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 588
5
Diseases
6
Unique genes
0.357
Avg. similarity score
Blomstrand lethal chondrodysplasia
Most-connected disease (4 links)
Disease
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Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Blomstrand lethal chondrodysplasia
Eiken skeletal dysplasia
Eiken syndrome
Primary failure of tooth eruption
Rickets
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Blomstrand lethal chondrodysplasia | 4 | 4 | 1 |
| Eiken skeletal dysplasia | 4 | 4 | 1 |
| Eiken syndrome | 4 | 4 | 1 |
| Primary failure of tooth eruption | 4 | 4 | 1 |
| Rickets | 4 | 4 | 6 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| PTH1R | 5 / 5 | Blomstrand lethal chondrodysplasia, Eiken skeletal dysplasia, Eiken syndrome, Primary failure of tooth eruption and 1 more |
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 ⇵ |
|---|---|---|---|---|---|
| Parathyroid hormone synthesis, secretion and action | KEGG | 4 / 115 | 69.6× | 1.18e-7 | 6.47e-6 ✓ sig. |
| Endocrine and other factor-regulated calcium reabsorption | KEGG | 3 / 53 | 113× | 1.61e-6 | 6.29e-5 ✓ sig. |
| Vitamin D (calciferol) metabolism | Reactome | 2 / 11 | 364× | 1.14e-5 | 3.25e-4 ✓ sig. |
| Class B/2 (Secretin family receptors) | Reactome | 2 / 18 | 222× | 3.17e-5 | 7.59e-4 ✓ sig. |
| Defective CYP27B1 causes Rickets vitamin D-dependent 1A (VDDR1A) | Reactome | 1 / 1 | 2,002× | 5.00e-4 | 6.67e-3 ✓ sig. |
| Beta oxidation of myristoyl-CoA to lauroyl-CoA | Reactome | 1 / 3 | 667× | 1.50e-3 | 1.54e-2 ✓ sig. |
| Beta oxidation of palmitoyl-CoA to myristoyl-CoA | Reactome | 1 / 3 | 667× | 1.50e-3 | 1.54e-2 ✓ sig. |
| ADORA2B mediated anti-inflammatory cytokines production | Reactome | 2 / 128 | 31.3× | 1.64e-3 | 1.65e-2 ✓ sig. |
| G alpha (s) signalling events | Reactome | 2 / 140 | 28.6× | 1.96e-3 | 1.88e-2 ✓ sig. |
| Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA | Reactome | 1 / 5 | 400× | 2.50e-3 | 2.23e-2 ✓ sig. |
| Beta oxidation of octanoyl-CoA to hexanoyl-CoA | Reactome | 1 / 5 | 400× | 2.50e-3 | 2.23e-2 ✓ sig. |
| Beta oxidation of hexanoyl-CoA to butanoyl-CoA | Reactome | 1 / 5 | 400× | 2.50e-3 | 2.23e-2 ✓ sig. |
| Acyl chain remodeling of CL | Reactome | 1 / 5 | 400× | 2.50e-3 | 2.23e-2 ✓ sig. |
| Vitamins | Reactome | 1 / 6 | 334× | 2.99e-3 | 2.54e-2 ✓ sig. |
| mitochondrial fatty acid beta-oxidation of unsaturated fatty acids | Reactome | 1 / 6 | 334× | 2.99e-3 | 2.54e-2 ✓ 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 ⇵ |
|---|---|---|---|---|---|
| bone mineralization | GO:0030282 | 3 / 56 | 167× | 5.07e-7 | 4.93e-5 ✓ sig. |
| positive regulation of vitamin D receptor signaling pathway | GO:0070564 | 2 / 6 | 1,038× | 1.29e-6 | 1.06e-4 ✓ sig. |
| positive regulation of inositol phosphate biosynthetic process | GO:0060732 | 2 / 7 | 890× | 1.80e-6 | 1.39e-4 ✓ sig. |
| intracellular calcium ion homeostasis | GO:0006874 | 3 / 113 | 82.7× | 4.25e-6 | 2.78e-4 ✓ sig. |
| skeletal system development | GO:0001501 | 3 / 151 | 61.9× | 1.02e-5 | 5.50e-4 ✓ sig. |
| positive regulation of keratinocyte differentiation | GO:0045618 | 2 / 20 | 311× | 1.63e-5 | 7.92e-4 ✓ sig. |
| response to vitamin D | GO:0033280 | 2 / 21 | 297× | 1.80e-5 | 8.55e-4 ✓ sig. |
| decidualization | GO:0046697 | 2 / 25 | 249× | 2.57e-5 | 1.11e-3 ✓ sig. |
| bone resorption | GO:0045453 | 2 / 26 | 240× | 2.78e-5 | 1.18e-3 ✓ sig. |
| calcium ion homeostasis | GO:0055074 | 2 / 42 | 148× | 7.36e-5 | 2.46e-3 ✓ sig. |
| positive regulation of bone mineralization | GO:0030501 | 2 / 42 | 148× | 7.36e-5 | 2.46e-3 ✓ sig. |
| negative regulation of cell population proliferation | GO:0008285 | 3 / 444 | 21.0× | 2.53e-4 | 5.99e-3 ✓ sig. |
| macromolecule biosynthetic process | GO:0009059 | 1 / 1 | 3,115× | 3.21e-4 | 7.04e-3 ✓ sig. |
| nuclear receptor-mediated bile acid signaling pathway | GO:0038185 | 1 / 2 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| negative regulation of phosphate transmembrane transport | GO:2000186 | 1 / 2 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Blomstrand lethal chondrodysplasia | Eiken skeletal dysplasia | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Blomstrand lethal chondrodysplasia | Primary failure of tooth eruption | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Blomstrand lethal chondrodysplasia | Eiken syndrome | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Eiken skeletal dysplasia | Primary failure of tooth eruption | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Eiken skeletal dysplasia | Eiken syndrome | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Eiken syndrome | Primary failure of tooth eruption | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Blomstrand lethal chondrodysplasia | Rickets | 0.143 | 1 | 3.87e-4 | 7.33e-4 ✓ sig. |
| Eiken skeletal dysplasia | Rickets | 0.143 | 1 | 3.87e-4 | 7.33e-4 ✓ sig. |
| Eiken syndrome | Rickets | 0.143 | 1 | 3.87e-4 | 7.33e-4 ✓ sig. |
| Primary failure of tooth eruption | Rickets | 0.143 | 1 | 3.87e-4 | 7.33e-4 ✓ sig. |