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 152
9
Diseases
38
Unique genes
0.137
Avg. similarity score
Night blindness, congenital stationary
Most-connected disease (8 links)
Disease
Searched: inherited retinal dystrophy
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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inherited retinal dystrophy
Night blindness, congenital stationary
Congenital stationary night blindness
Oguchi disease
GRM6-related retinopathy
NYX-related retinopathy
TRPM1-related retinopathy
GPR179-related retinopathy
retinitis pigmentosa 47
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Night blindness, congenital stationary | 8 | 8 | 25 |
| Congenital stationary night blindness | 7 | 7 | 12 |
| Oguchi disease | 7 | 7 | 14 |
| GRM6-related retinopathy | 3 | 3 | 1 |
| NYX-related retinopathy | 3 | 3 | 1 |
| TRPM1-related retinopathy | 3 | 3 | 1 |
| inherited retinal dystrophy | 3 | 3 | 15 |
| GPR179-related retinopathy | 2 | 2 | 1 |
| retinitis pigmentosa 47 | 2 | 2 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| GNAT1 | 4 / 9 | Congenital stationary night blindness, inherited retinal dystrophy, Night blindness, congenital stationary, Oguchi disease |
| GRM6 | 4 / 9 | Congenital stationary night blindness, GRM6-related retinopathy, Night blindness, congenital stationary, Oguchi disease |
| NYX | 4 / 9 | Congenital stationary night blindness, Night blindness, congenital stationary, NYX-related retinopathy, Oguchi disease |
| PDE6B | 4 / 9 | Congenital stationary night blindness, inherited retinal dystrophy, Night blindness, congenital stationary, Oguchi disease |
| SLC24A1 | 4 / 9 | Congenital stationary night blindness, inherited retinal dystrophy, Night blindness, congenital stationary, Oguchi disease |
| TRPM1 | 4 / 9 | Congenital stationary night blindness, Night blindness, congenital stationary, Oguchi disease, TRPM1-related retinopathy |
| CACNA1F | 3 / 9 | Congenital stationary night blindness, Night blindness, congenital stationary, Oguchi disease |
| GNB3 | 3 / 9 | Congenital stationary night blindness, Night blindness, congenital stationary, Oguchi disease |
| GPR179 | 3 / 9 | Congenital stationary night blindness, GPR179-related retinopathy, Night blindness, congenital stationary |
| LRIT3 | 3 / 9 | Congenital stationary night blindness, Night blindness, congenital stationary, Oguchi disease |
| RHO | 3 / 9 | Congenital stationary night blindness, Night blindness, congenital stationary, Oguchi disease |
| SAG | 3 / 9 | Night blindness, congenital stationary, Oguchi disease, retinitis pigmentosa 47 |
| CABP4 | 2 / 9 | Congenital stationary night blindness, Night blindness, congenital stationary |
| GRK1 | 2 / 9 | Night blindness, congenital stationary, Oguchi disease |
| GUCY2D | 2 / 9 | Night blindness, congenital stationary, Oguchi disease |
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 ⇵ |
|---|---|---|---|---|---|
| Axon guidance | KEGG | 8 / 183 | 3.1× | 4.19e-3 | 3.95e-2 ✓ sig. |
| MET activates PTK2 signaling | Reactome | 3 / 30 | 7.1× | 8.27e-3 | 6.22e-2 |
| Small cell lung cancer | KEGG | 5 / 93 | 3.8× | 9.76e-3 | 6.90e-2 |
| Purine salvage | Reactome | 2 / 13 | 11.0× | 1.37e-2 | 8.47e-2 |
| RAF-independent MAPK1/3 activation | Reactome | 2 / 13 | 11.0× | 1.37e-2 | 8.47e-2 |
| Signaling by FGFR2 amplification mutants | Reactome | 1 / 1 | 71.5× | 1.40e-2 | 8.58e-2 |
| Signaling by FGFR2 fusions | Reactome | 1 / 1 | 71.5× | 1.40e-2 | 8.58e-2 |
| Negative regulation of MAPK pathway | Reactome | 3 / 38 | 5.6× | 1.58e-2 | 9.30e-2 |
| Gastric cancer | KEGG | 6 / 150 | 2.9× | 1.88e-2 | 1.03e-1 |
| Type I diabetes mellitus | KEGG | 3 / 44 | 4.9× | 2.34e-2 | 1.16e-1 |
| RORA activates gene expression | Reactome | 2 / 18 | 7.9× | 2.57e-2 | 1.22e-1 |
| Elastic fibre formation | Reactome | 2 / 18 | 7.9× | 2.57e-2 | 1.22e-1 |
| PCP/CE pathway | Reactome | 2 / 18 | 7.9× | 2.57e-2 | 1.22e-1 |
| Acetylation | Reactome | 1 / 2 | 35.7× | 2.78e-2 | 1.28e-1 |
| Defective ABCC9 causes dilated cardiomyopathy 10, familial atrial fibrillation 12 and hypertrichotic osteochondrodysplasia | Reactome | 1 / 2 | 35.7× | 2.78e-2 | 1.28e-1 |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| ureteric bud development | GO:0001657 | 6 / 41 | 16.3× | 1.67e-6 | 1.27e-4 ✓ sig. |
| branching involved in ureteric bud morphogenesis | GO:0001658 | 6 / 45 | 14.8× | 2.94e-6 | 2.00e-4 ✓ sig. |
| metanephros development | GO:0001656 | 5 / 38 | 14.6× | 2.18e-5 | 9.76e-4 ✓ sig. |
| animal organ morphogenesis | GO:0009887 | 8 / 130 | 6.8× | 2.31e-5 | 1.01e-3 ✓ sig. |
| camera-type eye development | GO:0043010 | 6 / 74 | 9.0× | 5.40e-5 | 1.94e-3 ✓ sig. |
| gland morphogenesis | GO:0022612 | 3 / 9 | 37.1× | 5.76e-5 | 2.03e-3 ✓ sig. |
| mesenchymal to epithelial transition | GO:0060231 | 3 / 11 | 30.3× | 1.12e-4 | 3.35e-3 ✓ sig. |
| ventricular zone neuroblast division | GO:0021847 | 2 / 3 | 74.2× | 2.40e-4 | 5.84e-3 ✓ sig. |
| regulation of signal transduction | GO:0009966 | 6 / 101 | 6.6× | 3.02e-4 | 6.91e-3 ✓ sig. |
| axon guidance | GO:0007411 | 8 / 192 | 4.6× | 3.52e-4 | 7.67e-3 ✓ sig. |
| lung development | GO:0030324 | 6 / 108 | 6.2× | 4.34e-4 | 8.85e-3 ✓ sig. |
| eye morphogenesis | GO:0048592 | 2 / 4 | 55.6× | 4.76e-4 | 9.48e-3 ✓ sig. |
| regulation of epidermal cell differentiation | GO:0045604 | 2 / 4 | 55.6× | 4.76e-4 | 9.48e-3 ✓ sig. |
| positive regulation of epithelial cell proliferation | GO:0050679 | 5 / 73 | 7.6× | 5.07e-4 | 9.84e-3 ✓ sig. |
| positive regulation of bone mineralization | GO:0030501 | 4 / 42 | 10.6× | 5.41e-4 | 1.03e-2 ✓ sig. |