Disease Clusters?
Groups of diseases that share a large number of curated genes with each other, computed via label propagation over the shared-gene similarity graph. See also Shared-Gene Disease Pairs for pairwise comparisons.
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Cluster 127
10
Diseases
705
Unique genes
0.159
Avg. similarity score
Bone fragility with contractures, arterial rupture, and deafness
Most-connected disease (7 links)
Disease
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Bone fragility with contractures, arterial rupture, and deafness
Osteoporosis-pseudoglioma syndrome
Larsen syndrome
Osteogenesis imperfecta
Cole-carpenter syndrome
Desbuquois syndrome
Osteoporosis
ehlers-danlos syndrome, spondylodysplastic type, 1
neurodevelopmental disorder with hypotonia, facial dysmorphism, and brain abnormalities
skeletal dysplasia, mild, with joint laxity and advanced bone age
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Bone fragility with contractures, arterial rupture, and deafness | 7 | 7 | 49 |
| Osteoporosis-pseudoglioma syndrome | 7 | 7 | 49 |
| Larsen syndrome | 4 | 4 | 17 |
| Osteogenesis imperfecta | 4 | 4 | 39 |
| Cole-carpenter syndrome | 3 | 3 | 3 |
| Desbuquois syndrome | 3 | 3 | 567 |
| Osteoporosis | 3 | 3 | 146 |
| ehlers-danlos syndrome, spondylodysplastic type, 1 | 3 | 3 | 1 |
| neurodevelopmental disorder with hypotonia, facial dysmorphism, and brain abnormalities | 1 | 1 | 1 |
| skeletal dysplasia, mild, with joint laxity and advanced bone age | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| P4HB | 6 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Cole-carpenter syndrome, Desbuquois syndrome, Osteogenesis imperfecta and 2 more |
| B4GALT7 | 5 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, ehlers-danlos syndrome, spondylodysplastic type, 1, Larsen syndrome and 1 more |
| COL1A1 | 5 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis and 1 more |
| COL1A2 | 5 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis and 1 more |
| CRTAP | 5 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Cole-carpenter syndrome, Desbuquois syndrome, Osteogenesis imperfecta and 1 more |
| GORAB | 5 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Larsen syndrome, Osteoporosis and 1 more |
| IFITM5 | 5 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis and 1 more |
| LRP5 | 5 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis and 1 more |
| PLS3 | 5 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis and 1 more |
| SEC24D | 5 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Cole-carpenter syndrome, Desbuquois syndrome, Osteogenesis imperfecta and 1 more |
| SERPINF1 | 5 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis and 1 more |
| SP7 | 5 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis and 1 more |
| WNT1 | 5 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis and 1 more |
| XYLT2 | 5 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Larsen syndrome, Osteogenesis imperfecta and 1 more |
| ALPL | 4 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome |
| B3GALT6 | 4 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Larsen syndrome, Osteoporosis-pseudoglioma syndrome |
| B3GAT3 | 4 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Larsen syndrome, Osteoporosis-pseudoglioma syndrome |
| BMP1 | 4 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome |
| CCDC134 | 4 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome |
| CHST3 | 4 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Larsen syndrome, Osteoporosis-pseudoglioma syndrome |
| CREB3L1 | 4 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome |
| FKBP10 | 4 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome |
| KDELR2 | 4 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome |
| MBTPS2 | 4 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome |
| MESD | 4 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome |
| P3H1 | 4 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome |
| PLOD2 | 4 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome |
| PPIB | 4 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome |
| SERPINH1 | 4 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome |
| SPARC | 4 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome |
| TENT5A | 4 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome |
| TMEM38B | 4 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome |
| XYLT1 | 4 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Larsen syndrome, Osteoporosis-pseudoglioma syndrome |
| COPB2 | 3 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis, Osteoporosis-pseudoglioma syndrome |
