.85) | 1.63E-28 | |
| 7 | mmu05135 | Yersinia infection | Inhibited | 116 | 35 (30.17) | 1.61E-26 | |
| 8 | mmu05235 | PD-L1/PD-1 checkpoint pathway in cancer | Inhibited | 84 | 31 (36.91) | 1.94E-26 | |
| 9 | mmu05168 | Herpes simplex virus 1 infection | Inhibited | 340 | 50 (14.71) | 6.55E-24 | |
| 10 | mmu04621 | NOD-like receptor signaling pathway | Activated | 148 | 33 (22.30) | 1.24E-20 | |
| 11 | mmu05140 | Leishmaniasis | Inhibited | 66 | 23 (34.85) | 3.92E-19 | |
| 12 | mmu05164 | Influenza A | Inhibited | 143 | 31 (21.68) | 7.33E-19 | |
| 13 | mmu05152 | Tuberculosis | Inhibited | 158 | 31 (19.62) | 1.74E-17 | |
| 14 | mmu05133 | Pertussis | Inhibited | 67 | 21 (31.34) | 2.00E-16 | |
| 15 | mmu05145 | Toxoplasmosis | Inhibited | 105 | 23 (21.91) | 1.60E-14 | |
| 16 | mmu04064 | NF-kappa B signaling pathway | Inhibited | 92 | 22 (23.91) | 5.09E-14 | |
| 17 | mmu05132 | Salmonella infection | Inhibited | 193 | 26 (13.47) | 5.18E-11 | |
| 18 | mmu04933 | AGE-RAGE signaling pathway in diabetics | Activated | 98 | 18 (18.37) | 1.58E-09 | |
| 19 | mmu05134 | Legionellosis | Inhibited | 51 | 13 (25.49) | 7.03E-09 | |
| 20 | mmu04010 | MAPK signaling pathway | Inhibited | 281 | 22 (7.83) | 6.66E-06 | |
| 21 | mmu05144 | Malaria | Inhibited | 48 | 9 (18.75) | 2.00E-05 | |
| 22 | mmu05143 | African trypanosomiasis | Inhibited | 31 | 7 (22.58) | 0.000149 | |
| 23 | mmu05010 | Alzheimer disease | Activated | 311 | 13 (4.18) | 0.158326 | |
| Pathways identified from GSE22873_A (KO Ager vs. WT) | |||||||
| 1 | mmu04933 | AGE-RAGE signaling pathway in diabetics | Activated | 98 | 10 (10.20) | 0.002314 | |
| 2 | mmu05150 | Staphylococcus aureus infection | Activated | 76 | 3 (3.95) | 0.476408 | |
| 3 | mmu05010 | Alzheimer disease | Activated | 311 | 8 (2.57) | 0.638874 | |
True positive knockout (TPKO) signaling pathway (pGFdr < 0.001 or 0.005) and false negative knockout (FNKO) signaling pathway (pGFdr > 0.005) are distinguishable. Bold pathways are discussed in the main text.