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 192
8
Diseases
7
Unique genes
0.314
Avg. similarity score
X-linked ocular abinism
Most-connected disease (5 links)
Disease
Searched: Cone-rod synaptic disorder
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Cone-rod synaptic disorder
X-linked ocular abinism
Ocular albinism
Early-onset severe hermansky-pudlak syndrome with hearing loss due to ap3d1 deficiency
Ocular albinism with sensorineural deafness
hermansky-pudlak syndrome 10
GPR143-related foveal hypoplasia
Usher syndrome type 2D
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| X-linked ocular abinism | 5 | 5 | 2 |
| Ocular albinism | 4 | 4 | 5 |
| Early-onset severe hermansky-pudlak syndrome with hearing loss due to ap3d1 deficiency | 3 | 3 | 1 |
| Ocular albinism with sensorineural deafness | 3 | 3 | 1 |
| hermansky-pudlak syndrome 10 | 3 | 3 | 1 |
| GPR143-related foveal hypoplasia | 2 | 2 | 1 |
| Cone-rod synaptic disorder | 1 | 1 | 2 |
| Usher syndrome type 2D | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| AP3D1 | 4 / 8 | Early-onset severe hermansky-pudlak syndrome with hearing loss due to ap3d1 deficiency, hermansky-pudlak syndrome 10, Ocular albinism with sensorineural deafness, X-linked ocular abinism |
| GPR143 | 3 / 8 | GPR143-related foveal hypoplasia, Ocular albinism, X-linked ocular abinism |
| CABP4 | 2 / 8 | Cone-rod synaptic disorder, Ocular albinism |
| WHRN | 2 / 8 | Ocular albinism, Usher syndrome type 2D |
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 ⇵ |
|---|---|---|---|---|---|
| Insulin secretion | KEGG | 2 / 86 | 39.9× | 1.04e-3 | 1.43e-2 ✓ sig. |
| Amine ligand-binding receptors | Reactome | 1 / 7 | 245× | 4.07e-3 | 3.88e-2 ✓ sig. |
| Calcium signaling pathway | KEGG | 2 / 254 | 13.5× | 8.72e-3 | 6.44e-2 |
| Glycogen breakdown (glycogenolysis) | Reactome | 1 / 16 | 107× | 9.29e-3 | 6.69e-2 |
| Phase 2 - plateau phase | Reactome | 1 / 25 | 68.6× | 1.45e-2 | 8.76e-2 |
| Phase 0 - rapid depolarisation | Reactome | 1 / 44 | 39.0× | 2.54e-2 | 1.21e-1 |
| Cortisol synthesis and secretion | KEGG | 1 / 65 | 26.4× | 3.73e-2 | 1.49e-1 |
| GnRH secretion | KEGG | 1 / 65 | 26.4× | 3.73e-2 | 1.49e-1 |
| Renin secretion | KEGG | 1 / 69 | 24.9× | 3.95e-2 | 1.54e-1 |
| Arrhythmogenic right ventricular cardiomyopathy | KEGG | 1 / 86 | 20.0× | 4.91e-2 | 1.73e-1 |
| Cardiac muscle contraction | KEGG | 1 / 87 | 19.7× | 4.96e-2 | 1.74e-1 |
| GABAergic synapse | KEGG | 1 / 89 | 19.3× | 5.07e-2 | 1.76e-1 |
| GnRH signaling pathway | KEGG | 1 / 93 | 18.4× | 5.30e-2 | 1.80e-1 |
| Aldosterone synthesis and secretion | KEGG | 1 / 98 | 17.5× | 5.58e-2 | 1.84e-1 |
| Hypertrophic cardiomyopathy | KEGG | 1 / 99 | 17.3× | 5.63e-2 | 1.86e-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 ⇵ |
|---|---|---|---|---|---|
| melanosome organization | GO:0032438 | 2 / 25 | 214× | 3.59e-5 | 1.43e-3 ✓ sig. |
| visual perception | GO:0007601 | 3 / 215 | 37.2× | 5.08e-5 | 1.86e-3 ✓ sig. |
| regulation of melanosome transport | GO:1902908 | 1 / 1 | 2,670× | 3.75e-4 | 8.02e-3 ✓ sig. |
| neurotransmitter receptor transport, postsynaptic endosome to lysosome | GO:0098943 | 1 / 2 | 1,335× | 7.49e-4 | 1.28e-2 ✓ sig. |
| paranodal junction maintenance | GO:1990227 | 1 / 2 | 1,335× | 7.49e-4 | 1.28e-2 ✓ sig. |
| eye pigment biosynthetic process | GO:0006726 | 1 / 2 | 1,335× | 7.49e-4 | 1.28e-2 ✓ sig. |
| cerebellar Purkinje cell layer formation | GO:0021694 | 1 / 2 | 1,335× | 7.49e-4 | 1.28e-2 ✓ sig. |
| regulation of melanosome organization | GO:1903056 | 1 / 2 | 1,335× | 7.49e-4 | 1.28e-2 ✓ sig. |
| synaptic vesicle budding from endosome | GO:0016182 | 1 / 3 | 890× | 1.12e-3 | 1.66e-2 ✓ sig. |
| zinc ion import into lysosome | GO:0140916 | 1 / 4 | 667× | 1.50e-3 | 1.95e-2 ✓ sig. |
| positive regulation of NK T cell differentiation | GO:0051138 | 1 / 4 | 667× | 1.50e-3 | 1.95e-2 ✓ sig. |
| synaptic vesicle coating | GO:0016183 | 1 / 5 | 534× | 1.87e-3 | 2.24e-2 ✓ sig. |
| synaptic vesicle membrane organization | GO:0048499 | 1 / 5 | 534× | 1.87e-3 | 2.24e-2 ✓ sig. |
| melanosome localization | GO:0032400 | 1 / 5 | 534× | 1.87e-3 | 2.24e-2 ✓ sig. |
| calcium ion-regulated exocytosis of neurotransmitter | GO:0048791 | 1 / 5 | 534× | 1.87e-3 | 2.24e-2 ✓ sig. |