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 402
5
Diseases
3
Unique genes
0.357
Avg. similarity score
Au-kline syndrome
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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Au-kline syndrome
X-linked distal spinal muscular atrophy
X-linked distal spinal muscular atrophy type 3
menkes disease
neurodevelopmental disorder-craniofacial dysmorphism-cardiac defect-hip dysplasia syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Au-kline syndrome | 4 | 4 | 3 |
| X-linked distal spinal muscular atrophy | 3 | 3 | 1 |
| X-linked distal spinal muscular atrophy type 3 | 3 | 3 | 1 |
| menkes disease | 3 | 3 | 1 |
| neurodevelopmental disorder-craniofacial dysmorphism-cardiac defect-hip dysplasia syndrome | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| ATP7A | 4 / 5 | Au-kline syndrome, menkes disease, X-linked distal spinal muscular atrophy, X-linked distal spinal muscular atrophy type 3 |
| HNRNPK | 2 / 5 | Au-kline syndrome, neurodevelopmental disorder-craniofacial dysmorphism-cardiac defect-hip dysplasia syndrome |
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 ⇵ |
|---|---|---|---|---|---|
| Ion influx/efflux at host-pathogen interface | Reactome | 1 / 4 | 1,001× | 9.99e-4 | 1.35e-2 ✓ sig. |
| Processing of Capped Intron-Containing Pre-mRNA | Reactome | 1 / 37 | 108× | 9.21e-3 | 6.53e-2 |
| SUMOylation of ubiquitinylation proteins | Reactome | 1 / 38 | 105× | 9.46e-3 | 6.63e-2 |
| SUMOylation of RNA binding proteins | Reactome | 1 / 47 | 85.2× | 1.17e-2 | 7.53e-2 |
| Ion transport by P-type ATPases | Reactome | 1 / 56 | 71.5× | 1.39e-2 | 8.32e-2 |
| Mineral absorption | KEGG | 1 / 61 | 65.6× | 1.52e-2 | 8.75e-2 |
| Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha | Reactome | 1 / 66 | 60.7× | 1.64e-2 | 9.17e-2 |
| Renal cell carcinoma | KEGG | 1 / 70 | 57.2× | 1.74e-2 | 9.51e-2 |
| Platinum drug resistance | KEGG | 1 / 75 | 53.4× | 1.86e-2 | 9.87e-2 |
| HIF-1 signaling pathway | KEGG | 1 / 110 | 36.4× | 2.72e-2 | 1.22e-1 |
| HCMV Late Events | Reactome | 1 / 116 | 34.5× | 2.87e-2 | 1.26e-1 |
| Ubiquitin mediated proteolysis | KEGG | 1 / 142 | 28.2× | 3.51e-2 | 1.41e-1 |
| Spliceosome | KEGG | 1 / 162 | 24.7× | 3.99e-2 | 1.52e-1 |
| mRNA Splicing - Major Pathway | Reactome | 1 / 183 | 21.9× | 4.50e-2 | 1.62e-1 |
| Viral carcinogenesis | KEGG | 1 / 205 | 19.5× | 5.03e-2 | 1.72e-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 ⇵ |
|---|---|---|---|---|---|
| regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator | GO:1902165 | 1 / 1 | 6,229× | 1.61e-4 | 4.31e-3 ✓ sig. |
| negative regulation of catecholamine metabolic process | GO:0045914 | 1 / 2 | 3,115× | 3.21e-4 | 7.03e-3 ✓ sig. |
| negative regulation of RNA metabolic process | GO:0051253 | 1 / 2 | 3,115× | 3.21e-4 | 7.03e-3 ✓ sig. |
| copper ion export | GO:0060003 | 1 / 3 | 2,076× | 4.82e-4 | 9.31e-3 ✓ sig. |
| L-tryptophan metabolic process | GO:0006568 | 1 / 3 | 2,076× | 4.82e-4 | 9.31e-3 ✓ sig. |
| epinephrine metabolic process | GO:0042414 | 1 / 3 | 2,076× | 4.82e-4 | 9.31e-3 ✓ sig. |
| positive regulation of low-density lipoprotein particle clearance | GO:1905581 | 1 / 4 | 1,557× | 6.42e-4 | 1.13e-2 ✓ sig. |
| tyrosine metabolic process | GO:0006570 | 1 / 5 | 1,246× | 8.03e-4 | 1.30e-2 ✓ sig. |
| T-helper cell differentiation | GO:0042093 | 1 / 5 | 1,246× | 8.03e-4 | 1.30e-2 ✓ sig. |
| negative regulation of gene expression | GO:0010629 | 2 / 339 | 36.7× | 9.73e-4 | 1.48e-2 ✓ sig. |
| copper ion import | GO:0015677 | 1 / 7 | 890× | 1.12e-3 | 1.62e-2 ✓ sig. |
| regulation of cellular response to hypoxia | GO:1900037 | 1 / 7 | 890× | 1.12e-3 | 1.62e-2 ✓ sig. |
| pyramidal neuron development | GO:0021860 | 1 / 8 | 779× | 1.28e-3 | 1.75e-2 ✓ sig. |
| regulation of gene expression | GO:0010468 | 2 / 402 | 31.0× | 1.37e-3 | 1.82e-2 ✓ sig. |
| regulatory ncRNA-mediated heterochromatin formation | GO:0031048 | 1 / 9 | 692× | 1.44e-3 | 1.87e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| menkes disease | X-linked distal spinal muscular atrophy | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| menkes disease | X-linked distal spinal muscular atrophy type 3 | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| X-linked distal spinal muscular atrophy | X-linked distal spinal muscular atrophy type 3 | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Au-kline syndrome | X-linked distal spinal muscular atrophy | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |
| Au-kline syndrome | menkes disease | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |
| Au-kline syndrome | X-linked distal spinal muscular atrophy type 3 | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |
| Au-kline syndrome | neurodevelopmental disorder-craniofacial dysmorphism-cardiac defect-hip dysplasia syndrome | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |