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 401
5
Diseases
14
Unique genes
0.235
Avg. similarity score
Bmpr1a-related juvenile polyposis
Most-connected disease (4 links)
Disease
Searched: juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome
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Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome
Bmpr1a-related juvenile polyposis
Ductal carcinoma of breast
Myhre syndrome
juvenile polyposis syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Bmpr1a-related juvenile polyposis | 4 | 4 | 2 |
| Ductal carcinoma of breast | 3 | 3 | 12 |
| Myhre syndrome | 3 | 3 | 1 |
| juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome | 3 | 3 | 1 |
| juvenile polyposis syndrome | 1 | 1 | 2 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| SMAD4 | 4 / 5 | Bmpr1a-related juvenile polyposis, Ductal carcinoma of breast, juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome, Myhre syndrome |
| BMPR1A | 2 / 5 | Bmpr1a-related juvenile polyposis, juvenile polyposis 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 ⇵ |
|---|---|---|---|---|---|
| Adherens junction | KEGG | 3 / 93 | 27.7× | 1.54e-4 | 3.09e-3 ✓ sig. |
| Pathways in cancer | KEGG | 5 / 533 | 8.0× | 2.42e-4 | 4.43e-3 ✓ sig. |
| Signaling by BMP | Reactome | 2 / 28 | 61.3× | 4.69e-4 | 7.51e-3 ✓ sig. |
| Gastric cancer | KEGG | 3 / 150 | 17.2× | 6.28e-4 | 9.43e-3 ✓ sig. |
| Hippo signaling pathway | KEGG | 3 / 157 | 16.4× | 7.18e-4 | 1.04e-2 ✓ sig. |
| Cell adhesion molecules | KEGG | 3 / 160 | 16.1× | 7.58e-4 | 1.09e-2 ✓ sig. |
| Bladder cancer | KEGG | 2 / 41 | 41.8× | 1.01e-3 | 1.35e-2 ✓ sig. |
| Biosynthesis of EPA-derived SPMs | Reactome | 1 / 1 | 858× | 1.17e-3 | 1.51e-2 ✓ sig. |
| Biosynthesis of DPAn-3 SPMs | Reactome | 1 / 1 | 858× | 1.17e-3 | 1.51e-2 ✓ sig. |
| Human cytomegalovirus infection | KEGG | 3 / 226 | 11.4× | 2.05e-3 | 2.32e-2 ✓ sig. |
| Endometrial cancer | KEGG | 2 / 59 | 29.1× | 2.08e-3 | 2.34e-2 ✓ sig. |
| Biosynthesis of electrophilic ω-3 PUFA oxo-derivatives | Reactome | 1 / 2 | 429× | 2.33e-3 | 2.55e-2 ✓ sig. |
| Response of EIF2AK4 (GCN2) to amino acid deficiency | Reactome | 1 / 3 | 286× | 3.49e-3 | 3.41e-2 ✓ sig. |
| Response of EIF2AK1 (HRI) to heme deficiency | Reactome | 1 / 3 | 286× | 3.49e-3 | 3.41e-2 ✓ sig. |
| Biosynthesis of DHA-derived SPMs | Reactome | 1 / 3 | 286× | 3.49e-3 | 3.41e-2 ✓ sig. |
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 cardiac muscle cell apoptotic process | GO:0010665 | 2 / 2 | 1,335× | 5.21e-7 | 4.83e-5 ✓ sig. |
| outflow tract septum morphogenesis | GO:0003148 | 3 / 28 | 143× | 1.08e-6 | 8.89e-5 ✓ sig. |
| positive regulation of SMAD protein signal transduction | GO:0060391 | 3 / 42 | 95.3× | 3.78e-6 | 2.41e-4 ✓ sig. |
| mesendoderm development | GO:0048382 | 2 / 7 | 381× | 1.09e-5 | 5.62e-4 ✓ sig. |
| regulation of cell population proliferation | GO:0042127 | 4 / 201 | 26.6× | 1.20e-5 | 6.03e-4 ✓ sig. |
| dorsal aorta morphogenesis | GO:0035912 | 2 / 8 | 334× | 1.46e-5 | 7.03e-4 ✓ sig. |
| cellular response to growth factor stimulus | GO:0071363 | 3 / 76 | 52.7× | 2.28e-5 | 9.94e-4 ✓ sig. |
| response to selenium ion | GO:0010269 | 2 / 11 | 243× | 2.86e-5 | 1.18e-3 ✓ sig. |
| positive regulation of vascular associated smooth muscle cell apoptotic process | GO:1905461 | 2 / 11 | 243× | 2.86e-5 | 1.18e-3 ✓ sig. |
| BMP signaling pathway | GO:0030509 | 3 / 88 | 45.5× | 3.54e-5 | 1.39e-3 ✓ sig. |
| heart development | GO:0007507 | 4 / 273 | 19.6× | 3.97e-5 | 1.52e-3 ✓ sig. |
| epithelial to mesenchymal transition involved in endocardial cushion formation | GO:0003198 | 2 / 13 | 205× | 4.05e-5 | 1.54e-3 ✓ sig. |
| ventricular trabecula myocardium morphogenesis | GO:0003222 | 2 / 15 | 178× | 5.44e-5 | 1.93e-3 ✓ sig. |
| cardiac conduction system development | GO:0003161 | 2 / 16 | 167× | 6.22e-5 | 2.13e-3 ✓ sig. |
| transforming growth factor beta receptor signaling pathway | GO:0007179 | 3 / 112 | 35.8× | 7.27e-5 | 2.39e-3 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome | Myhre syndrome | 0.500 | 1 | 6.49e-5 | 2.33e-4 ✓ sig. |
| Bmpr1a-related juvenile polyposis | Myhre syndrome | 0.333 | 1 | 1.30e-4 | 3.93e-4 ✓ sig. |
| Bmpr1a-related juvenile polyposis | juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome | 0.333 | 1 | 1.30e-4 | 3.93e-4 ✓ sig. |
| Bmpr1a-related juvenile polyposis | juvenile polyposis syndrome | 0.250 | 1 | 2.60e-4 | 6.51e-4 ✓ sig. |
| Ductal carcinoma of breast | juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome | 0.077 | 1 | 7.79e-4 | 1.40e-3 ✓ sig. |
| Ductal carcinoma of breast | Myhre syndrome | 0.077 | 1 | 7.79e-4 | 1.40e-3 ✓ sig. |
| Bmpr1a-related juvenile polyposis | Ductal carcinoma of breast | 0.071 | 1 | 1.56e-3 | 2.38e-3 ✓ sig. |