Table 1. Significant pathways with P<0.01 by pathway analysis of BMD genes using the “best SNP per gene” method.
| Classifications | Pathway ID | Pathway Name | C | O | E | R | rawP | adjP |
|---|---|---|---|---|---|---|---|---|
| Immune diseases | hsa05323 | Rheumatoid arthritis | 91 | 16 | 2.61 | 6.14 | 6.45E-09 | 3.50E-07 |
| Environmental Information Processing | hsa04310 | Wnt signaling pathway | 150 | 20 | 4.3 | 4.66 | 1.26E-08 | 4.16E-07 |
| Immune diseases | hsa04940 | Type I diabetes mellitus | 43 | 11 | 1.23 | 8.93 | 2.52E-08 | 6.24E-07 |
| Environmental Information Processing | hsa04350 | TGF-beta signaling pathway | 84 | 14 | 2.41 | 5.82 | 1.14E-07 | 1.88E-06 |
| Cardiovascular diseases | hsa05416 | Viral myocarditis | 70 | 12 | 2 | 5.99 | 6.63E-07 | 9.38E-06 |
| Immune diseases | hsa05330 | Allograft rejection | 37 | 9 | 1.06 | 8.49 | 7.60E-07 | 9.41E-06 |
| Endocrine system | hsa04916 | Melanogenesis | 101 | 14 | 2.89 | 4.84 | 1.17E-06 | 1.29E-05 |
| Cellular Processes | hsa04510 | Focal adhesion | 200 | 20 | 5.73 | 3.49 | 1.46E-06 | 1.45E-05 |
| Immune diseases | hsa05332 | Graft-versus-host disease | 41 | 9 | 1.17 | 7.67 | 1.93E-06 | 1.74E-05 |
| Cancers: Specific types | hsa05217 | Basal cell carcinoma | 55 | 10 | 1.57 | 6.35 | 3.24E-06 | 2.47E-05 |
| Infectious diseases: Bacterial | hsa05150 | Staphylococcus aureus infection | 55 | 10 | 1.57 | 6.35 | 3.24E-06 | 2.47E-05 |
| Cellular Processes | hsa04114 | Oocyte meiosis | 112 | 14 | 3.21 | 4.37 | 4.10E-06 | 2.71E-05 |
| Environmental Information Processing | hsa04340 | Hedgehog signaling pathway | 56 | 10 | 1.6 | 6.24 | 3.85E-06 | 2.71E-05 |
| Infectious diseases: Parasitic | hsa05140 | Leishmaniasis | 72 | 11 | 2.06 | 5.34 | 6.21E-06 | 3.84E-05 |
| Cardiovascular diseases | hsa05412 | Arrhythmogenic right ventricular cardiomyopathy (ARVC) | 74 | 11 | 2.12 | 5.19 | 8.15E-06 | 4.75E-05 |
| Environmental Information Processing | hsa04060 | Cytokine-cytokine receptor interaction | 265 | 22 | 7.59 | 2.9 | 9.53E-06 | 5.18E-05 |
| Cancers: Specific types | hsa05210 | Colorectal cancer | 62 | 10 | 1.78 | 5.63 | 9.94E-06 | 5.18E-05 |
| Immune diseases | hsa05320 | Autoimmune thyroid disease | 52 | 9 | 1.49 | 6.04 | 1.53E-05 | 7.57E-05 |
| Immune diseases | hsa05310 | Asthma | 30 | 7 | 0.86 | 8.15 | 1.77E-05 | 8.01E-05 |
| Nervous system | hsa04722 | Neurotrophin signaling pathway | 127 | 14 | 3.64 | 3.85 | 1.78E-05 | 8.01E-05 |
| Immune system | hsa04062 | Chemokine signaling pathway | 189 | 17 | 5.41 | 3.14 | 3.48E-05 | 1.00E-04 |
| Infectious diseases: Parasitic | hsa05145 | Toxoplasmosis | 132 | 14 | 3.78 | 3.7 | 2.75E-05 | 1.00E-04 |
| Immune system | hsa04672 | Intestinal immune network for IgA production | 48 | 8 | 1.37 | 5.82 | 6.03E-05 | 2.00E-04 |
| Cellular Processes | hsa04520 | Adherens junction | 73 | 10 | 2.09 | 4.78 | 4.33E-05 | 2.00E-04 |
| Circulatory system | hsa04270 | Vascular smooth muscle contraction | 116 | 12 | 3.32 | 3.61 | 1.00E-04 | 3.00E-04 |
| Cardiovascular diseases | hsa05410 | Hypertrophic cardiomyopathy (HCM) | 83 | 10 | 2.38 | 4.21 | 1.00E-04 | 3.00E-04 |
