Table 2. Significant pathways with P<0.01 by pathway analysis of BMD genes using the meta-analysis method.
| Classifications | Pathway ID | Pathway Name | C | O | E | R | rawP | adjP | Shared |
|---|---|---|---|---|---|---|---|---|---|
| Immune diseases | hsa05323 | Rheumatoid arthritis | 91 | 12 | 1.61 | 7.45 | 7.60E-08 | 2.43E-06 | Y |
| Environmental Information Processing | hsa04060 | Cytokine-cytokine receptor interaction | 265 | 19 | 4.69 | 4.05 | 3.31E-07 | 5.30E-06 | Y |
| Immune diseases | hsa04940 | Type I diabetes mellitus | 43 | 8 | 0.76 | 10.52 | 7.77E-07 | 9.95E-06 | Y |
| Immune diseases | hsa05320 | Autoimmune thyroid disease | 52 | 8 | 0.92 | 8.7 | 3.50E-06 | 3.73E-05 | Y |
| Environmental Information Processing | hsa04010 | MAPK signaling pathway | 268 | 17 | 4.74 | 3.59 | 7.08E-06 | 6.47E-05 | Y |
| Cellular Processes | hsa04145 | Phagosome | 153 | 12 | 2.71 | 4.43 | 1.97E-05 | 1.00E-04 | Y |
| Cellular Processes | hsa04510 | Focal adhesion | 200 | 14 | 3.54 | 3.96 | 1.50E-05 | 1.00E-04 | Y |
| Environmental Information Processing | hsa04310 | Wnt signaling pathway | 150 | 12 | 2.65 | 4.52 | 1.61E-05 | 1.00E-04 | Y |
| Cardiovascular diseases | hsa05416 | Viral myocarditis | 70 | 8 | 1.24 | 6.46 | 3.32E-05 | 2.00E-04 | Y |
| Cellular Processes | hsa04810 | Regulation of actin cytoskeleton | 213 | 14 | 3.77 | 3.72 | 3.03E-05 | 2.00E-04 | Y |
| Immune diseases | hsa05330 | Allograft rejection | 37 | 6 | 0.65 | 9.17 | 4.38E-05 | 2.00E-04 | Y |
| Infectious diseases: Parasitic | hsa05140 | Leishmaniasis | 72 | 8 | 1.27 | 6.28 | 4.08E-05 | 2.00E-04 | Y |
| Immune diseases | hsa05332 | Graft-versus-host disease | 41 | 6 | 0.73 | 8.27 | 7.98E-05 | 3.00E-04 | Y |
| Infectious diseases: Parasitic | hsa05145 | Toxoplasmosis | 132 | 10 | 2.34 | 4.28 | 1.00E-04 | 4.00E-04 | Y |
| Immune diseases | hsa05310 | Asthma | 30 | 5 | 0.53 | 9.42 | 2.00E-04 | 6.00E-04 | Y |
| Immune system | hsa04672 | Intestinal immune network for IgA production | 48 | 6 | 0.85 | 7.07 | 2.00E-04 | 6.00E-04 | Y |
| Immune system | hsa04062 | Chemokine signaling pathway | 189 | 12 | 3.34 | 3.59 | 2.00E-04 | 6.00E-04 | Y |
| Metabolism | hsa00250 | Alanine, aspartate and glutamate metabolism | 32 | 5 | 0.57 | 8.83 | 2.00E-04 | 6.00E-04 | N |
| Cellular Processes | hsa04142 | Lysosome | 121 | 9 | 2.14 | 4.2 | 3.00E-04 | 9.00E-04 | N |
| Immune system | hsa04612 | Antigen processing and presentation | 76 | 7 | 1.34 | 5.21 | 4.00E-04 | 1.10E-03 | Y |
| Infectious diseases: Bacterial | hsa05150 | Staphylococcus aureus infection | 55 | 6 | 0.97 | 6.17 | 4.00E-04 | 1.10E-03 | Y |
| Nervous system | hsa04722 | Neurotrophin signaling pathway | 127 | 9 | 2.25 | 4.01 | 4.00E-04 | 1.10E-03 | Y |
| Environmental Information Processing | hsa04514 | Cell adhesion molecules (CAMs) | 133 | 9 | 2.35 | 3.82 | 6.00E-04 | 1.50E-03 | Y |
| Environmental Information Processing | hsa04350 | TGF-beta signaling pathway | 84 | 7 | 1.49 | 4.71 | 7.00E-04 | 1.70E-03 | Y |
| Environmental Information Processing | hsa04512 | ECM-receptor interaction | 85 | 7 | 1.5 | 4.65 | 8.00E-04 | 1.90E-03 | Y |
| Cellular Processes | hsa04144 | Endocytosis | 201 | 11 | 3.56 | 3.09 | 1.00E-03 | 2.20E-03 | Y |
| Genetic Information Processing | hsa03050 | Proteasome | 44 | 5 | 0.78 | 6.42 | 1.00E-03 | 2.20E-03 | Y |
| Immune system | hsa04670 | Leukocyte transendothelial migration | 116 | 8 | 2.05 | 3.9 | 1.10E-03 | 2.30E-03 | N |
| Cancers: Specific types | hsa05220 | Chronic myeloid leukemia | 73 | 6 | 1.29 | 4.65 | 1.90E-03 | 3.80E-03 | Y |
| Cellular Processes | hsa04520 | Adherens junction | 73 | 6 | 1.29 | 4.65 | 1.90E-03 | 3.80E-03 | Y |
| Development | hsa04380 | Osteoclast differentiation | 128 | 8 | 2.26 | 3.53 | 2.10E-03 | 4.10E-03 | Y |
| Cellular Processes | hsa04530 | Tight junction | 132 | 8 | 2.34 | 3.43 | 2.50E-03 | 4.70E-03 | Y |
| Infectious diseases: Viral | hsa05160 | Hepatitis C | 134 | 8 | 2.37 | 3.37 | 2.70E-03 | 4.90E-03 | N |
| Cancers: Specific types | hsa05217 | Basal cell carcinoma | 55 | 5 | 0.97 | 5.14 | 2.90E-03 | 5.20E-03 | Y |
| Environmental Information Processing | hsa04340 | Hedgehog signaling pathway | 56 | 5 | 0.99 | 5.05 | 3.10E-03 | 5.40E-03 | Y |
| Cellular Processes | hsa04114 | Oocyte meiosis | 112 | 7 | 1.98 | 3.53 | 3.90E-03 | 6.60E-03 | Y |
| Genetic Information Processing | hsa03013 | RNA transport | 151 | 8 | 2.67 | 2.99 | 5.60E-03 | 9.00E-03 | Y |
| Genetic Information Processing | hsa03010 | Ribosome | 92 | 6 | 1.63 | 3.69 | 5.90E-03 | 9.20E-03 | N |
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. Y, this pathway is shared in pathway analysis of BMD genes using the “best SNP per gene” method; N, this pathway is not shared in pathway analysis of BMD genes using the “best SNP per gene” method;