Table 2.
The enriched KEGG and Reactome pathways.
| Module No. | KEGG | Frequency | P-value corrected with Bonferroni step down | Reactome | Frequency | P-value corrected with Bonferroni step down |
|---|---|---|---|---|---|---|
| M1 | Vasopressin-regulated water reabsorption | 26 | 1.13E-33 | Peptide ligand-binding receptors | 22 | 9.62E-30 |
| Calcium signaling pathway | 21 | 2.76E-28 | Platelet activation, signaling, and aggregation | 10 | 2.76E-08 | |
| cGMP-PKG signaling pathway | 7 | 2.56E-05 | Thrombin signaling through proteinase activated receptors (PARs) | 7 | 2.49E-10 | |
| M2 | PI3K-Akt signaling pathway | 30 | 2.16E-24 | Immune system | 49 | 9.78E-28 |
| Pathways in cancer | 30 | 1.26E-22 | Innate immune system | 38 | 1.31E-25 | |
| Ras signaling pathway | 29 | 2.10E-28 | Adaptive immune system | 35 | 6.87E-23 | |
| M3 | Cell cycle | 10 | 1.71E-11 | Cell cycle | 28 | 4.52E-31 |
| Vasopressin-regulated water reabsorption | 2 | 2.42E-02 | Cell cycle, mitotic | 27 | 4.64E-31 | |
| Bladder cancer | 2 | 4.17E-02 | M Phase | 12 | 1.80E-10 | |
| M4 | Neuroactive ligand–receptor interaction | 16 | 3.08E-22 | G alpha (s) signaling events | 23 | 1.04E-47 |
| – | – | – | GPCR ligand binding | 21 | 1.91E-29 | |
| – | – | – | Class B/2 (secretin family receptors) | 10 | 5.73E-16 | |
| M5 | Chemokine signaling pathway | 25 | 1.78E-29 | Signaling by GPCR | 68 | 2.40E-78 |
| Neuroactive ligand-receptor interaction | 25 | 2.85E-25 | GPCR downstream signaling | 63 | 2.90E-70 | |
| Cytokine-cytokine receptor interaction | 20 | 4.75E-18 | G alpha (i) signaling events | 63 | 1.24E-110 | |
| M6 | Thyroid hormone signaling pathway | 12 | 1.56E-12 | Generic transcription pathway | 46 | 3.10E-54 |
| Notch signaling pathway | 8 | 8.68E-10 | Developmental biology | 28 | 1.47E-24 | |
| Maturity onset diabetes of the young | 3 | 7.71E-03 | Nuclear receptor transcription pathway | 27 | 4.31E-53 | |
| M7 | Regulation of actin cytoskeleton | 9 | 1.74E-06 | Signaling by Rho GTPases | 52 | 1.49E-77 |
| Pancreatic cancer | 3 | 3.45E-02 | Rho GTPase cycle | 51 | 1.99E-104 | |
| – | – | – | G alpha (12/13) signaling events | 17 | 1.45E-25 | |
| M8 | Ubiquitin mediated proteolysis | 8 | 2.36E-12 | Association of TriC/CCT with target proteins during biosynthesis | 4 | 1.40E-07 |
| Circadian rhythm | 2 | 1.19E-03 | Protein folding | 4 | 1.44E-06 | |
| – | – | – | Chaperonin-mediated protein folding | 4 | 1.04E-06 | |
| M9 | Jak-STAT signaling pathway | 37 | 2.06E-50 | Immune system | 57 | 3.06E-41 |
| Cytokine–cytokine receptor interaction | 36 | 1.80E-39 | Cytokine signaling in immune system | 53 | 1.54E-67 | |
| Measles | 26 | 9.44E-32 | Interferon signaling | 31 | 1.08E-35 | |
| M10 | MAPK signaling pathway | 25 | 3.59E-24 | Innate immune system | 31 | 2.54E-21 |
| Pathways in cancer | 23 | 7.36E-17 | Toll-like receptors cascades | 19 | 1.54E-20 | |
| PI3K-Akt signaling pathway | 22 | 7.01E-17 | Toll like receptor 3 (TLR3) cascade | 18 | 7.97E-22 | |
| M11 | Wnt signaling pathway | 33 | 6.80E-57 | Signaling by Wnt | 30 | 1.06E-37 |
| Pathways in cancer | 28 | 2.05E-31 | TCF dependent signaling in response to WNT | 23 | 1.72E-28 | |
| Melanogenesis | 26 | 2.21E-44 | Class B/2 (secretin family receptors) | 18 | 1.63E-27 | |
| M12 | – | – | – | Amyloids | 5 | 1.21E-09 |
| – | – | – | Disease | 5 | 8.05E-05 |
The statistically significantly enriched KEGG and Reactome pathways were identified by ClueGO. The top three representative pathways identified in each module (M1–M12) of the SHIDEG-PPIN proximal neighborhood network are given together with their corrected p-values. The highlighted pathway names were found to be enriched in more than one module.