| CSGALNACT1 | 3 / 10 | Desbuquois syndrome, Larsen syndrome, skeletal dysplasia, mild, with joint laxity and advanced bone age |
| LIFR | 3 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteoporosis-pseudoglioma syndrome |
| NBAS | 3 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteoporosis-pseudoglioma syndrome |
| P4HA1 | 3 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Larsen syndrome, Osteoporosis-pseudoglioma syndrome |
| PHLDB1 | 3 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome |
| PLOD3 | 3 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Larsen syndrome, Osteoporosis-pseudoglioma syndrome |
| SGMS2 | 3 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteoporosis-pseudoglioma syndrome |
| SLC10A7 | 3 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteoporosis-pseudoglioma syndrome |
| TAPT1 | 3 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteoporosis-pseudoglioma syndrome |
| AMBN | 2 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome |
| ANO5 | 2 / 10 | Desbuquois syndrome, Osteogenesis imperfecta |
| ANTXR2 | 2 / 10 | Desbuquois syndrome, Osteoporosis |
| BMP2 | 2 / 10 | Desbuquois syndrome, Osteoporosis |
| CA2 | 2 / 10 | Desbuquois syndrome, Osteoporosis |
| CANT1 | 2 / 10 | Desbuquois syndrome, Larsen syndrome |
| COL11A1 | 2 / 10 | Desbuquois syndrome, Osteogenesis imperfecta |
| DSPP | 2 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome |
| EMILIN1 | 2 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome |
| FGFR3 | 2 / 10 | Desbuquois syndrome, Larsen syndrome |
| FLNB | 2 / 10 | Desbuquois syndrome, Larsen syndrome |
| GALNT3 | 2 / 10 | Desbuquois syndrome, Osteoporosis |
| GPC6 | 2 / 10 | Desbuquois syndrome, Osteoporosis |
| GZF1 | 2 / 10 | Desbuquois syndrome, Larsen syndrome |
| IDH2 | 2 / 10 | Desbuquois syndrome, Osteoporosis |
| IGF1R | 2 / 10 | Desbuquois syndrome, Osteoporosis |
| IL1RN | 2 / 10 | Desbuquois syndrome, Osteoporosis |
| KIF22 | 2 / 10 | Desbuquois syndrome, Larsen syndrome |
| KIF5B | 2 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome |
| KL | 2 / 10 | Desbuquois syndrome, Osteoporosis |
| MECOM | 2 / 10 | Desbuquois syndrome, Osteoporosis |
| MIA3 | 2 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome |
| OFD1 | 2 / 10 | Desbuquois syndrome, Osteoporosis |
| PGGHG | 2 / 10 | Osteogenesis imperfecta, Osteoporosis |
| PIEZO2 | 2 / 10 | Larsen syndrome, Osteoporosis |
| PPP1R21 | 2 / 10 | Desbuquois syndrome, neurodevelopmental disorder with hypotonia, facial dysmorphism, and brain abnormalities |
| SEC16B | 2 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome |
| SFRP4 | 2 / 10 | Desbuquois syndrome, Osteoporosis |
| SKI | 2 / 10 | Desbuquois syndrome, Larsen syndrome |
| TGFB1 | 2 / 10 | Desbuquois syndrome, Osteoporosis |
| TNFRSF11A | 2 / 10 | Desbuquois syndrome, Osteoporosis |
| TNFRSF11B | 2 / 10 | Desbuquois syndrome, Osteoporosis |
| TNFSF11 | 2 / 10 | Desbuquois syndrome, Osteoporosis |
| WNT11 | 2 / 10 | Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome |
What do these columns mean?
- Connections in cluster
- How many other members this disease has a shared-gene link to (the node size in the network above). The most-connected diseases are the cluster's core.
- Significant partners
- How many of those links are statistically significant (FDR q < 0.05).
- Curated genes
- Distinct curated genes linked to that disease in GeDiPNet.
- Member diseases (Top shared genes)
- How many of this cluster's diseases are linked to the gene, out of the cluster's total. Genes shared by many members are the most direct explanation of why they group together.
- Overlap genes (x / y)
- x = genes shared between this cluster and the pathway/GO term; y = that pathway/GO term's total gene count. A higher x relative to y (and to the cluster's own size) means a tighter biological match.
- Cluster gene count
- Total distinct genes across every disease in this cluster -- the "n" used in the significance test below.
- Fold enrichment
- Observed overlap divided by the overlap expected by chance, given the cluster's gene count, the pathway/term's size and the gene universe tested. 5× means five times more shared genes than random. Tells strong hits apart when q-values are all vanishingly small.
- P-value / FDR q-value
- Is this pathway/GO term's overlap with the cluster more than chance? Upper-tail hypergeometric test, Benjamini-Hochberg corrected across every tested pathway/term (prefer the q-value -- it accounts for testing many at once).
- Shared genes (Pairs within this cluster)
- Number of curated genes the two diseases in that row have in common.
- Similarity score (Pairs within this cluster)
- Jaccard-based gene overlap between the two specific diseases in that row -- same metric as the main Shared-Gene Disease Pairs page.
