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 397
6
Diseases
4
Unique genes
0.364
Avg. similarity score
Abnormal muscle tone
Most-connected disease (5 links)
Disease
Searched: Lack of speech
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Lack of speech
Abnormal muscle tone
Beukes hip dysplasia
Developmental delay and epilepsy
Poor weight gain
Neurodevelopmental disorder with microcephaly, movement abnormalities, and seizures
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Abnormal muscle tone | 5 | 5 | 4 |
| Beukes hip dysplasia | 4 | 4 | 1 |
| Developmental delay and epilepsy | 4 | 4 | 1 |
| Lack of speech | 4 | 4 | 1 |
| Poor weight gain | 4 | 4 | 1 |
| Neurodevelopmental disorder with microcephaly, movement abnormalities, and seizures | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| UFSP2 | 5 / 6 | Abnormal muscle tone, Beukes hip dysplasia, Developmental delay and epilepsy, Lack of speech and 1 more |
| CHKA | 2 / 6 | Abnormal muscle tone, Neurodevelopmental disorder with microcephaly, movement abnormalities, and seizures |
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 ⇵ |
|---|---|---|---|---|---|
| Hypusine synthesis from eIF5A-lysine | Reactome | 1 / 4 | 751× | 1.33e-3 | 1.41e-2 ✓ sig. |
| Presynaptic depolarization and calcium channel opening | Reactome | 1 / 12 | 250× | 3.99e-3 | 3.12e-2 ✓ sig. |
| Synthesis of PE | Reactome | 1 / 12 | 250× | 3.99e-3 | 3.12e-2 ✓ sig. |
| Phase 2 - plateau phase | Reactome | 1 / 25 | 120× | 8.30e-3 | 5.06e-2 |
| Synthesis of PC | Reactome | 1 / 28 | 107× | 9.29e-3 | 5.43e-2 |
| Phase 0 - rapid depolarisation | Reactome | 1 / 44 | 68.2× | 1.46e-2 | 7.13e-2 |
| Arrhythmogenic right ventricular cardiomyopathy | KEGG | 1 / 86 | 34.9× | 2.83e-2 | 1.05e-1 |
| Cardiac muscle contraction | KEGG | 1 / 87 | 34.5× | 2.87e-2 | 1.05e-1 |
| Choline metabolism in cancer | KEGG | 1 / 99 | 30.3× | 3.26e-2 | 1.13e-1 |
| Hypertrophic cardiomyopathy | KEGG | 1 / 99 | 30.3× | 3.26e-2 | 1.13e-1 |
| Glycerophospholipid metabolism | KEGG | 1 / 102 | 29.4× | 3.35e-2 | 1.15e-1 |
| Dilated cardiomyopathy | KEGG | 1 / 105 | 28.6× | 3.45e-2 | 1.17e-1 |
| Adrenergic signaling in cardiomyocytes | KEGG | 1 / 154 | 19.5× | 5.03e-2 | 1.45e-1 |
| Oxytocin signaling pathway | KEGG | 1 / 154 | 19.5× | 5.03e-2 | 1.45e-1 |
| MAPK signaling pathway | KEGG | 1 / 299 | 10.0× | 9.59e-2 | 2.11e-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 ⇵ |
|---|---|---|---|---|---|
| spermidine metabolic process | GO:0008216 | 1 / 1 | 4,672× | 2.14e-4 | 5.31e-3 ✓ sig. |
| spermidine catabolic process | GO:0046203 | 1 / 2 | 2,336× | 4.28e-4 | 8.53e-3 ✓ sig. |
| membrane depolarization during bundle of His cell action potential | GO:0086048 | 1 / 3 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| calcium ion transmembrane transport via high voltage-gated calcium channel | GO:0061577 | 1 / 3 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| regulation of membrane repolarization during action potential | GO:0098903 | 1 / 3 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| negative regulation of proteolysis involved in protein catabolic process | GO:1903051 | 1 / 4 | 1,168× | 8.56e-4 | 1.33e-2 ✓ sig. |
| lipid droplet disassembly | GO:1905691 | 1 / 7 | 667× | 1.50e-3 | 1.82e-2 ✓ sig. |
| CDP-choline pathway | GO:0006657 | 1 / 7 | 667× | 1.50e-3 | 1.82e-2 ✓ sig. |
| regulation of type II interferon production | GO:0032649 | 1 / 10 | 467× | 2.14e-3 | 2.19e-2 ✓ sig. |
| regulation of intracellular estrogen receptor signaling pathway | GO:0033146 | 1 / 10 | 467× | 2.14e-3 | 2.19e-2 ✓ sig. |
| regulation of calcium ion transmembrane transport via high voltage-gated calcium channel | GO:1902514 | 1 / 12 | 389× | 2.57e-3 | 2.40e-2 ✓ sig. |
| phosphatidylethanolamine biosynthetic process | GO:0006646 | 1 / 12 | 389× | 2.57e-3 | 2.40e-2 ✓ sig. |
| calcium ion transport into cytosol | GO:0060402 | 1 / 14 | 334× | 2.99e-3 | 2.59e-2 ✓ sig. |
| regulation of ventricular cardiac muscle cell membrane repolarization | GO:0060307 | 1 / 21 | 222× | 4.49e-3 | 3.17e-2 ✓ sig. |
| ribosome disassembly | GO:0032790 | 1 / 22 | 212× | 4.70e-3 | 3.25e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Beukes hip dysplasia | Developmental delay and epilepsy | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Beukes hip dysplasia | Lack of speech | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Beukes hip dysplasia | Poor weight gain | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Developmental delay and epilepsy | Lack of speech | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Developmental delay and epilepsy | Poor weight gain | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Lack of speech | Poor weight gain | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Abnormal muscle tone | Neurodevelopmental disorder with microcephaly, movement abnormalities, and seizures | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |
| Abnormal muscle tone | Beukes hip dysplasia | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |
| Abnormal muscle tone | Developmental delay and epilepsy | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |
| Abnormal muscle tone | Lack of speech | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |
| Abnormal muscle tone | Poor weight gain | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |