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 84
12
Diseases
42
Unique genes
0.311
Avg. similarity score
Cone-rod dystrophy, x-linked
Most-connected disease (7 links)
Disease
Searched: Aland island eye disease
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Aland island eye disease
Cone-rod dystrophy, x-linked
X-linked cone-rod dystrophy
Ocular albinism
CACNA1F-related retinopathy
Ciliary dyskinesia with retinitis pigmentosa
RPGR-related retinopathy
Retinitis pigmentosa, x-linked, and sinorespiratory infections with or without deafness
Ocular hypotension
Usher syndrome type 2D
Cone-rod synaptic disorder
Diabetic macular edema
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Cone-rod dystrophy, x-linked | 7 | 7 | 2 |
| X-linked cone-rod dystrophy | 6 | 6 | 2 |
| Ocular albinism | 5 | 5 | 5 |
| Aland island eye disease | 4 | 4 | 1 |
| CACNA1F-related retinopathy | 4 | 4 | 1 |
| Ciliary dyskinesia with retinitis pigmentosa | 4 | 4 | 1 |
| RPGR-related retinopathy | 4 | 4 | 1 |
| Retinitis pigmentosa, x-linked, and sinorespiratory infections with or without deafness | 4 | 4 | 1 |
| Ocular hypotension | 2 | 2 | 36 |
| Usher syndrome type 2D | 2 | 2 | 1 |
| Cone-rod synaptic disorder | 1 | 1 | 2 |
| Diabetic macular edema | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| CACNA1F | 5 / 12 | Aland island eye disease, CACNA1F-related retinopathy, Cone-rod dystrophy, x-linked, Ocular albinism and 1 more |
| RPGR | 5 / 12 | Ciliary dyskinesia with retinitis pigmentosa, Cone-rod dystrophy, x-linked, Retinitis pigmentosa, x-linked, and sinorespiratory infections with or without deafness, RPGR-related retinopathy and 1 more |
| WHRN | 3 / 12 | Ocular albinism, Ocular hypotension, Usher syndrome type 2D |
| CABP4 | 2 / 12 | Cone-rod synaptic disorder, Ocular albinism |
| MRPL19 | 2 / 12 | Diabetic macular edema, Ocular hypotension |
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)
None of these pathways reaches significance (all FDR q ≥ 0.05). They’re the best candidates found, but treat them as weak evidence for why this cluster groups together.
| Pathway ⇵ | Source ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Rap1 signaling pathway | KEGG | 4 / 211 | 5.4× | 6.15e-3 | 5.20e-2 |
| Signaling by VEGF | Reactome | 1 / 2 | 143× | 6.98e-3 | 5.64e-2 |
| Caspase activation via Dependence Receptors in the absence of ligand | Reactome | 1 / 4 | 71.5× | 1.39e-2 | 8.64e-2 |
| NGF processing | Reactome | 1 / 4 | 71.5× | 1.39e-2 | 8.64e-2 |
| VEGF ligand-receptor interactions | Reactome | 1 / 5 | 57.2× | 1.74e-2 | 9.88e-2 |
| Amine ligand-binding receptors | Reactome | 1 / 7 | 40.9× | 2.42e-2 | 1.20e-1 |
| Non-small cell lung cancer | KEGG | 2 / 73 | 7.8× | 2.68e-2 | 1.26e-1 |
| Sema4D mediated inhibition of cell attachment and migration | Reactome | 1 / 8 | 35.7× | 2.76e-2 | 1.28e-1 |
| Netrin-1 signaling | Reactome | 1 / 8 | 35.7× | 2.76e-2 | 1.28e-1 |
| VEGF binds to VEGFR leading to receptor dimerization | Reactome | 1 / 8 | 35.7× | 2.76e-2 | 1.28e-1 |
| Pancreatic cancer | KEGG | 2 / 77 | 7.4× | 2.96e-2 | 1.33e-1 |
| DSCAM interactions | Reactome | 1 / 9 | 31.8× | 3.10e-2 | 1.37e-1 |
| Insulin secretion | KEGG | 2 / 86 | 6.7× | 3.63e-2 | 1.49e-1 |
| Colorectal cancer | KEGG | 2 / 87 | 6.6× | 3.70e-2 | 1.50e-1 |
| Regulation of gene expression by Hypoxia-inducible Factor | Reactome | 1 / 11 | 26.0× | 3.78e-2 | 1.52e-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 ⇵ |
|---|---|---|---|---|---|
| bone trabecula morphogenesis | GO:0061430 | 2 / 4 | 222× | 2.95e-5 | 1.25e-3 ✓ sig. |
| positive regulation of cold-induced thermogenesis | GO:0120162 | 4 / 102 | 17.4× | 7.98e-5 | 2.66e-3 ✓ sig. |
| positive regulation of axon extension involved in axon guidance | GO:0048842 | 2 / 7 | 127× | 1.03e-4 | 3.20e-3 ✓ sig. |
| ossification involved in bone maturation | GO:0043931 | 2 / 12 | 74.2× | 3.21e-4 | 7.28e-3 ✓ sig. |
| dendrite self-avoidance | GO:0070593 | 2 / 16 | 55.6× | 5.80e-4 | 1.09e-2 ✓ sig. |
| axon guidance | GO:0007411 | 4 / 192 | 9.3× | 8.91e-4 | 1.45e-2 ✓ sig. |
| eye photoreceptor cell development | GO:0042462 | 2 / 21 | 42.4× | 1.01e-3 | 1.57e-2 ✓ sig. |
| visual perception | GO:0007601 | 4 / 215 | 8.3× | 1.35e-3 | 1.87e-2 ✓ sig. |
| regulation of monoatomic ion transmembrane transporter activity | GO:0032412 | 1 / 1 | 445× | 2.25e-3 | 2.50e-2 ✓ sig. |
| basophil chemotaxis | GO:0002575 | 1 / 1 | 445× | 2.25e-3 | 2.50e-2 ✓ sig. |
| positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway | GO:0038033 | 1 / 1 | 445× | 2.25e-3 | 2.50e-2 ✓ sig. |
| leukocyte aggregation | GO:0070486 | 1 / 1 | 445× | 2.25e-3 | 2.50e-2 ✓ sig. |
| peptidyl-tyrosine sulfation | GO:0006478 | 1 / 1 | 445× | 2.25e-3 | 2.50e-2 ✓ sig. |
| regulation of melanosome transport | GO:1902908 | 1 / 1 | 445× | 2.25e-3 | 2.50e-2 ✓ sig. |
| regulation of synaptic vesicle exocytosis | GO:2000300 | 2 / 38 | 23.4× | 3.29e-3 | 3.08e-2 ✓ sig. |