Table 2.
Twenty pathways from each dataset, sorted by increasing p-values.
| Ingenuity canonical pathways | P-value | adj. P-value | Ratio | Ratio (# molecules) | P > NP (# proteins) | NP > P (# proteins) |
|---|---|---|---|---|---|---|
| Proteomics | ||||||
| EIF2 signaling | 1.00E−13 | 3.98E−11 | 0.08 | 17/224 | 5 | 12 |
| Acute phase response signaling | 2.29E−09 | 3.98E−07 | 0.07 | 12/180 | 0 | 12 |
| LXR/RXR activation | 6.61E−09 | 7.59E−07 | 0.08 | 10/121 | 0 | 10 |
| FXR/RXR activation | 9.77E−09 | 8.32E−07 | 0.08 | 10/126 | 0 | 10 |
| Regulation of eIF4 and p70S6K signaling | 1.41E−06 | 9.77E−05 | 0.05 | 9/166 | 3 | 6 |
| Production of nitric oxide and reactive oxygen species in macrophages | 4.17E−06 | 2.34E−04 | 0.05 | 9/189 | 2 | 7 |
| Clathrin-mediated endocytosis signaling | 4.90E−06 | 2.40E−04 | 0.05 | 9/183 | 3 | 6 |
| Phagosome maturation | 6.61E−06 | 2.82E−04 | 0.05 | 8/151 | 6 | 2 |
| Atherosclerosis signaling | 1.95E−05 | 7.41E−04 | 0.06 | 7/127 | 1 | 6 |
| Lipid antigen presentation by CD1 | 2.29E−05 | 7.76E−04 | 0.15 | 4/26 | 3 | 1 |
| mTOR signaling | 7.08E−05 | 2.14E−03 | 0.04 | 8/210 | 2 | 6 |
| CDK5 signaling | 7.41E−05 | 2.14E−03 | 0.06 | 6/108 | 4 | 2 |
| Antigen presentation pathway | 1.17E−04 | 3.02E−03 | 0.10 | 4/39 | 1 | 3 |
| Thiosulfate disproportionation III (rhodanese) | 1.26E−04 | 3.02E−03 | 0.67 | 2/3 | 0 | 2 |
| IL-12 signaling and production in macrophages | 2.34E−04 | 5.37E−03 | 0.05 | 6/133 | 0 | 6 |
| Virus entry via endocytic pathways | 5.37E−04 | 1.15E−02 | 0.05 | 5/102 | 2 | 3 |
| Systemic lupus erythematosus signaling | 7.59E−04 | 1.51E−02 | 0.03 | 7/229 | 1 | 6 |
| Coagulation system | 1.51E−03 | 2.69E−02 | 0.09 | 3/35 | 0 | 3 |
| Synaptic long term potentiation | 1.55E−03 | 2.69E−02 | 0.04 | 5/129 | 3 | 2 |
| PPARα/RXRα activation | 1.58E−03 | 2.69E−02 | 0.03 | 6/191 | 2 | 4 |
| Ingenuity canonical pathways | P-value | adj. P-value | Ratio | Ratio (# molecules) | P > NP (# RNA) | NP > P (# RNA) |
|---|---|---|---|---|---|---|
| RNAseq | ||||||
| Primary immunodeficiency signaling | 6.61E−04 | 1.83E−01 | 0.16 | 8/50 | 2 | 6 |
| B cell receptor signaling | 1.02E−03 | 1.83E−01 | 0.09 | 17/186 | 9 | 8 |
| Molecular mechanisms of cancer | 1.12E−03 | 1.83E−01 | 0.07 | 29/400 | 14 | 15 |
| IL-7 signaling pathway | 3.31E−03 | 4.11E−01 | 0.16 | 9/78 | 2 | 7 |
| Triacylglycerol biosynthesis | 6.92E−03 | 5.58E−01 | 0.14 | 6/44 | 4 | 2 |
| Opioid signaling pathway | 8.51E−03 | 5.58E−01 | 0.07 | 18/247 | 13 | 5 |
| Retinoate biosynthesis I | 9.77E−03 | 5.58E−01 | 0.15 | 5/34 | 3 | 2 |
| Synaptogenesis signaling pathway | 1.12E−02 | 5.58E−01 | 0.07 | 21/312 | 14 | 7 |
| Hematopoiesis from pluripotent stem cells | 1.17E−02 | 5.58E−01 | 0.12 | 6/49 | 1 | 5 |
| GABA receptor signaling | 1.20E−02 | 5.58E−01 | 0.09 | 9/95 | 7 | 2 |
| B cell development | 1.23E−02 | 5.58E−01 | 0.14 | 5/36 | 3 | 2 |
| Bladder cancer signaling | 1.35E−02 | 5.61E−01 | 0.09 | 9/97 | 7 | 2 |
| Cell Cycle: G1/S checkpoint regulation | 1.55E−02 | 5.69E−01 | 0.10 | 7/67 | 3 | 4 |
| Regulation of the epithelial mesenchymal transition in development pathway | 1.70E−02 | 5.69E−01 | 0.10 | 8/84 | 4 | 4 |
| Inhibition of matrix metalloproteases | 1.74E−02 | 5.69E−01 | 0.13 | 5/39 | 3 | 2 |
| PKCθ signaling in T lymphocytes | 1.86E−02 | 5.79E−01 | 0.08 | 12/155 | 8 | 4 |
| Nicotine degradation III | 2.34E−02 | 6.35E−01 | 0.10 | 6/57 | 5 | 1 |
| Role of osteoblasts, osteoclasts and chondrocytes in rheumatoid arthritis | 2.45E−02 | 6.35E−01 | 0.07 | 15/218 | 9 | 6 |
| Oncostatin M signaling | 2.51E−02 | 6.35E−01 | 0.17 | 5/43 | 3 | 2 |
| Melatonin degradation I | 2.95E−02 | 6.35E−01 | 0.10 | 6/60 | 5 | 1 |
| Ingenuity canonical pathways | P-value | adj. P-value | Ratio | Ratio (# molecules) | P > NP (# microRNA) | NP > P (# microRNA) |
|---|---|---|---|---|---|---|
| microRNAseq | ||||||
| No pathways detected | ||||||
P progressor, NP nonprogressor.