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 316
7
Diseases
7
Unique genes
0.255
Avg. similarity score
Abnormality of movement
Most-connected disease (4 links)
Disease
Searched: Stereotypic behavior
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Stereotypic behavior
Abnormality of movement
Axial hypotonia
Neurodevelopmental disorder with hypotonia and autistic features with or without hyperkinetic movements
Short foot
Neurodevelopmental disorder with seizures and nonepileptic hyperkinetic movements
Neurodevelopmental disorder with spasticity, cataracts, and cerebellar hypoplasia
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Abnormality of movement | 4 | 4 | 6 |
| Stereotypic behavior | 4 | 4 | 2 |
| Axial hypotonia | 3 | 3 | 2 |
| Neurodevelopmental disorder with hypotonia and autistic features with or without hyperkinetic movements | 3 | 3 | 1 |
| Short foot | 2 | 2 | 1 |
| Neurodevelopmental disorder with seizures and nonepileptic hyperkinetic movements | 1 | 1 | 1 |
| Neurodevelopmental disorder with spasticity, cataracts, and cerebellar hypoplasia | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| VAMP2 | 4 / 7 | Abnormality of movement, Axial hypotonia, Neurodevelopmental disorder with hypotonia and autistic features with or without hyperkinetic movements, Stereotypic behavior |
| DROSHA | 3 / 7 | Abnormality of movement, Short foot, Stereotypic behavior |
| CACNA1B | 2 / 7 | Abnormality of movement, Neurodevelopmental disorder with seizures and nonepileptic hyperkinetic movements |
| MED27 | 2 / 7 | Axial hypotonia, Neurodevelopmental disorder with spasticity, cataracts, and cerebellar hypoplasia |
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 ⇵ |
|---|---|---|---|---|---|
| Presynaptic depolarization and calcium channel opening | Reactome | 2 / 12 | 286× | 1.92e-5 | 5.02e-4 ✓ sig. |
| Toxicity of tetanus toxin (TeNT) | Reactome | 1 / 1 | 1,716× | 5.83e-4 | 7.52e-3 ✓ sig. |
| Synaptic vesicle cycle | KEGG | 2 / 79 | 43.4× | 8.78e-4 | 1.03e-2 ✓ sig. |
| Toxicity of botulinum toxin type B (BoNT/B) | Reactome | 1 / 3 | 572× | 1.75e-3 | 1.73e-2 ✓ sig. |
| Toxicity of botulinum toxin type G (BoNT/G) | Reactome | 1 / 3 | 572× | 1.75e-3 | 1.73e-2 ✓ sig. |
| Cholinergic synapse | KEGG | 2 / 115 | 29.8× | 1.85e-3 | 1.80e-2 ✓ sig. |
| Toxicity of botulinum toxin type D (BoNT/D) | Reactome | 1 / 5 | 343× | 2.91e-3 | 2.49e-2 ✓ sig. |
| Toxicity of botulinum toxin type F (BoNT/F) | Reactome | 1 / 5 | 343× | 2.91e-3 | 2.49e-2 ✓ sig. |
| Oxytocin signaling pathway | KEGG | 2 / 154 | 22.3× | 3.29e-3 | 2.72e-2 ✓ sig. |
| CaMK IV-mediated phosphorylation of CREB | Reactome | 1 / 6 | 286× | 3.49e-3 | 2.83e-2 ✓ sig. |
| CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde | Reactome | 1 / 6 | 286× | 3.49e-3 | 2.83e-2 ✓ sig. |
| trans-Golgi Network Vesicle Budding | Reactome | 1 / 7 | 245× | 4.07e-3 | 3.17e-2 ✓ sig. |
| Synthesis of PE | Reactome | 1 / 12 | 143× | 6.97e-3 | 4.53e-2 ✓ sig. |
| GABA synthesis, release, reuptake and degradation | Reactome | 1 / 13 | 132× | 7.55e-3 | 4.77e-2 ✓ sig. |
| Calcium signaling pathway | KEGG | 2 / 254 | 13.5× | 8.72e-3 | 5.22e-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 ⇵ |
|---|---|---|---|---|---|
| calcium ion import across plasma membrane | GO:0098703 | 2 / 28 | 191× | 4.53e-5 | 1.71e-3 ✓ sig. |
| regulation of delayed rectifier potassium channel activity | GO:1902259 | 1 / 2 | 1,335× | 7.49e-4 | 1.23e-2 ✓ sig. |
| regulation of histamine secretion by mast cell | GO:1903593 | 1 / 3 | 890× | 1.12e-3 | 1.55e-2 ✓ sig. |
| membrane depolarization during bundle of His cell action potential | GO:0086048 | 1 / 3 | 890× | 1.12e-3 | 1.55e-2 ✓ sig. |
| calcium ion transmembrane transport via high voltage-gated calcium channel | GO:0061577 | 1 / 3 | 890× | 1.12e-3 | 1.55e-2 ✓ sig. |
| regulation of membrane repolarization during action potential | GO:0098903 | 1 / 3 | 890× | 1.12e-3 | 1.55e-2 ✓ sig. |
| positive regulation of calcium ion-dependent exocytosis of neurotransmitter | GO:1903235 | 1 / 3 | 890× | 1.12e-3 | 1.55e-2 ✓ sig. |
| regulation of miRNA metabolic process | GO:2000628 | 1 / 3 | 890× | 1.12e-3 | 1.55e-2 ✓ sig. |
| calcium ion transmembrane transport | GO:0070588 | 2 / 149 | 35.8× | 1.29e-3 | 1.68e-2 ✓ sig. |
| calcium ion transport | GO:0006816 | 2 / 157 | 34.0× | 1.43e-3 | 1.79e-2 ✓ sig. |
| eosinophil degranulation | GO:0043308 | 1 / 6 | 445× | 2.25e-3 | 2.24e-2 ✓ sig. |
| positive regulation of myeloid dendritic cell cytokine production | GO:0002735 | 1 / 7 | 381× | 2.62e-3 | 2.44e-2 ✓ sig. |
| regulation of T cell differentiation in thymus | GO:0033081 | 1 / 7 | 381× | 2.62e-3 | 2.44e-2 ✓ sig. |
| lipid droplet disassembly | GO:1905691 | 1 / 7 | 381× | 2.62e-3 | 2.44e-2 ✓ sig. |
| neutrophil degranulation | GO:0043312 | 1 / 7 | 381× | 2.62e-3 | 2.44e-2 ✓ sig. |