Table 2.
Top pathways for the genes linked to mSNPs categorized by the number of counts in COSMIC
| COSMIC singletons (7290) | 2–4 COSMIC counts (8430) | 5–9 COSMIC counts (5340) | 10–19 COSMIC counts (2747) | >19 COSMIC counts (968) | |||||
|---|---|---|---|---|---|---|---|---|---|
| KEGG pathway | P-value | KEGG pathway | P-value | KEGG pathway | P-value | KEGG pathway | P-value | KEGG pathway | P-value |
| Pancreatic secretion | 0.00000058 | Endocytosis | 0.00011 | Ascorbate and aldarate metabolism | 0.00078 | Adherens junction | 0.00015 | Drug metabolism—cytochrome P450 | 0.0000083 |
| Endocytosis | 0.000087 | Pancreatic secretion | 0.00033 | Pancreatic secretion | 0.00085 | Fc gamma R-mediated phagocytosis | 0.00035 | Metabolism of xenobiotics by cytochrome P450 | 0.000023 |
| Calcium signaling pathway | 0.00057 | Hematopoietic cell lineage | 0.0027 | Endocrine and other factor-regulated calcium reabsorption | 0.0028 | Pentose and glucuronate interconversions | 0.00051 | Pentose and glucuronate interconversions | 0.000034 |
| Gastric acid secretion | 0.0015 | Epstein-Barr virus infection | 0.0036 | Fc gamma R-mediated phagocytosis | 0.0031 | Pathways in cancer | 0.0023 | Ascorbate and aldarate metabolism | 0.000048 |
| Neuroactive ligand-receptor interaction | 0.0022 | Renin secretion | 0.0068 | Protein digestion and absorption | 0.0041 | Cell adhesion molecules | 0.0026 | Chemical carcinogenesis | 0.000058 |
| Endocrine and other factor-regulated calcium reabsorption | 0.0037 | Leukocyte transendothelial migration | 0.0082 | Pentose and glucuronate interconversions | 0.0042 | Endometrial cancer | 0.0027 | Endometrial cancer | 0.00006 |
| Leukocyte transendothelial migration | 0.004 | TNF signaling pathway | 0.0086 | Long-term depression | 0.0044 | Long-term depression | 0.0052 | Prostate cancer | 0.00017 |
| Carbohydrate digestion and absorption | 0.0064 | Synaptic vesicle cycle | 0.0096 | Cell adhesion molecules | 0.0079 | Serotonergic synapse | 0.0055 | Porphyrin and chlorophyl metabolism | 0.00025 |
| Thyroid hormone synthesis | 0.0098 | Proximal tubule bicarbonate reclamation | 0.0099 | Metabolism of xenobiotics by cytochrome P450 | 0.0087 | Axon guidance | 0.0056 | Adherens junction | 0.00027 |
| Fc gamma R-mediated phagocytosis | 0.01 | Calcium signaling pathway | 0.017 | Inflammatory mediator regulation of TRP channels | 0.0097 | Proteoglycans in cancer | 0.0068 | Pathways in cancer | 0.00032 |
| Starch and sucrose metabolism | 0.013 | Endocrine and other factor-regulated calcium reabsorption | 0.018 | Endocytosis | 0.016 | Focal adhesion | 0.007 | Drug metabolism—other enzymes | 0.00052 |
| Protein digestion and absorption | 0.015 | Biosynthesis of antibiotics | 0.02 | Chemical carcinogenesis | 0.017 | ECM-receptor interaction | 0.0072 | Central carbon metabolism in cancer | 0.0016 |
| Glycerolipid metabolism | 0.016 | Gastric acid secretion | 0.031 | cAMP signaling pathway | 0.019 | Prostate cancer | 0.0083 | Retinol metabolism | 0.0016 |
| Synaptic vesicle cycle | 0.018 | Fc gamma R-mediated phagocytosis | 0.036 | Axon guidance | 0.021 | Endocrine and other factor-regulated calcium reabsorption | 0.012 | Proteoglycans in cancer | 0.0017 |
| TGF-beta signaling pathway | 0.018 | Circadian entrainment | 0.041 | Thyroid hormone signaling pathway | 0.023 | HIF-1 signaling pathway | 0.012 | Arrhythmogenic right ventricular cardiomyopathy | 0.0023 |
| cAMP signaling pathway | 0.019 | Cell adhesion molecules | 0.044 | Thyroid hormone synthesis | 0.024 | Morphine addiction | 0.012 | Thyroid hormone signaling pathway | 0.0026 |
| Cell adhesion molecules | 0.02 | Long-term depression | 0.045 | Insulin secretion | 0.024 | GnRH signaling pathway | 0.012 | Thyroid cancer | 0.0034 |
| Epstein-Barr virus infection | 0.028 | Glycerolipid metabolism | 0.045 | Bladder cancer | 0.024 | Ascorbate and aldarate metabolism | 0.013 | Colorectal cancer | 0.0046 |
| Phosphatidylinositol signaling system | 0.028 | Mineral absorption | 0.049 | Epstein-Barr virus infection | 0.025 | Arrhythmogenic right ventricular cardiomyopathy | 0.016 | Cell adhesion molecules | 0.0071 |
| Mucin type O-Glycan biosynthesis | 0.033 | Inflammatory mediator regulation of TRP channels | 0.049 | Histidine metabolism | 0.026 | Leukocyte transendothelial migration | 0.017 | Steroid hormone biosynthesis | 0.01 |
| Renin secretion | 0.041 | Adherens junction | 0.053 | TNF signaling pathway | 0.027 | Vibrio cholera infection | 0.017 | Melanoma | 0.011 |
| Aldosterone synthesis and secretion | 0.044 | Complement and coagulation cascades | 0.054 | Calcium signaling pathway | 0.027 | Biosynthesis of antibiotics | 0.019 | Calcium signaling pathway | 0.012 |
| Salivary secretion | 0.046 | Epithelial cell signaling in Helicobacter pylori infection | 0.055 | Purine metabolism | 0.028 | Fc epsilon RI signaling pathway | 0.019 | Bladder cancer | 0.019 |
| Signaling pathways regulating pluripotency of stem cells | 0.047 | p53 signaling pathway | 0.055 | Circadian entrainment | 0.028 | Cholinergic synapse | 0.02 | Hepatitis B | 0.019 |
| AMPK signaling pathway | 0.049 | Arrhythmogenic right ventricular cardiomyopathy | 0.055 | Salivary secretion | 0.029 | Type II diabetes mellitus | 0.02 | MAPK signaling pathway | 0.024 |
| Aldosterone-regulated sodium reabsorption | 0.049 | Protein digestion and absorption | 0.055 | Drug metabolism—cytochrome P450 | 0.029 | Circadian entrainment | 0.02 | Oxytocin signaling pathway | 0.025 |
| Olfactory transduction | 0.05 | Salivary secretion | 0.057 | Adherens junction | 0.029 | Calcium signaling pathway | 0.021 | B cell receptor signaling pathway | 0.027 |
| Hippo signaling pathway | 0.055 | NF-kappa B signaling pathway | 0.069 | Inositol phosphate metabolism | 0.039 | Thyroid cancer | 0.041 | Cholinergic synapse | 0.04 |
Number of genes used in pathway analysis is shown in parenthesis.