Enriched Pathways (why this cluster is grouped, biologically)
| Pathway ⇵ | Source ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Proteoglycans in cancer | KEGG | 55 / 204 | 4.6× | 1.82e-22 | 2.28e-19 ✓ sig. |
| Pathways in cancer | KEGG | 91 / 533 | 2.9× | 5.03e-21 | 4.71e-18 ✓ sig. |
| Signaling pathways regulating pluripotency of stem cells | KEGG | 41 / 144 | 4.9× | 5.71e-18 | 3.25e-15 ✓ sig. |
| Breast cancer | KEGG | 41 / 148 | 4.7× | 1.70e-17 | 8.84e-15 ✓ sig. |
| Hepatocellular carcinoma | KEGG | 44 / 170 | 4.4× | 1.87e-17 | 9.66e-15 ✓ sig. |
| Parathyroid hormone synthesis, secretion and action | KEGG | 36 / 115 | 5.3× | 2.10e-17 | 1.07e-14 ✓ sig. |
| Gastric cancer | KEGG | 41 / 150 | 4.7× | 2.88e-17 | 1.42e-14 ✓ sig. |
| Hedgehog 'off' state | Reactome | 24 / 56 | 7.3× | 1.40e-15 | 5.25e-13 ✓ sig. |
| Melanogenesis | KEGG | 31 / 101 | 5.2× | 6.76e-15 | 2.23e-12 ✓ sig. |
| Signaling by high-kinase activity BRAF mutants | Reactome | 17 / 36 | 8.0× | 2.90e-12 | 5.75e-10 ✓ sig. |
| Chronic myeloid leukemia | KEGG | 24 / 77 | 5.3× | 5.41e-12 | 1.02e-9 ✓ sig. |
| Endocrine resistance | KEGG | 27 / 99 | 4.6× | 8.69e-12 | 1.57e-9 ✓ sig. |
| AGE-RAGE signaling pathway in diabetic complications | KEGG | 27 / 101 | 4.6× | 1.45e-11 | 2.50e-9 ✓ sig. |
| Human papillomavirus infection | KEGG | 53 / 333 | 2.7× | 2.15e-11 | 3.57e-9 ✓ sig. |
| MAP2K and MAPK activation | Reactome | 17 / 40 | 7.2× | 2.40e-11 | 3.93e-9 ✓ sig. |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| skeletal system development | GO:0001501 | 72 / 151 | 12.6× | 9.38e-62 | 4.00e-57 ✓ sig. |
| ossification | GO:0001503 | 43 / 110 | 10.4× | 1.20e-32 | 7.76e-29 ✓ sig. |
| embryonic limb morphogenesis | GO:0030326 | 33 / 59 | 14.8× | 8.07e-32 | 4.71e-28 ✓ sig. |
| embryonic digit morphogenesis | GO:0042733 | 31 / 57 | 14.4× | 1.91e-29 | 9.41e-26 ✓ sig. |
| cartilage development | GO:0051216 | 35 / 89 | 10.4× | 6.76e-27 | 2.66e-23 ✓ sig. |
| bone development | GO:0060348 | 32 / 76 | 11.2× | 8.02e-26 | 2.75e-22 ✓ sig. |
| bone mineralization | GO:0030282 | 28 / 56 | 13.3× | 2.34e-25 | 7.64e-22 ✓ sig. |
| positive regulation of gene expression | GO:0010628 | 75 / 504 | 3.9× | 8.23e-25 | 2.52e-21 ✓ sig. |
| embryonic hindlimb morphogenesis | GO:0035116 | 20 / 29 | 18.3× | 1.91e-22 | 4.39e-19 ✓ sig. |
| positive regulation of transcription by RNA polymerase II | GO:0045944 | 114 / 1,208 | 2.5× | 3.79e-20 | 6.40e-17 ✓ sig. |
| chondrocyte differentiation | GO:0002062 | 25 / 61 | 10.9× | 4.20e-20 | 7.03e-17 ✓ sig. |
| osteoblast differentiation | GO:0001649 | 35 / 137 | 6.8× | 8.92e-20 | 1.40e-16 ✓ sig. |
| bone morphogenesis | GO:0060349 | 19 / 32 | 15.7× | 1.56e-19 | 2.36e-16 ✓ sig. |
| cilium assembly | GO:0060271 | 44 / 237 | 4.9× | 1.11e-18 | 1.47e-15 ✓ sig. |
| heart development | GO:0007507 | 47 / 273 | 4.6× | 1.74e-18 | 2.24e-15 ✓ sig. |