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 40
16
Diseases
18
Unique genes
0.247
Avg. similarity score
Central areolar choroidal dystrophy
Most-connected disease (8 links)
Disease
Searched: cone dystrophy 3
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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cone dystrophy 3
Central areolar choroidal dystrophy
Choroidal dystrophy
Choroidal sclerosis
PRPH2-related retinopathy
Choroideremia
GUCY2D-related dominant retinopathy
GUCY2D-related recessive retinopathy
Retinal cone dystrophy
Retinitis pigmentosa, digenic
Retinitis punctata albescens
CACNA2D4-related retinopathy
PRPF8-related retinopathy
RDH5-related retinopathy
TOPORS-related retinopathy
TTLL5-related retinopathy
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Central areolar choroidal dystrophy | 8 | 8 | 5 |
| Choroidal dystrophy | 8 | 8 | 2 |
| Choroidal sclerosis | 7 | 7 | 2 |
| PRPH2-related retinopathy | 6 | 6 | 1 |
| Choroideremia | 5 | 5 | 5 |
| GUCY2D-related dominant retinopathy | 5 | 5 | 1 |
| GUCY2D-related recessive retinopathy | 5 | 5 | 1 |
| Retinal cone dystrophy | 4 | 4 | 5 |
| Retinitis pigmentosa, digenic | 3 | 3 | 2 |
| Retinitis punctata albescens | 3 | 3 | 6 |
| CACNA2D4-related retinopathy | 1 | 1 | 1 |
| PRPF8-related retinopathy | 1 | 1 | 1 |
| RDH5-related retinopathy | 1 | 1 | 1 |
| TOPORS-related retinopathy | 1 | 1 | 1 |
| TTLL5-related retinopathy | 1 | 1 | 1 |
| cone dystrophy 3 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| PRPH2 | 7 / 16 | Central areolar choroidal dystrophy, Choroidal dystrophy, Choroidal sclerosis, Choroideremia and 3 more |
| GUCY2D | 6 / 16 | Central areolar choroidal dystrophy, Choroidal dystrophy, Choroidal sclerosis, GUCY2D-related dominant retinopathy and 2 more |
| CACNA2D4 | 2 / 16 | CACNA2D4-related retinopathy, Retinal cone dystrophy |
| EYS | 2 / 16 | Central areolar choroidal dystrophy, Retinitis punctata albescens |
| GUCA1A | 2 / 16 | Central areolar choroidal dystrophy, cone dystrophy 3 |
| PRPF8 | 2 / 16 | Choroideremia, PRPF8-related retinopathy |
| RDH5 | 2 / 16 | RDH5-related retinopathy, Retinitis punctata albescens |
| TOPORS | 2 / 16 | Choroideremia, TOPORS-related retinopathy |
| TTLL5 | 2 / 16 | Central areolar choroidal dystrophy, TTLL5-related retinopathy |
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 ⇵ |
|---|---|---|---|---|---|
| The canonical retinoid cycle in rods (twilight vision) | Reactome | 4 / 20 | 133× | 1.69e-8 | 1.35e-6 ✓ sig. |
| Phototransduction | KEGG | 3 / 29 | 69.0× | 1.01e-5 | 3.44e-4 ✓ sig. |
| Inactivation, recovery and regulation of the phototransduction cascade | Reactome | 3 / 33 | 60.7× | 1.50e-5 | 4.78e-4 ✓ sig. |
| Retinoid cycle disease events | Reactome | 2 / 13 | 103× | 1.64e-4 | 3.36e-3 ✓ sig. |
| The retinoid cycle in cones (daylight vision) | Reactome | 1 / 8 | 83.4× | 1.19e-2 | 7.79e-2 |
| Activation of the phototransduction cascade | Reactome | 1 / 9 | 74.1× | 1.34e-2 | 8.37e-2 |
| Opsins | Reactome | 1 / 10 | 66.7× | 1.49e-2 | 8.91e-2 |
| Purine metabolism | KEGG | 2 / 128 | 10.4× | 1.54e-2 | 9.12e-2 |
| SUMOylation of immune response proteins | Reactome | 1 / 11 | 60.7× | 1.64e-2 | 9.46e-2 |
| TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain | Reactome | 1 / 14 | 47.7× | 2.08e-2 | 1.08e-1 |
| VxPx cargo-targeting to cilium | Reactome | 1 / 21 | 31.8× | 3.10e-2 | 1.35e-1 |
| RA biosynthesis pathway | Reactome | 1 / 22 | 30.3× | 3.25e-2 | 1.38e-1 |
| Phase 2 - plateau phase | Reactome | 1 / 25 | 26.7× | 3.68e-2 | 1.48e-1 |
| Endogenous sterols | Reactome | 1 / 25 | 26.7× | 3.68e-2 | 1.48e-1 |
| Carboxyterminal post-translational modifications of tubulin | Reactome | 1 / 27 | 24.7× | 3.97e-2 | 1.54e-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 ⇵ |
|---|---|---|---|---|---|
| visual perception | GO:0007601 | 12 / 215 | 57.9× | 6.90e-20 | 1.08e-16 ✓ sig. |
| detection of light stimulus involved in visual perception | GO:0050908 | 5 / 24 | 216× | 1.90e-11 | 6.50e-9 ✓ sig. |
| photoreceptor cell outer segment organization | GO:0035845 | 3 / 15 | 208× | 3.39e-7 | 3.41e-5 ✓ sig. |
| retina development in camera-type eye | GO:0060041 | 4 / 85 | 48.9× | 1.16e-6 | 9.46e-5 ✓ sig. |
| protein heterooligomerization | GO:0051291 | 2 / 15 | 138× | 9.13e-5 | 2.89e-3 ✓ sig. |
| protein homooligomerization | GO:0051260 | 3 / 130 | 24.0× | 2.49e-4 | 5.99e-3 ✓ sig. |
| phototransduction | GO:0007602 | 2 / 34 | 61.1× | 4.83e-4 | 9.51e-3 ✓ sig. |
| retinoid metabolic process | GO:0001523 | 2 / 38 | 54.6× | 6.04e-4 | 1.11e-2 ✓ sig. |
| response to low light intensity stimulus | GO:0009645 | 1 / 1 | 1,038× | 9.63e-4 | 1.50e-2 ✓ sig. |
| pigment granule maturation | GO:0048757 | 1 / 1 | 1,038× | 9.63e-4 | 1.50e-2 ✓ sig. |
| pigment cell differentiation | GO:0050931 | 1 / 1 | 1,038× | 9.63e-4 | 1.50e-2 ✓ sig. |
| gamma-aminobutyric acid secretion, neurotransmission | GO:0061534 | 1 / 2 | 519× | 1.93e-3 | 2.26e-2 ✓ sig. |
| rod bipolar cell differentiation | GO:1904389 | 1 / 2 | 519× | 1.93e-3 | 2.26e-2 ✓ sig. |
| thermotaxis | GO:0043052 | 1 / 2 | 519× | 1.93e-3 | 2.26e-2 ✓ sig. |
| positive regulation of guanylate cyclase activity | GO:0031284 | 1 / 2 | 519× | 1.93e-3 | 2.26e-2 ✓ sig. |