| Cellular Processes | hsa04530 | Tight junction | 132 | 13 | 3.78 | 3.44 | 1.00E-04 | 3.00E-04 |
| Cellular Processes | hsa04145 | Phagosome | 153 | 14 | 4.38 | 3.2 | 1.00E-04 | 3.00E-04 |
| Genetic Information Processing | hsa03040 | Spliceosome | 127 | 13 | 3.64 | 3.57 | 7.62E-05 | 3.00E-04 |
| Cancers: Specific types | hsa05221 | Acute myeloid leukemia | 57 | 8 | 1.63 | 4.9 | 2.00E-04 | 6.00E-04 |
| Cellular Processes | hsa04110 | Cell cycle | 124 | 12 | 3.55 | 3.38 | 2.00E-04 | 6.00E-04 |
| Immune system | hsa04612 | Antigen processing and presentation | 76 | 9 | 2.18 | 4.14 | 3.00E-04 | 8.00E-04 |
| Cardiovascular diseases | hsa05414 | Dilated cardiomyopathy | 90 | 10 | 2.58 | 3.88 | 3.00E-04 | 8.00E-04 |
| Genetic Information Processing | hsa03013 | RNA transport | 151 | 13 | 4.32 | 3.01 | 4.00E-04 | 1.10E-03 |
| Cellular Processes | hsa04810 | Regulation of actin cytoskeleton | 213 | 16 | 6.1 | 2.62 | 5.00E-04 | 1.30E-03 |
| Environmental Information Processing | hsa04514 | Cell adhesion molecules (CAMs) | 133 | 12 | 3.81 | 3.15 | 5.00E-04 | 1.30E-03 |
| Endocrine system | hsa04910 | Insulin signaling pathway | 138 | 12 | 3.95 | 3.04 | 6.00E-04 | 1.50E-03 |
| Environmental Information Processing | hsa04512 | ECM-receptor interaction | 85 | 9 | 2.43 | 3.7 | 7.00E-04 | 1.60E-03 |
| Cancers: Specific types | hsa05213 | Endometrial cancer | 52 | 7 | 1.49 | 4.7 | 7.00E-04 | 1.60E-03 |
| Cellular Processes | hsa04144 | Endocytosis | 201 | 15 | 5.76 | 2.61 | 7.00E-04 | 1.60E-03 |
| Environmental Information Processing | hsa04010 | MAPK signaling pathway | 268 | 18 | 7.67 | 2.35 | 8.00E-04 | 1.80E-03 |
| Cancers: Specific types | hsa05215 | Prostate cancer | 89 | 9 | 2.55 | 3.53 | 1.00E-03 | 2.30E-03 |
| Cancers: Specific types | hsa05220 | Chronic myeloid leukemia | 73 | 8 | 2.09 | 3.83 | 1.10E-03 | 2.40E-03 |
| Development | hsa04380 | Osteoclast differentiation | 128 | 11 | 3.67 | 3 | 1.20E-03 | 2.60E-03 |
| Genetic Information Processing | hsa03050 | Proteasome | 44 | 6 | 1.26 | 4.76 | 1.50E-03 | 3.20E-03 |
| Environmental Information Processing | hsa04070 | Phosphatidylinositol signaling system | 78 | 8 | 2.23 | 3.58 | 1.80E-03 | 3.70E-03 |
| Immune diseases | hsa05322 | Systemic lupus erythematosus | 136 | 11 | 3.89 | 2.82 | 1.90E-03 | 3.80E-03 |
| Neurodegenerative diseases | hsa05016 | Huntington's disease | 183 | 13 | 5.24 | 2.48 | 2.50E-03 | 5.00E-03 |
| Endocrine system | hsa04914 | Progesterone-mediated oocyte maturation | 86 | 8 | 2.46 | 3.25 | 3.30E-03 | 6.40E-03 |
| Environmental Information Processing | hsa04150 | mTOR signaling pathway | 52 | 6 | 1.49 | 4.03 | 3.60E-03 | 6.90E-03 |
| Environmental Information Processing | hsa04020 | Calcium signaling pathway | 177 | 12 | 5.07 | 2.37 | 5.20E-03 | 9.70E-03 |
C, the number of reference genes in the category; O, the number of genes in the gene set and also in the category; E, expected number in the category; R, the ratio of enrichment, rawP, the p value from hypergeometric test; adjP, the p value adjusted by the multiple test adjustment.