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 374
5
Diseases
4
Unique genes
0.361
Avg. similarity score
cerebral arteriopathy, autosomal dominant, with subcortical infarcts and leukoencephalopathy, type 1
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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cerebral arteriopathy, autosomal dominant, with subcortical infarcts and leukoencephalopathy, type 1
cerebral arteriopathy, autosomal recessive, with subcortical infarcts and leukoencephalopathy 1
inherited thrombocytopenia
Cerebral arteriopathy with subcortical infarcts and leukoencephalopathy
Myofibromatosis
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| cerebral arteriopathy, autosomal dominant, with subcortical infarcts and leukoencephalopathy, type 1 | 4 | 4 | 1 |
| cerebral arteriopathy, autosomal recessive, with subcortical infarcts and leukoencephalopathy 1 | 4 | 4 | 1 |
| inherited thrombocytopenia | 4 | 4 | 1 |
| Cerebral arteriopathy with subcortical infarcts and leukoencephalopathy | 3 | 3 | 3 |
| Myofibromatosis | 3 | 3 | 2 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| NOTCH3 | 5 / 5 | Cerebral arteriopathy with subcortical infarcts and leukoencephalopathy, cerebral arteriopathy, autosomal dominant, with subcortical infarcts and leukoencephalopathy, type 1, cerebral arteriopathy, autosomal recessive, with subcortical infarcts and leukoencephalopathy 1, inherited thrombocytopenia and 1 more |
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 ⇵ |
|---|---|---|---|---|---|
| Defective LFNG causes SCDO3 | Reactome | 1 / 5 | 601× | 1.66e-3 | 2.00e-2 ✓ sig. |
| Pre-NOTCH Processing in Golgi | Reactome | 1 / 6 | 500× | 2.00e-3 | 2.28e-2 ✓ sig. |
| Noncanonical activation of NOTCH3 | Reactome | 1 / 8 | 375× | 2.66e-3 | 2.83e-2 ✓ sig. |
| MicroRNAs in cancer | KEGG | 2 / 311 | 19.3× | 3.87e-3 | 3.69e-2 ✓ sig. |
| Human papillomavirus infection | KEGG | 2 / 333 | 18.0× | 4.43e-3 | 4.05e-2 ✓ sig. |
| NOTCH3 Intracellular Domain Regulates Transcription | Reactome | 1 / 18 | 167× | 5.98e-3 | 4.92e-2 ✓ sig. |
| NOTCH3 Activation and Transmission of Signal to the Nucleus | Reactome | 1 / 19 | 158× | 6.31e-3 | 5.10e-2 |
| Notch-HLH transcription pathway | Reactome | 1 / 28 | 107× | 9.29e-3 | 6.56e-2 |
| Downstream signal transduction | Reactome | 1 / 29 | 104× | 9.62e-3 | 6.71e-2 |
| Pre-NOTCH Transcription and Translation | Reactome | 1 / 31 | 96.9× | 1.03e-2 | 7.00e-2 |
| Signaling by PDGF | Reactome | 1 / 33 | 91.0× | 1.09e-2 | 7.25e-2 |
| Pathways in cancer | KEGG | 2 / 533 | 11.3× | 1.11e-2 | 7.32e-2 |
| Notch signaling pathway | KEGG | 1 / 62 | 48.4× | 2.05e-2 | 1.04e-1 |
| Degradation of the extracellular matrix | Reactome | 1 / 70 | 42.9× | 2.31e-2 | 1.12e-1 |
| Central carbon metabolism in cancer | KEGG | 1 / 71 | 42.3× | 2.34e-2 | 1.13e-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 ⇵ |
|---|---|---|---|---|---|
| positive regulation of smooth muscle cell proliferation | GO:0048661 | 2 / 52 | 180× | 4.54e-5 | 1.68e-3 ✓ sig. |
| cell migration involved in coronary angiogenesis | GO:0060981 | 1 / 1 | 4,672× | 2.14e-4 | 5.28e-3 ✓ sig. |
| metanephric glomerular mesangial cell proliferation involved in metanephros development | GO:0072262 | 1 / 1 | 4,672× | 2.14e-4 | 5.28e-3 ✓ sig. |
| smooth muscle cell chemotaxis | GO:0071670 | 1 / 2 | 2,336× | 4.28e-4 | 8.59e-3 ✓ sig. |
| cell migration involved in vasculogenesis | GO:0035441 | 1 / 2 | 2,336× | 4.28e-4 | 8.59e-3 ✓ sig. |
| glomerular capillary formation | GO:0072104 | 1 / 3 | 1,557× | 6.42e-4 | 1.13e-2 ✓ sig. |
| positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway | GO:0035793 | 1 / 3 | 1,557× | 6.42e-4 | 1.13e-2 ✓ sig. |
| positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway | GO:0038091 | 1 / 3 | 1,557× | 6.42e-4 | 1.13e-2 ✓ sig. |
| metanephric glomerular capillary formation | GO:0072277 | 1 / 3 | 1,557× | 6.42e-4 | 1.13e-2 ✓ sig. |
| smooth muscle adaptation | GO:0014805 | 1 / 4 | 1,168× | 8.56e-4 | 1.36e-2 ✓ sig. |
| platelet-derived growth factor receptor-beta signaling pathway | GO:0035791 | 1 / 6 | 779× | 1.28e-3 | 1.75e-2 ✓ sig. |
| chorionic trophoblast cell differentiation | GO:0060718 | 1 / 6 | 779× | 1.28e-3 | 1.75e-2 ✓ sig. |
| neuroblast differentiation | GO:0014016 | 1 / 7 | 667× | 1.50e-3 | 1.91e-2 ✓ sig. |
| positive regulation of DNA biosynthetic process | GO:2000573 | 1 / 12 | 389× | 2.57e-3 | 2.58e-2 ✓ sig. |
| cardiac myofibril assembly | GO:0055003 | 1 / 13 | 359× | 2.78e-3 | 2.71e-2 ✓ sig. |