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 573
5
Diseases
19
Unique genes
0.179
Avg. similarity score
Autoimmune neurological syndrome
Most-connected disease (3 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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Autoimmune neurological syndrome
Delta-sarcoglycan-related limb-girdle muscular dystrophy r6
Dilated cardiomyopathy 1L
Salivary gland disease
Epileptic encephalopathy, early infantile, 47
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Autoimmune neurological syndrome | 3 | 3 | 16 |
| Delta-sarcoglycan-related limb-girdle muscular dystrophy r6 | 3 | 3 | 1 |
| Dilated cardiomyopathy 1L | 3 | 3 | 1 |
| Salivary gland disease | 2 | 2 | 4 |
| Epileptic encephalopathy, early infantile, 47 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| SGCD | 4 / 5 | Autoimmune neurological syndrome, Delta-sarcoglycan-related limb-girdle muscular dystrophy r6, Dilated cardiomyopathy 1L, Salivary gland disease |
| FGF12 | 2 / 5 | Autoimmune neurological syndrome, Epileptic encephalopathy, early infantile, 47 |
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 ⇵ |
|---|---|---|---|---|---|
| Arrhythmogenic right ventricular cardiomyopathy | KEGG | 2 / 86 | 14.7× | 8.01e-3 | 4.96e-2 ✓ sig. |
| Hypertrophic cardiomyopathy | KEGG | 2 / 99 | 12.8× | 1.05e-2 | 5.86e-2 |
| Dilated cardiomyopathy | KEGG | 2 / 105 | 12.0× | 1.18e-2 | 6.27e-2 |
| Uptake and function of anthrax toxins | Reactome | 1 / 13 | 48.6× | 2.04e-2 | 8.67e-2 |
| Sodium/Calcium exchangers | Reactome | 1 / 13 | 48.6× | 2.04e-2 | 8.67e-2 |
| Reduction of cytosolic Ca++ levels | Reactome | 1 / 14 | 45.2× | 2.19e-2 | 9.03e-2 |
| Pink/Parkin Mediated Mitophagy | Reactome | 1 / 22 | 28.7× | 3.43e-2 | 1.17e-1 |
| JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 | Reactome | 1 / 23 | 27.5× | 3.58e-2 | 1.19e-1 |
| Budding and maturation of HIV virion | Reactome | 1 / 29 | 21.8× | 4.49e-2 | 1.36e-1 |
| Sealing of the nuclear envelope (NE) by ESCRT-III | Reactome | 1 / 31 | 20.4× | 4.80e-2 | 1.41e-1 |
| Endosomal Sorting Complex Required For Transport (ESCRT) | Reactome | 1 / 32 | 19.8× | 4.95e-2 | 1.44e-1 |
| FCERI mediated MAPK activation | Reactome | 1 / 32 | 19.8× | 4.95e-2 | 1.44e-1 |
| Phase 0 - rapid depolarisation | Reactome | 1 / 44 | 14.4× | 6.74e-2 | 1.72e-1 |
| Virion - Hepatitis viruses | KEGG | 1 / 48 | 13.2× | 7.33e-2 | 1.80e-1 |
| Endocrine and other factor-regulated calcium reabsorption | KEGG | 1 / 53 | 11.9× | 8.07e-2 | 1.90e-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 ⇵ |
|---|---|---|---|---|---|
| late endosome to vacuole transport via multivesicular body sorting pathway | GO:0032511 | 2 / 12 | 164× | 6.43e-5 | 2.23e-3 ✓ sig. |
| cardiac muscle cell development | GO:0055013 | 2 / 25 | 78.7× | 2.90e-4 | 6.62e-3 ✓ sig. |
| calcium ion homeostasis | GO:0055074 | 2 / 42 | 46.8× | 8.23e-4 | 1.31e-2 ✓ sig. |
| cardiac muscle contraction | GO:0060048 | 2 / 43 | 45.7× | 8.63e-4 | 1.34e-2 ✓ sig. |
| regulation of systemic arterial blood pressure by baroreceptor feedback | GO:0003025 | 1 / 1 | 984× | 1.02e-3 | 1.48e-2 ✓ sig. |
| glossopharyngeal nerve development | GO:0021563 | 1 / 1 | 984× | 1.02e-3 | 1.48e-2 ✓ sig. |
| vagus nerve development | GO:0021564 | 1 / 1 | 984× | 1.02e-3 | 1.48e-2 ✓ sig. |
| regulation of voltage-gated sodium channel activity | GO:1905150 | 1 / 1 | 984× | 1.02e-3 | 1.48e-2 ✓ sig. |
| relaxation of smooth muscle | GO:0044557 | 1 / 1 | 984× | 1.02e-3 | 1.48e-2 ✓ sig. |
| JNK cascade | GO:0007254 | 2 / 61 | 32.2× | 1.73e-3 | 1.97e-2 ✓ sig. |
| smooth muscle cell apoptotic process | GO:0034390 | 1 / 2 | 492× | 2.03e-3 | 2.14e-2 ✓ sig. |
| coronary vasculature morphogenesis | GO:0060977 | 1 / 2 | 492× | 2.03e-3 | 2.14e-2 ✓ sig. |
| intrinsic apoptotic signaling pathway in response to hydrogen peroxide | GO:0036481 | 1 / 3 | 328× | 3.05e-3 | 2.62e-2 ✓ sig. |
| calcium ion export | GO:1901660 | 1 / 3 | 328× | 3.05e-3 | 2.62e-2 ✓ sig. |
| regulation of neuronal action potential | GO:0098908 | 1 / 4 | 246× | 4.06e-3 | 3.03e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Delta-sarcoglycan-related limb-girdle muscular dystrophy r6 | Dilated cardiomyopathy 1L | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Delta-sarcoglycan-related limb-girdle muscular dystrophy r6 | Salivary gland disease | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |
| Dilated cardiomyopathy 1L | Salivary gland disease | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |
| Autoimmune neurological syndrome | Epileptic encephalopathy, early infantile, 47 | 0.059 | 1 | 1.03e-3 | 1.57e-3 ✓ sig. |
| Autoimmune neurological syndrome | Delta-sarcoglycan-related limb-girdle muscular dystrophy r6 | 0.059 | 1 | 1.03e-3 | 1.57e-3 ✓ sig. |
| Autoimmune neurological syndrome | Dilated cardiomyopathy 1L | 0.059 | 1 | 1.03e-3 | 1.57e-3 ✓ sig. |