Table 3.
Canonical pathways affected by OVX and OVX in the context of CBA
| Ingenuity Canonical Pathway | P Value of Overlap | Ratio |
|---|---|---|
| OVX effects | ||
| Acute phase response signaling | 6.57E-13 | 13/179 |
| LXR/RXR activation* | 2.23E-09 | 9/121 |
| FXR/RXR activation* | 3.19E-09 | 9/126 |
| Clathrin-mediated endocytosis signaling* | 1.30E-07 | 9/193 |
| Coagulation system | 3.55E-07 | 5/35 |
| Atherosclerosis signaling | 1.66E-05 | 6/127 |
| Neuroprotective role of THOP1 in Alzheimer’s disease | 1.34E-04 | 5/116 |
| Production of nitric oxide and reactive oxygen species in macrophages | 1.48E-04 | 6/188 |
| IL-12 signaling and production in macrophages | 2.45E-04 | 5/132 |
| Intrinsic prothrombin activation pathway | 7.43E-04 | 3/42 |
| Sirtuin signaling pathway* | 1.48E-03 | 6/291 |
| Extrinsic prothrombin activation pathway | 2.04E-03 | 2/16 |
| Caveolar-mediated endocytosis signaling | 3.66E-03 | 3/73 |
| Macropinocytosis signaling | 4.10E-03 | 3/76 |
| Acetyl-CoA biosynthesis III (from Citrate)* | 4.22E-03 | 1/1 |
| Apelin liver signaling pathway | 5.37E-03 | 2/26 |
| Xenobiotic metabolism AHR signaling pathway* | 5.61E-03 | 3/85 |
| Palmitate biosynthesis I (animals)* | 8.43E-03 | 1/2 |
| Fatty acid biosynthesis Initiation II* | 8.43E-03 | 1/2 |
| PPARα/RXRα activation* | 8.64E-03 | 4/190 |
| Xenobiotic metabolism PXR signaling pathway | 8.95E-03 | 4/192 |
| OVX in the context of CBA | ||
| Mitochondrial dysfunction | 1.05E-12 | 13/171 |
| Oxidative phosphorylation | 7.55E-11 | 10/109 |
| Sirtuin signaling pathway* | 8.18E-10 | 13/291 |
| Glutaryl-CoA degradation | 7.21E-07 | 4/16 |
| Valine degradation I | 1.52E-06 | 4/19 |
| Tryptophan degradation III (eukaryotic) | 3.42E-06 | 4/23 |
| Ketolysis | 1.09E-05 | 3/10 |
| Fatty acid β-oxidation I | 1.35E-05 | 4/32 |
| Ketogenesis | 1.49E-05 | 3/11 |
| LXR/RXR activation* | 1.99E-05 | 6/121 |
| Mevalonate pathway I | 3.26E-05 | 3/14 |
| Isoleucine degradation I | 4.99E-05 | 3/16 |
| Biotin-carboxyl carrier protein assembly | 6.20E-05 | 2/3 |
| Stearate biosynthesis I (animals) | 6.88E-05 | 4/48 |
| Superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate) | 7.22E-05 | 3/18 |
| TCA cycle II (eukaryotic) | 1.75E-04 | 3/24 |
| NRF2-mediated oxidative stress response | 2.35E-04 | 6/189 |
| Superpathway of cholesterol biosynthesis | 3.12E-04 | 3/29 |
| Ethanol degradation II | 4.19E-04 | 3/32 |
| Iron homeostasis signaling pathway | 4.21E-04 | 5/137 |
| Acetyl-CoA biosynthesis I (pyruvate dehydrogenase complex) | 4.29E-04 | 2/7 |
| AMPK signaling | 4.57E-04 | 6/214 |
| Noradrenaline and adrenaline degradation | 5.47E-04 | 3/35 |
| Superoxide radicals degradation | 5.70E-04 | 2/8 |
| Xenobiotic metabolism AHR signaling pathway* | 6.29E-04 | 4/85 |
| Sucrose degradation V (mammalian) | 7.31E-04 | 2/9 |
| Folate transformations I | 7.31E-04 | 2/9 |
| Glycine betaine degradation | 9.10E-04 | 2/10 |
| Acyl-CoA hydrolysis | 1.56E-03 | 2/13 |
| PPARα/RXRα activation* | 1.82E-03 | 5/190 |
| Clathrin-mediated endocytosis signaling* | 1.95E-03 | 5/193 |
| FXR/RXR activation* | 2.70E-03 | 4/126 |
| Serotonin degradation | 3.60E-03 | 3/67 |
| LPS/IL-1 mediated inhibition of RXR function | 3.71E-03 | 5/224 |
| Aryl hydrocarbon receptor signaling | 4.24E-03 | 4/143 |
| Acetyl-CoA biosynthesis III (from citrate)* | 4.57E-03 | 1/1 |
| Glycolysis I | 6.27E-03 | 2/26 |
| Gluconeogenesis I | 6.27E-03 | 2/26 |
| Palmitate biosynthesis I (animals)* | 9.13E-03 | 1/2 |
| Fatty acid biosynthesis initiation II* | 9.13E-03 | 1/2 |
| Glycine biosynthesis I | 9.13E-03 | 1/2 |
Ratio is the number of differentially expressed proteins in our data set that were implicated in the pathway relative to the total number of proteins in that pathway. AHR, aryl hydrocarbon receptor; AMPK, adenosine monophosphate-activated protein kinase; CBA, chronic binge alcohol; FXR, farnesoid X receptor; LXR, liver X receptor; OVX, ovariectomy; PPARα, peroxisome proliferator-activated receptor alpha; RXR, retinoid X receptor. Only pathways with P value of overlap 10−3 are shown. *Pathways that are enriched in both comparisons.