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 407
5
Diseases
50
Unique genes
0.239
Avg. similarity score
Malignant peripheral nerve sheath tumor
Most-connected disease (3 links)
Disease
Searched: Small vessel stroke
Pinned (dragged)
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Small vessel stroke
Malignant peripheral nerve sheath tumor
Malignant triton tumor
Carasil syndrome
spinocerebellar ataxia, autosomal recessive 31
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Malignant peripheral nerve sheath tumor | 3 | 3 | 2 |
| Malignant triton tumor | 3 | 3 | 2 |
| Small vessel stroke | 3 | 3 | 50 |
| Carasil syndrome | 2 | 2 | 1 |
| spinocerebellar ataxia, autosomal recessive 31 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| HTRA1 | 4 / 5 | Carasil syndrome, Malignant peripheral nerve sheath tumor, Malignant triton tumor, Small vessel stroke |
| SH3PXD2A | 3 / 5 | Malignant peripheral nerve sheath tumor, Malignant triton tumor, Small vessel stroke |
| ATG7 | 2 / 5 | Small vessel stroke, spinocerebellar ataxia, autosomal recessive 31 |
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 ⇵ |
|---|---|---|---|---|---|
| Inflammatory mediator regulation of TRP channels | KEGG | 4 / 99 | 9.7× | 7.48e-4 | 1.08e-2 ✓ sig. |
| RAF/MAP kinase cascade | Reactome | 4 / 124 | 7.7× | 1.73e-3 | 2.05e-2 ✓ sig. |
| Unblocking of NMDA receptors, glutamate binding and activation | Reactome | 2 / 22 | 21.8× | 3.72e-3 | 3.57e-2 ✓ sig. |
| Oxytocin signaling pathway | KEGG | 4 / 154 | 6.2× | 3.79e-3 | 3.61e-2 ✓ sig. |
| Defective GFPT1 causes CMSTA1 | Reactome | 1 / 1 | 240× | 4.16e-3 | 3.86e-2 ✓ sig. |
| GnRH signaling pathway | KEGG | 3 / 93 | 7.7× | 6.77e-3 | 5.36e-2 |
| phospho-PLA2 pathway | Reactome | 1 / 2 | 120× | 8.31e-3 | 6.14e-2 |
| Glutamatergic synapse | KEGG | 3 / 116 | 6.2× | 1.24e-2 | 7.93e-2 |
| Biosynthesis of aspirin-triggered D-series resolvins | Reactome | 1 / 3 | 80.1× | 1.24e-2 | 7.94e-2 |
| Ferroptosis | KEGG | 2 / 42 | 11.4× | 1.32e-2 | 8.22e-2 |
| Phase 0 - rapid depolarisation | Reactome | 2 / 44 | 10.9× | 1.44e-2 | 8.66e-2 |
| Arachidonic acid metabolism | Reactome | 1 / 4 | 60.1× | 1.66e-2 | 9.42e-2 |
| Biosynthesis of D-series resolvins | Reactome | 1 / 4 | 60.1× | 1.66e-2 | 9.42e-2 |
| Biosynthesis of E-series 18(R)-resolvins | Reactome | 1 / 4 | 60.1× | 1.66e-2 | 9.42e-2 |
| Invadopodia formation | Reactome | 1 / 4 | 60.1× | 1.66e-2 | 9.42e-2 |
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 neuronal synaptic plasticity | GO:0048168 | 2 / 26 | 28.7× | 2.19e-3 | 2.41e-2 ✓ sig. |
| regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum | GO:0010880 | 2 / 28 | 26.7× | 2.54e-3 | 2.64e-2 ✓ sig. |
| dADP biosynthetic process | GO:0006173 | 1 / 1 | 374× | 2.68e-3 | 2.70e-2 ✓ sig. |
| ERBB3 signaling pathway | GO:0038129 | 1 / 1 | 374× | 2.68e-3 | 2.70e-2 ✓ sig. |
| positive regulation of peptidyl-tyrosine autophosphorylation | GO:1900086 | 1 / 1 | 374× | 2.68e-3 | 2.70e-2 ✓ sig. |
| chemical synaptic transmission | GO:0007268 | 4 / 236 | 6.3× | 3.62e-3 | 3.18e-2 ✓ sig. |
| blood vessel diameter maintenance | GO:0097746 | 2 / 37 | 20.2× | 4.40e-3 | 3.48e-2 ✓ sig. |
| mammary gland development | GO:0030879 | 2 / 37 | 20.2× | 4.40e-3 | 3.48e-2 ✓ sig. |
| retrograde axonal protein transport | GO:0099642 | 1 / 2 | 187× | 5.34e-3 | 3.86e-2 ✓ sig. |
| negative regulation of Kit signaling pathway | GO:1900235 | 1 / 2 | 187× | 5.34e-3 | 3.86e-2 ✓ sig. |
| positive regulation of protein modification process | GO:0031401 | 1 / 2 | 187× | 5.34e-3 | 3.86e-2 ✓ sig. |
| ultradian rhythm | GO:0007624 | 1 / 2 | 187× | 5.34e-3 | 3.86e-2 ✓ sig. |
| phosphatidylglycerol catabolic process | GO:0034478 | 1 / 2 | 187× | 5.34e-3 | 3.86e-2 ✓ sig. |
| regulation of relaxation of cardiac muscle | GO:1901897 | 1 / 2 | 187× | 5.34e-3 | 3.86e-2 ✓ sig. |
| response to chlorate | GO:0010157 | 1 / 2 | 187× | 5.34e-3 | 3.86e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Malignant peripheral nerve sheath tumor | Malignant triton tumor | 0.667 | 2 | 8.44e-9 | 6.82e-8 ✓ sig. |
| Malignant peripheral nerve sheath tumor | Small vessel stroke | 0.039 | 2 | 1.03e-5 | 5.11e-5 ✓ sig. |
| Malignant triton tumor | Small vessel stroke | 0.039 | 2 | 1.03e-5 | 5.11e-5 ✓ sig. |
| Carasil syndrome | Malignant peripheral nerve sheath tumor | 0.333 | 1 | 1.30e-4 | 3.93e-4 ✓ sig. |
| Carasil syndrome | Malignant triton tumor | 0.333 | 1 | 1.30e-4 | 3.93e-4 ✓ sig. |
| Small vessel stroke | spinocerebellar ataxia, autosomal recessive 31 | 0.020 | 1 | 3.25e-3 | 4.24e-3 ✓ sig. |