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 518
5
Diseases
80
Unique genes
0.192
Avg. similarity score
Dystonia
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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Dystonia
Dystonia musculorum deformans
Focal dystonia
Genetic torsion dystonia
Dystonia 37, early-onset, with striatal lesions
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Dystonia | 4 | 4 | 80 |
| Dystonia musculorum deformans | 3 | 3 | 9 |
| Focal dystonia | 3 | 3 | 1 |
| Genetic torsion dystonia | 3 | 3 | 9 |
| Dystonia 37, early-onset, with striatal lesions | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| GNAL | 4 / 5 | Dystonia, Dystonia musculorum deformans, Focal dystonia, Genetic torsion dystonia |
| COL6A3 | 3 / 5 | Dystonia, Dystonia musculorum deformans, Genetic torsion dystonia |
| GCH1 | 3 / 5 | Dystonia, Dystonia musculorum deformans, Genetic torsion dystonia |
| HPCA | 3 / 5 | Dystonia, Dystonia musculorum deformans, Genetic torsion dystonia |
| SGCE | 3 / 5 | Dystonia, Dystonia musculorum deformans, Genetic torsion dystonia |
| TAF1 | 3 / 5 | Dystonia, Dystonia musculorum deformans, Genetic torsion dystonia |
| THAP1 | 3 / 5 | Dystonia, Dystonia musculorum deformans, Genetic torsion dystonia |
| TOR1A | 3 / 5 | Dystonia, Dystonia musculorum deformans, Genetic torsion dystonia |
| TUBB4A | 3 / 5 | Dystonia, Dystonia musculorum deformans, Genetic torsion dystonia |
| NUP54 | 2 / 5 | Dystonia, Dystonia 37, early-onset, with striatal lesions |
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 ⇵ |
|---|---|---|---|---|---|
| Folate biosynthesis | KEGG | 5 / 28 | 26.8× | 1.01e-6 | 4.19e-5 ✓ sig. |
| Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation | Reactome | 3 / 11 | 40.9× | 4.52e-5 | 1.01e-3 ✓ sig. |
| Catecholamine biosynthesis | Reactome | 2 / 4 | 75.1× | 2.61e-4 | 4.04e-3 ✓ sig. |
| Ion transport by P-type ATPases | Reactome | 4 / 56 | 10.7× | 5.15e-4 | 6.82e-3 ✓ sig. |
| Efferocytosis | KEGG | 6 / 157 | 5.7× | 6.14e-4 | 7.83e-3 ✓ sig. |
| Thyroid hormone signaling pathway | KEGG | 5 / 122 | 6.2× | 1.30e-3 | 1.39e-2 ✓ sig. |
| Metal ion SLC transporters | Reactome | 2 / 9 | 33.4× | 1.53e-3 | 1.56e-2 ✓ sig. |
| Insulin secretion | KEGG | 4 / 86 | 7.0× | 2.56e-3 | 2.28e-2 ✓ sig. |
| Presynaptic depolarization and calcium channel opening | Reactome | 2 / 12 | 25.0× | 2.77e-3 | 2.41e-2 ✓ sig. |
| Bile secretion | KEGG | 4 / 90 | 6.7× | 3.02e-3 | 2.55e-2 ✓ sig. |
| Regulation of insulin secretion | Reactome | 2 / 16 | 18.8× | 4.95e-3 | 3.64e-2 ✓ sig. |
| Inhibition of PKR | Reactome | 1 / 1 | 150× | 6.66e-3 | 4.40e-2 ✓ sig. |
| Defective SLC2A1 causes GLUT1 deficiency syndrome 1 (GLUT1DS1) | Reactome | 1 / 1 | 150× | 6.66e-3 | 4.40e-2 ✓ sig. |
| Defective SLC20A2 causes idiopathic basal ganglia calcification 1 (IBGC1) | Reactome | 1 / 1 | 150× | 6.66e-3 | 4.40e-2 ✓ sig. |
| Serotonergic synapse | KEGG | 4 / 115 | 5.2× | 7.22e-3 | 4.64e-2 ✓ sig. |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| tetrahydrobiopterin biosynthetic process | GO:0006729 | 4 / 8 | 117× | 2.15e-8 | 3.43e-6 ✓ sig. |
| neuromuscular process controlling posture | GO:0050884 | 4 / 15 | 62.3× | 4.10e-7 | 4.12e-5 ✓ sig. |
| autophagy | GO:0006914 | 9 / 221 | 9.5× | 4.31e-7 | 4.29e-5 ✓ sig. |
| autophagy of mitochondrion | GO:0000422 | 4 / 25 | 37.4× | 3.68e-6 | 2.47e-4 ✓ sig. |
| dopamine biosynthetic process | GO:0042416 | 3 / 9 | 77.9× | 6.23e-6 | 3.77e-4 ✓ sig. |
| regulation of SNARE complex assembly | GO:0035542 | 3 / 12 | 58.4× | 1.62e-5 | 7.89e-4 ✓ sig. |
| amino acid metabolic process | GO:0006520 | 4 / 37 | 25.3× | 1.85e-5 | 8.72e-4 ✓ sig. |
| regulation of respiratory gaseous exchange by nervous system process | GO:0002087 | 3 / 13 | 53.9× | 2.10e-5 | 9.59e-4 ✓ sig. |
| regulation of resting membrane potential | GO:0060075 | 3 / 13 | 53.9× | 2.10e-5 | 9.59e-4 ✓ sig. |
| positive regulation of ATP biosynthetic process | GO:2001171 | 3 / 14 | 50.1× | 2.66e-5 | 1.14e-3 ✓ sig. |
| negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway | GO:1903377 | 3 / 14 | 50.1× | 2.66e-5 | 1.14e-3 ✓ sig. |
| endosomal vesicle fusion | GO:0034058 | 3 / 15 | 46.7× | 3.31e-5 | 1.35e-3 ✓ sig. |
| pteridine-containing compound metabolic process | GO:0042558 | 2 / 3 | 156× | 5.41e-5 | 1.96e-3 ✓ sig. |
| regulation of synaptic vesicle transport | GO:1902803 | 2 / 3 | 156× | 5.41e-5 | 1.96e-3 ✓ sig. |
| mitochondrion to lysosome vesicle-mediated transport | GO:0099074 | 2 / 3 | 156× | 5.41e-5 | 1.96e-3 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Dystonia musculorum deformans | Genetic torsion dystonia | 0.900 | 9 | 7.09e-33 | 1.48e-31 ✓ sig. |
| Dystonia | Dystonia musculorum deformans | 0.111 | 9 | 1.64e-21 | 2.52e-20 ✓ sig. |
| Dystonia | Genetic torsion dystonia | 0.111 | 9 | 1.64e-21 | 2.52e-20 ✓ sig. |
| Dystonia musculorum deformans | Focal dystonia | 0.100 | 1 | 5.81e-4 | 1.00e-3 ✓ sig. |
| Focal dystonia | Genetic torsion dystonia | 0.100 | 1 | 5.81e-4 | 1.00e-3 ✓ sig. |
| Dystonia | Dystonia 37, early-onset, with striatal lesions | 0.012 | 1 | 5.17e-3 | 6.16e-3 ✓ sig. |
| Dystonia | Focal dystonia | 0.012 | 1 | 5.17e-3 | 6.16e-3 ✓ sig. |