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 241
7
Diseases
16
Unique genes
0.235
Avg. similarity score
Blindness
Most-connected disease (5 links)
Disease
Searched: RPE65-related dominant retinopathy
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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RPE65-related dominant retinopathy
Blindness
RPE65-related recessive retinopathy
Retinitis pigmentosa with choroidal involvement
Congenital blindness
AIPL1-related retinopathy
LCA5-related retinopathy
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Blindness | 5 | 5 | 14 |
| RPE65-related dominant retinopathy | 4 | 4 | 1 |
| RPE65-related recessive retinopathy | 4 | 4 | 1 |
| Retinitis pigmentosa with choroidal involvement | 4 | 4 | 1 |
| Congenital blindness | 3 | 3 | 3 |
| AIPL1-related retinopathy | 1 | 1 | 1 |
| LCA5-related retinopathy | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| RPE65 | 5 / 7 | Blindness, Congenital blindness, Retinitis pigmentosa with choroidal involvement, RPE65-related dominant retinopathy and 1 more |
| AIPL1 | 2 / 7 | AIPL1-related retinopathy, Blindness |
| LCA5 | 2 / 7 | Blindness, LCA5-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 | 3 / 20 | 113× | 2.18e-6 | 1.02e-4 ✓ sig. |
| Phototransduction | KEGG | 2 / 29 | 51.8× | 6.62e-4 | 1.03e-2 ✓ sig. |
| Inactivation, recovery and regulation of the phototransduction cascade | Reactome | 2 / 33 | 45.5× | 8.58e-4 | 1.25e-2 ✓ sig. |
| Activation of the phototransduction cascade | Reactome | 1 / 9 | 83.4× | 1.19e-2 | 7.90e-2 |
| Purine metabolism | KEGG | 2 / 128 | 11.7× | 1.23e-2 | 8.06e-2 |
| Opsins | Reactome | 1 / 10 | 75.1× | 1.32e-2 | 8.41e-2 |
| Purine ribonucleoside monophosphate biosynthesis | Reactome | 1 / 12 | 62.6× | 1.59e-2 | 9.38e-2 |
| Passive transport by Aquaporins | Reactome | 1 / 12 | 62.6× | 1.59e-2 | 9.38e-2 |
| Retinoid cycle disease events | Reactome | 1 / 13 | 57.7× | 1.72e-2 | 9.84e-2 |
| Processing of SMDT1 | Reactome | 1 / 16 | 46.9× | 2.11e-2 | 1.10e-1 |
| VxPx cargo-targeting to cilium | Reactome | 1 / 21 | 35.7× | 2.76e-2 | 1.28e-1 |
| Cholesterol biosynthesis | Reactome | 1 / 21 | 35.7× | 2.76e-2 | 1.28e-1 |
| Antifolate resistance | KEGG | 1 / 30 | 25.0× | 3.93e-2 | 1.55e-1 |
| One carbon pool by folate | KEGG | 1 / 38 | 19.8× | 4.95e-2 | 1.76e-1 |
| Molecules associated with elastic fibres | Reactome | 1 / 38 | 19.8× | 4.95e-2 | 1.76e-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 | 8 / 215 | 43.5× | 3.20e-12 | 1.34e-9 ✓ sig. |
| photoreceptor cell maintenance | GO:0045494 | 4 / 45 | 104× | 5.23e-8 | 7.10e-6 ✓ sig. |
| phototransduction, visible light | GO:0007603 | 3 / 13 | 270× | 1.47e-7 | 1.70e-5 ✓ sig. |
| camera-type eye development | GO:0043010 | 4 / 74 | 63.1× | 3.98e-7 | 3.95e-5 ✓ sig. |
| regulation of opsin-mediated signaling pathway | GO:0022400 | 2 / 10 | 234× | 3.08e-5 | 1.29e-3 ✓ sig. |
| sensory perception of light stimulus | GO:0050953 | 2 / 13 | 180× | 5.33e-5 | 1.96e-3 ✓ sig. |
| retina homeostasis | GO:0001895 | 2 / 15 | 156× | 7.17e-5 | 2.44e-3 ✓ sig. |
| retinal metabolic process | GO:0042574 | 2 / 19 | 123× | 1.17e-4 | 3.49e-3 ✓ sig. |
| response to light stimulus | GO:0009416 | 2 / 28 | 83.4× | 2.56e-4 | 6.22e-3 ✓ sig. |
| retinoid metabolic process | GO:0001523 | 2 / 38 | 61.5× | 4.75e-4 | 9.55e-3 ✓ sig. |
| zeaxanthin biosynthetic process | GO:1901827 | 1 / 1 | 1,168× | 8.56e-4 | 1.41e-2 ✓ sig. |
| regulation of plasma membrane sterol distribution | GO:0097036 | 1 / 1 | 1,168× | 8.56e-4 | 1.41e-2 ✓ sig. |
| mitochondrial threonyl-tRNA aminoacylation | GO:0070159 | 1 / 1 | 1,168× | 8.56e-4 | 1.41e-2 ✓ sig. |
| ciliary basal body-plasma membrane docking | GO:0097711 | 1 / 2 | 584× | 1.71e-3 | 2.14e-2 ✓ sig. |
| rod bipolar cell differentiation | GO:1904389 | 1 / 2 | 584× | 1.71e-3 | 2.14e-2 ✓ sig. |