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 424
5
Diseases
22
Unique genes
0.088
Avg. similarity score
Developmental regression
Most-connected disease (4 links)
Disease
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Developmental regression
Focal onset epileptic seizure
Cognitive impairment with or without cerebellar ataxia
intellectual disability, autosomal dominant 42
Hepatoencephalopathy due to combined oxidative phosphorylation defect
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Developmental regression | 4 | 4 | 18 |
| Focal onset epileptic seizure | 3 | 3 | 6 |
| Cognitive impairment with or without cerebellar ataxia | 2 | 2 | 1 |
| intellectual disability, autosomal dominant 42 | 2 | 2 | 1 |
| Hepatoencephalopathy due to combined oxidative phosphorylation defect | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| GNB1 | 3 / 5 | Developmental regression, Focal onset epileptic seizure, intellectual disability, autosomal dominant 42 |
| SCN8A | 3 / 5 | Cognitive impairment with or without cerebellar ataxia, Developmental regression, Focal onset epileptic seizure |
| GFM1 | 2 / 5 | Developmental regression, Hepatoencephalopathy due to combined oxidative phosphorylation defect |
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 ⇵ |
|---|---|---|---|---|---|
| Complex I biogenesis | Reactome | 4 / 55 | 39.7× | 2.71e-6 | 1.14e-4 ✓ sig. |
| Retrograde endocannabinoid signaling | KEGG | 4 / 149 | 14.7× | 1.40e-4 | 2.94e-3 ✓ sig. |
| Respiratory electron transport | Reactome | 3 / 83 | 19.7× | 4.46e-4 | 7.29e-3 ✓ sig. |
| Thermogenesis | KEGG | 4 / 234 | 9.3× | 7.79e-4 | 1.13e-2 ✓ sig. |
| Loss of MECP2 binding ability to 5hmC-DNA | Reactome | 1 / 1 | 546× | 1.83e-3 | 2.14e-2 ✓ sig. |
| Inhibition of PKR | Reactome | 1 / 1 | 546× | 1.83e-3 | 2.14e-2 ✓ sig. |
| MPS IIIA - Sanfilippo syndrome A | Reactome | 1 / 1 | 546× | 1.83e-3 | 2.14e-2 ✓ sig. |
| Oxidative phosphorylation | KEGG | 3 / 137 | 12.0× | 1.91e-3 | 2.20e-2 ✓ sig. |
| Phase 0 - rapid depolarisation | Reactome | 2 / 44 | 24.8× | 2.89e-3 | 3.00e-2 ✓ sig. |
| Alzheimer disease | KEGG | 4 / 388 | 5.6× | 4.94e-3 | 4.36e-2 ✓ sig. |
| Loss of MECP2 binding ability to 5mC-DNA | Reactome | 1 / 3 | 182× | 5.49e-3 | 4.65e-2 ✓ sig. |
| Breakdown of the nuclear lamina | Reactome | 1 / 3 | 182× | 5.49e-3 | 4.65e-2 ✓ sig. |
| Diabetic cardiomyopathy | KEGG | 3 / 205 | 8.0× | 5.94e-3 | 4.91e-2 ✓ sig. |
| MECP2 regulates neuronal receptors and channels | Reactome | 1 / 4 | 136× | 7.31e-3 | 5.62e-2 |
| Chemical carcinogenesis - reactive oxygen species | KEGG | 3 / 227 | 7.2× | 7.87e-3 | 5.91e-2 |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| mitochondrial respiratory chain complex I assembly | GO:0032981 | 3 / 40 | 63.7× | 1.36e-5 | 6.63e-4 ✓ sig. |
| mitochondrial electron transport, NADH to ubiquinone | GO:0006120 | 3 / 47 | 54.2× | 2.22e-5 | 9.75e-4 ✓ sig. |
| proton motive force-driven mitochondrial ATP synthesis | GO:0042776 | 3 / 64 | 39.8× | 5.63e-5 | 1.97e-3 ✓ sig. |
| aerobic respiration | GO:0009060 | 3 / 68 | 37.5× | 6.75e-5 | 2.25e-3 ✓ sig. |
| neuromuscular process controlling posture | GO:0050884 | 2 / 15 | 113× | 1.38e-4 | 3.83e-3 ✓ sig. |
| electron transport chain | GO:0022900 | 2 / 16 | 106× | 1.57e-4 | 4.25e-3 ✓ sig. |
| cardiac muscle cell action potential involved in contraction | GO:0086002 | 2 / 24 | 70.8× | 3.59e-4 | 7.58e-3 ✓ sig. |
| determination of adult lifespan | GO:0008340 | 2 / 38 | 44.7× | 9.07e-4 | 1.42e-2 ✓ sig. |
| associative learning | GO:0008306 | 2 / 40 | 42.5× | 1.00e-3 | 1.51e-2 ✓ sig. |
| response to hypoxia | GO:0001666 | 3 / 176 | 14.5× | 1.11e-3 | 1.61e-2 ✓ sig. |
| lateral geniculate nucleus development | GO:0021771 | 1 / 1 | 849× | 1.18e-3 | 1.66e-2 ✓ sig. |
| regulation of circadian sleep/wake cycle, REM sleep | GO:0042320 | 1 / 1 | 849× | 1.18e-3 | 1.66e-2 ✓ sig. |
| trans-synaptic signaling by BDNF | GO:0099191 | 1 / 1 | 849× | 1.18e-3 | 1.66e-2 ✓ sig. |
| proton transmembrane transport | GO:1902600 | 3 / 181 | 14.1× | 1.20e-3 | 1.69e-2 ✓ sig. |
| negative regulation of viral genome replication | GO:0045071 | 2 / 44 | 38.6× | 1.21e-3 | 1.70e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Developmental regression | Focal onset epileptic seizure | 0.087 | 2 | 1.93e-5 | 9.70e-5 ✓ sig. |
| Cognitive impairment with or without cerebellar ataxia | Focal onset epileptic seizure | 0.143 | 1 | 3.90e-4 | 8.52e-4 ✓ sig. |
| Focal onset epileptic seizure | intellectual disability, autosomal dominant 42 | 0.143 | 1 | 3.90e-4 | 8.52e-4 ✓ sig. |
| Cognitive impairment with or without cerebellar ataxia | Developmental regression | 0.053 | 1 | 1.17e-3 | 1.88e-3 ✓ sig. |
| Developmental regression | Hepatoencephalopathy due to combined oxidative phosphorylation defect | 0.053 | 1 | 1.17e-3 | 1.88e-3 ✓ sig. |
| Developmental regression | intellectual disability, autosomal dominant 42 | 0.053 | 1 | 1.17e-3 | 1.88e-3 ✓ sig. |