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 564
5
Diseases
6
Unique genes
0.259
Avg. similarity score
Ataxia with oculomotor apraxia
Most-connected disease (4 links)
Disease
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Ataxia with oculomotor apraxia
Cerebellar ataxia, intellectual disability, oculomotor apraxia, cerebellar cysts
Cerebellar dysplasia with cysts with or without retinal dystrophy
Poretti-boltshauser syndrome
Ataxia with oculomotor apraxia and hypoalbuminemia
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Ataxia with oculomotor apraxia | 4 | 4 | 5 |
| Cerebellar ataxia, intellectual disability, oculomotor apraxia, cerebellar cysts | 3 | 3 | 2 |
| Cerebellar dysplasia with cysts with or without retinal dystrophy | 3 | 3 | 1 |
| Poretti-boltshauser syndrome | 3 | 3 | 1 |
| Ataxia with oculomotor apraxia and hypoalbuminemia | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| LAMA1 | 4 / 5 | Ataxia with oculomotor apraxia, Cerebellar ataxia, intellectual disability, oculomotor apraxia, cerebellar cysts, Cerebellar dysplasia with cysts with or without retinal dystrophy, Poretti-boltshauser syndrome |
| APTX | 2 / 5 | Ataxia with oculomotor apraxia, Ataxia with oculomotor apraxia and hypoalbuminemia |
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 ⇵ |
|---|---|---|---|---|---|
| Base excision repair | KEGG | 2 / 44 | 91.0× | 1.95e-4 | 3.22e-3 ✓ sig. |
| Toxoplasmosis | KEGG | 2 / 112 | 35.7× | 1.26e-3 | 1.35e-2 ✓ sig. |
| APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway | Reactome | 1 / 7 | 286× | 3.49e-3 | 2.83e-2 ✓ sig. |
| Erythropoietin activates Phosphoinositide-3-kinase (PI3K) | Reactome | 1 / 12 | 167× | 5.98e-3 | 4.10e-2 ✓ sig. |
| G beta:gamma signalling through PI3Kgamma | Reactome | 1 / 25 | 80.1× | 1.24e-2 | 6.49e-2 |
| PI3K-Akt signaling pathway | KEGG | 2 / 361 | 11.1× | 1.25e-2 | 6.51e-2 |
| Laminin interactions | Reactome | 1 / 28 | 71.5× | 1.39e-2 | 6.94e-2 |
| MET activates PTK2 signaling | Reactome | 1 / 30 | 66.7× | 1.49e-2 | 7.22e-2 |
| GPVI-mediated activation cascade | Reactome | 1 / 34 | 58.9× | 1.69e-2 | 7.78e-2 |
| Synthesis of PIPs at the plasma membrane | Reactome | 1 / 51 | 39.2× | 2.52e-2 | 9.79e-2 |
| Ion transport by P-type ATPases | Reactome | 1 / 56 | 35.7× | 2.77e-2 | 1.03e-1 |
| Viral myocarditis | KEGG | 1 / 70 | 28.6× | 3.45e-2 | 1.17e-1 |
| Arrhythmogenic right ventricular cardiomyopathy | KEGG | 1 / 86 | 23.3× | 4.22e-2 | 1.31e-1 |
| ECM-receptor interaction | KEGG | 1 / 89 | 22.5× | 4.37e-2 | 1.34e-1 |
| Small cell lung cancer | KEGG | 1 / 93 | 21.5× | 4.56e-2 | 1.37e-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 ⇵ |
|---|---|---|---|---|---|
| DNA repair | GO:0006281 | 3 / 420 | 22.2× | 2.14e-4 | 5.32e-3 ✓ sig. |
| positive regulation of termination of DNA-templated transcription | GO:0060566 | 1 / 1 | 3,115× | 3.21e-4 | 7.04e-3 ✓ sig. |
| involuntary skeletal muscle contraction | GO:0003011 | 1 / 1 | 3,115× | 3.21e-4 | 7.04e-3 ✓ sig. |
| DNA damage response | GO:0006974 | 3 / 577 | 16.2× | 5.46e-4 | 1.00e-2 ✓ sig. |
| positive regulation of neuron projection development | GO:0010976 | 2 / 121 | 51.5× | 6.13e-4 | 1.09e-2 ✓ sig. |
| positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled | GO:2000806 | 1 / 3 | 1,038× | 9.63e-4 | 1.42e-2 ✓ sig. |
| positive regulation of phospholipid translocation | GO:0061092 | 1 / 4 | 779× | 1.28e-3 | 1.67e-2 ✓ sig. |
| retinal blood vessel morphogenesis | GO:0061304 | 1 / 6 | 519× | 1.93e-3 | 2.07e-2 ✓ sig. |
| regulation of basement membrane organization | GO:0110011 | 1 / 6 | 519× | 1.93e-3 | 2.07e-2 ✓ sig. |
| termination of RNA polymerase II transcription | GO:0006369 | 1 / 7 | 445× | 2.25e-3 | 2.24e-2 ✓ sig. |
| aminophospholipid translocation | GO:0140331 | 1 / 7 | 445× | 2.25e-3 | 2.24e-2 ✓ sig. |
| positive regulation of DNA-templated transcription initiation | GO:2000144 | 1 / 8 | 389× | 2.57e-3 | 2.40e-2 ✓ sig. |
| neurofilament cytoskeleton organization | GO:0060052 | 1 / 10 | 311× | 3.21e-3 | 2.69e-2 ✓ sig. |
| morphogenesis of an epithelial sheet | GO:0002011 | 1 / 10 | 311× | 3.21e-3 | 2.69e-2 ✓ sig. |
| branching involved in salivary gland morphogenesis | GO:0060445 | 1 / 12 | 260× | 3.85e-3 | 2.94e-2 ✓ sig. |