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 530
5
Diseases
22
Unique genes
0.239
Avg. similarity score
Synovitis, acne, pustulosis, hyperostosis, and osteitis
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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Synovitis, acne, pustulosis, hyperostosis, and osteitis
Adult polyglucosan body disease
Glycogen storage disease due to glycogen branching enzyme deficiency
Multiple pterygium syndrome
Exfoliation syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Synovitis, acne, pustulosis, hyperostosis, and osteitis | 4 | 4 | 22 |
| Adult polyglucosan body disease | 3 | 3 | 1 |
| Glycogen storage disease due to glycogen branching enzyme deficiency | 3 | 3 | 1 |
| Multiple pterygium syndrome | 3 | 3 | 1 |
| Exfoliation syndrome | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| GBE1 | 4 / 5 | Adult polyglucosan body disease, Glycogen storage disease due to glycogen branching enzyme deficiency, Multiple pterygium syndrome, Synovitis, acne, pustulosis, hyperostosis, and osteitis |
| LOXL1 | 2 / 5 | Exfoliation syndrome, Synovitis, acne, pustulosis, hyperostosis, and osteitis |
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 ⇵ |
|---|---|---|---|---|---|
| Glycogen storage disease type IV (GBE1) | Reactome | 1 / 3 | 182× | 5.49e-3 | 3.87e-2 ✓ sig. |
| Gap junction | KEGG | 2 / 89 | 12.3× | 1.14e-2 | 6.16e-2 |
| CREB1 phosphorylation through the activation of Adenylate Cyclase | Reactome | 1 / 7 | 78.0× | 1.28e-2 | 6.57e-2 |
| Inflammatory mediator regulation of TRP channels | KEGG | 2 / 99 | 11.0× | 1.40e-2 | 6.96e-2 |
| Melanogenesis | KEGG | 2 / 101 | 10.8× | 1.45e-2 | 7.12e-2 |
| HDL assembly | Reactome | 1 / 8 | 68.2× | 1.46e-2 | 7.13e-2 |
| Dilated cardiomyopathy | KEGG | 2 / 105 | 10.4× | 1.56e-2 | 7.44e-2 |
| WNT mediated activation of DVL | Reactome | 1 / 9 | 60.7× | 1.64e-2 | 7.63e-2 |
| Serotonergic synapse | KEGG | 2 / 115 | 9.5× | 1.85e-2 | 8.21e-2 |
| cGMP effects | Reactome | 1 / 11 | 49.6× | 2.00e-2 | 8.55e-2 |
| Presynaptic depolarization and calcium channel opening | Reactome | 1 / 12 | 45.5× | 2.18e-2 | 9.00e-2 |
| Serotonin receptors | Reactome | 1 / 12 | 45.5× | 2.18e-2 | 9.00e-2 |
| LGI-ADAM interactions | Reactome | 1 / 14 | 39.0× | 2.54e-2 | 9.82e-2 |
| Rap1 signalling | Reactome | 1 / 16 | 34.1× | 2.89e-2 | 1.06e-1 |
| Regulation of insulin secretion | Reactome | 1 / 16 | 34.1× | 2.89e-2 | 1.06e-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 ⇵ |
|---|---|---|---|---|---|
| response to cocaine | GO:0042220 | 2 / 35 | 48.5× | 7.69e-4 | 1.25e-2 ✓ sig. |
| presynaptic modulation of chemical synaptic transmission | GO:0099171 | 2 / 37 | 45.9× | 8.59e-4 | 1.33e-2 ✓ sig. |
| monocyte activation involved in immune response | GO:0002280 | 1 / 1 | 849× | 1.18e-3 | 1.59e-2 ✓ sig. |
| asymmetric protein localization involved in cell fate determination | GO:0045167 | 1 / 1 | 849× | 1.18e-3 | 1.59e-2 ✓ sig. |
| ER-dependent peroxisome organization | GO:0032581 | 1 / 1 | 849× | 1.18e-3 | 1.59e-2 ✓ sig. |
| ER-dependent peroxisome localization | GO:0106101 | 1 / 1 | 849× | 1.18e-3 | 1.59e-2 ✓ sig. |
| sphinganine metabolic process | GO:0006667 | 1 / 1 | 849× | 1.18e-3 | 1.59e-2 ✓ sig. |
| protein localization to cytoskeleton | GO:0044380 | 1 / 2 | 425× | 2.35e-3 | 2.30e-2 ✓ sig. |
| postsynapse assembly | GO:0099068 | 1 / 2 | 425× | 2.35e-3 | 2.30e-2 ✓ sig. |
| positive regulation of protein localization to presynapse | GO:1905386 | 1 / 2 | 425× | 2.35e-3 | 2.30e-2 ✓ sig. |
| protein deamination | GO:0018277 | 1 / 2 | 425× | 2.35e-3 | 2.30e-2 ✓ sig. |
| oviduct development | GO:0060066 | 1 / 3 | 283× | 3.53e-3 | 2.82e-2 ✓ sig. |
| skeletal muscle satellite cell activation | GO:0014719 | 1 / 3 | 283× | 3.53e-3 | 2.82e-2 ✓ sig. |
| cGMP metabolic process | GO:0046068 | 1 / 3 | 283× | 3.53e-3 | 2.82e-2 ✓ sig. |
| sensitization | GO:0046960 | 1 / 3 | 283× | 3.53e-3 | 2.82e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Adult polyglucosan body disease | Glycogen storage disease due to glycogen branching enzyme deficiency | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Adult polyglucosan body disease | Multiple pterygium syndrome | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Glycogen storage disease due to glycogen branching enzyme deficiency | Multiple pterygium syndrome | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Adult polyglucosan body disease | Synovitis, acne, pustulosis, hyperostosis, and osteitis | 0.043 | 1 | 1.42e-3 | 2.04e-3 ✓ sig. |
| Exfoliation syndrome | Synovitis, acne, pustulosis, hyperostosis, and osteitis | 0.043 | 1 | 1.42e-3 | 2.04e-3 ✓ sig. |
| Glycogen storage disease due to glycogen branching enzyme deficiency | Synovitis, acne, pustulosis, hyperostosis, and osteitis | 0.043 | 1 | 1.42e-3 | 2.04e-3 ✓ sig. |
| Multiple pterygium syndrome | Synovitis, acne, pustulosis, hyperostosis, and osteitis | 0.043 | 1 | 1.42e-3 | 2.04e-3 ✓ sig. |