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 400
5
Diseases
10
Unique genes
0.287
Avg. similarity score
RPE65-related dominant retinopathy
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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RPE65-related dominant retinopathy
RPE65-related recessive retinopathy
Retinitis pigmentosa with choroidal involvement
Congenital blindness
Congenital nystagmus
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| 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 |
| Congenital nystagmus | 3 | 3 | 8 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| RPE65 | 5 / 5 | Congenital blindness, Congenital nystagmus, Retinitis pigmentosa with choroidal involvement, RPE65-related dominant retinopathy 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 ⇵ |
|---|---|---|---|---|---|
| Melanin biosynthesis | Reactome | 2 / 5 | 480× | 6.23e-6 | 2.26e-4 ✓ sig. |
| The canonical retinoid cycle in rods (twilight vision) | Reactome | 2 / 20 | 120× | 1.18e-4 | 2.55e-3 ✓ sig. |
| Regulation of commissural axon pathfinding by SLIT and ROBO | Reactome | 1 / 3 | 400× | 2.50e-3 | 2.69e-2 ✓ sig. |
| ATF6 (ATF6-alpha) activates chaperones | Reactome | 1 / 4 | 300× | 3.33e-3 | 3.31e-2 ✓ sig. |
| Role of ABL in ROBO-SLIT signaling | Reactome | 1 / 4 | 300× | 3.33e-3 | 3.31e-2 ✓ sig. |
| SLIT2:ROBO1 increases RHOA activity | Reactome | 1 / 4 | 300× | 3.33e-3 | 3.31e-2 ✓ sig. |
| Aryl hydrocarbon receptor signalling | Reactome | 1 / 7 | 172× | 5.82e-3 | 4.84e-2 ✓ sig. |
| Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) | Reactome | 1 / 7 | 172× | 5.82e-3 | 4.84e-2 ✓ sig. |
| Regulation of expression of SLITs and ROBOs | Reactome | 1 / 8 | 150× | 6.64e-3 | 5.28e-2 |
| ATF6 (ATF6-alpha) activates chaperone genes | Reactome | 1 / 9 | 133× | 7.47e-3 | 5.69e-2 |
| Signaling by ROBO receptors | Reactome | 1 / 12 | 100× | 9.95e-3 | 6.82e-2 |
| Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) | Reactome | 1 / 14 | 85.8× | 1.16e-2 | 7.50e-2 |
| Phase I - Functionalization of compounds | Reactome | 1 / 21 | 57.2× | 1.74e-2 | 9.50e-2 |
| Xenobiotics | Reactome | 1 / 24 | 50.0× | 1.98e-2 | 1.02e-1 |
| Endogenous sterols | Reactome | 1 / 25 | 48.0× | 2.06e-2 | 1.05e-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 | 6 / 215 | 52.1× | 4.37e-10 | 1.07e-7 ✓ sig. |
| melanin biosynthetic process from tyrosine | GO:0006583 | 2 / 4 | 934× | 1.55e-6 | 1.17e-4 ✓ sig. |
| melanin biosynthetic process | GO:0042438 | 2 / 14 | 267× | 2.34e-5 | 1.01e-3 ✓ sig. |
| eye photoreceptor cell development | GO:0042462 | 2 / 21 | 178× | 5.38e-5 | 1.90e-3 ✓ sig. |
| sensory organ development | GO:0007423 | 2 / 27 | 138× | 8.98e-5 | 2.79e-3 ✓ sig. |
| pigmentation | GO:0043473 | 2 / 39 | 95.8× | 1.89e-4 | 4.86e-3 ✓ sig. |
| eye development | GO:0001654 | 2 / 49 | 76.3× | 2.99e-4 | 6.70e-3 ✓ sig. |
| cell population proliferation | GO:0008283 | 3 / 263 | 21.3× | 3.07e-4 | 6.84e-3 ✓ sig. |
| positive regulation of ATF6-mediated unfolded protein response | GO:1903893 | 1 / 1 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| pancreatic A cell development | GO:0003322 | 1 / 1 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| forebrain-midbrain boundary formation | GO:0021905 | 1 / 1 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| zeaxanthin biosynthetic process | GO:1901827 | 1 / 1 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| sensory organ morphogenesis | GO:0090596 | 1 / 1 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| mitochondrial threonyl-tRNA aminoacylation | GO:0070159 | 1 / 1 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| blood vessel development | GO:0001568 | 2 / 70 | 53.4× | 6.10e-4 | 1.10e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Retinitis pigmentosa with choroidal involvement | RPE65-related recessive retinopathy | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Retinitis pigmentosa with choroidal involvement | RPE65-related dominant retinopathy | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| RPE65-related dominant retinopathy | RPE65-related recessive retinopathy | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Congenital blindness | Retinitis pigmentosa with choroidal involvement | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |
| Congenital blindness | RPE65-related recessive retinopathy | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |
| Congenital blindness | RPE65-related dominant retinopathy | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |
| Congenital nystagmus | Retinitis pigmentosa with choroidal involvement | 0.111 | 1 | 5.20e-4 | 1.04e-3 ✓ sig. |
| Congenital nystagmus | RPE65-related dominant retinopathy | 0.111 | 1 | 5.20e-4 | 1.04e-3 ✓ sig. |
| Congenital nystagmus | RPE65-related recessive retinopathy | 0.111 | 1 | 5.20e-4 | 1.04e-3 ✓ sig. |