Table 1. MMnet is significantly enriched for variants that associate with different bone traits.
Single nucleotide polymorphisms (SNPs) significantly associated with the reported GWAS traits were interrogated in two datasets: the background dataset which includes all the eQTLs (posterior probability >80% see Materials and methods) and MMnet gene set. The enrichment was then tested over the background using a hypergeometric test. The significantly enriched traits are shown in bold.
| GWAS trait | Number of eQTLs genes (background) with at least one GWAS hit | Number of MMnet genes with at least one GWAS hit | Frequency (%) eQTLs genes (background) with at least one GWAS hit | Frequency (%) MMnet genes with at least one GWAS hit | P-value MMnet enrichment over background (hypergeometric test) |
|---|---|---|---|---|---|
| All GWAS combined | 299 | 41 | 20.3% | 27.7% | 0.0085 |
| Heel bone mineral density | 117 | 20 | 8.0% | 13.5% | 0.0045 |
| Osteoarthritis | 9 | 3 | 0.6% | 2.0% | 0.0083 |
| Psoriatic arthritis | 2 | 1 | 0.1% | 0.7% | 0.0101 |
| Body height | 165 | 24 | 11.2% | 16.2% | 0.0186 |
| Bone quantitative ultrasound measurement | 4 | 1 | 0.3% | 0.7% | 0.0527 |
| Bone density | 16 | 3 | 1.1% | 2.0% | 0.0686 |
| Hip bone mineral density | 5 | 1 | 0.3% | 0.7% | 0.0821 |
| Spine bone mineral density | 7 | 1 | 0.5% | 0.7% | 0.1509 |
| Bone fracture | 3 | 0 | 0.2% | 0.0% | 0.2727 |
| Ankylosing spondylitis | 4 | 0 | 0.3% | 0.0% | 0.3460 |
| Periodontitis | 4 | 0 | 0.3% | 0.0% | 0.3460 |
| Rheumatoid arthritis | 15 | 1 | 1.0% | 0.7% | 0.4550 |
| Adolescent idiopathic scoliosis | 60 | 5 | 4.1% | 3.4% | 0.5723 |
| Bone mineral content measurement | 1 | 1 | 0.1% | 0.7% | - |
| Lumbar disc degeneration | 1 | 1 | 0.1% | 0.7% | - |
| Osteitis deformans | 1 | 0 | 0.1% | 0.0% | - |