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 348
6
Diseases
14
Unique genes
0.226
Avg. similarity score
Cerebral cortical atrophy
Most-connected disease (5 links)
Disease
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Cerebral cortical atrophy
Caudate atrophy
Nasu-hakola disease
Polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy
Paraplegia
Proximal spinal muscular atrophy
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Cerebral cortical atrophy | 5 | 5 | 4 |
| Caudate atrophy | 3 | 3 | 1 |
| Nasu-hakola disease | 3 | 3 | 1 |
| Polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy | 3 | 3 | 2 |
| Paraplegia | 2 | 2 | 5 |
| Proximal spinal muscular atrophy | 2 | 2 | 6 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| TYROBP | 4 / 6 | Caudate atrophy, Cerebral cortical atrophy, Nasu-hakola disease, Polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy |
| SPG7 | 3 / 6 | Cerebral cortical atrophy, Paraplegia, Proximal spinal muscular atrophy |
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 ⇵ |
|---|---|---|---|---|---|
| Other semaphorin interactions | Reactome | 2 / 14 | 123× | 1.14e-4 | 2.49e-3 ✓ sig. |
| DAP12 interactions | Reactome | 2 / 21 | 81.7× | 2.62e-4 | 4.82e-3 ✓ sig. |
| DAP12 signaling | Reactome | 2 / 30 | 57.2× | 5.39e-4 | 8.44e-3 ✓ sig. |
| snRNP Assembly | Reactome | 2 / 53 | 32.4× | 1.68e-3 | 2.01e-2 ✓ sig. |
| Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | Reactome | 2 / 130 | 13.2× | 9.72e-3 | 6.74e-2 |
| Osteoclast differentiation | KEGG | 2 / 142 | 12.1× | 1.15e-2 | 7.47e-2 |
| Asparagine N-linked glycosylation | Reactome | 1 / 11 | 78.0× | 1.28e-2 | 7.89e-2 |
| Signal regulatory protein family interactions | Reactome | 1 / 12 | 71.5× | 1.39e-2 | 8.31e-2 |
| Mitochondrial tRNA aminoacylation | Reactome | 1 / 14 | 61.3× | 1.62e-2 | 9.12e-2 |
| Membrane binding and targetting of GAG proteins | Reactome | 1 / 14 | 61.3× | 1.62e-2 | 9.12e-2 |
| Processing of SMDT1 | Reactome | 1 / 16 | 53.6× | 1.85e-2 | 9.85e-2 |
| Elastic fibre formation | Reactome | 1 / 18 | 47.7× | 2.08e-2 | 1.05e-1 |
| Miscellaneous transport and binding events | Reactome | 1 / 25 | 34.3× | 2.88e-2 | 1.26e-1 |
| Budding and maturation of HIV virion | Reactome | 1 / 29 | 29.6× | 3.33e-2 | 1.37e-1 |
| Endosomal Sorting Complex Required For Transport (ESCRT) | Reactome | 1 / 32 | 26.8× | 3.67e-2 | 1.44e-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-templated transcription termination | GO:0006353 | 3 / 13 | 308× | 9.53e-8 | 1.16e-5 ✓ sig. |
| positive regulation of macrophage fusion | GO:0034241 | 2 / 5 | 534× | 5.21e-6 | 3.10e-4 ✓ sig. |
| microglial cell activation involved in immune response | GO:0002282 | 2 / 5 | 534× | 5.21e-6 | 3.10e-4 ✓ sig. |
| T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell | GO:0002291 | 2 / 8 | 334× | 1.46e-5 | 7.00e-4 ✓ sig. |
| nervous system development | GO:0007399 | 5 / 631 | 10.6× | 6.71e-5 | 2.24e-3 ✓ sig. |
| amyloid-beta clearance | GO:0097242 | 2 / 17 | 157× | 7.04e-5 | 2.33e-3 ✓ sig. |
| apoptotic cell clearance | GO:0043277 | 2 / 22 | 121× | 1.19e-4 | 3.46e-3 ✓ sig. |
| spliceosomal complex assembly | GO:0000245 | 2 / 28 | 95.3× | 1.95e-4 | 4.96e-3 ✓ sig. |
| spliceosomal snRNP assembly | GO:0000387 | 2 / 29 | 92.1× | 2.09e-4 | 5.21e-3 ✓ sig. |
| RNA splicing, via transesterification reactions | GO:0000375 | 2 / 30 | 89.0× | 2.24e-4 | 5.46e-3 ✓ sig. |
| response to axon injury | GO:0048678 | 2 / 37 | 72.2× | 3.42e-4 | 7.34e-3 ✓ sig. |
| pyroptotic inflammatory response | GO:0070269 | 2 / 40 | 66.7× | 4.00e-4 | 8.21e-3 ✓ sig. |
| semaphorin-plexin signaling pathway | GO:0071526 | 2 / 43 | 62.1× | 4.62e-4 | 9.08e-3 ✓ sig. |
| regulation of biological quality | GO:0065008 | 2 / 45 | 59.3× | 5.07e-4 | 9.66e-3 ✓ sig. |
| osteoclast differentiation | GO:0030316 | 2 / 49 | 54.5× | 6.01e-4 | 1.09e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Caudate atrophy | Nasu-hakola disease | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Caudate atrophy | Polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Nasu-hakola disease | Polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Caudate atrophy | Cerebral cortical atrophy | 0.200 | 1 | 2.60e-4 | 6.40e-4 ✓ sig. |
| Cerebral cortical atrophy | Nasu-hakola disease | 0.200 | 1 | 2.60e-4 | 6.40e-4 ✓ sig. |
| Cerebral cortical atrophy | Polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy | 0.167 | 1 | 5.19e-4 | 1.04e-3 ✓ sig. |
| Cerebral cortical atrophy | Paraplegia | 0.111 | 1 | 1.30e-3 | 2.04e-3 ✓ sig. |
| Cerebral cortical atrophy | Proximal spinal muscular atrophy | 0.100 | 1 | 1.56e-3 | 2.36e-3 ✓ sig. |
| Paraplegia | Proximal spinal muscular atrophy | 0.091 | 1 | 1.95e-3 | 2.81e-3 ✓ sig. |