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 560
5
Diseases
11
Unique genes
0.216
Avg. similarity score
Congenital hemihypertrophy
Most-connected disease (4 links)
Disease
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Congenital hemihypertrophy
Congenital joint contractures
Charcot-Marie-Tooth disease type 4C
Mononeuropathy of the median nerve, mild
Charcot-Marie-Tooth disease type 2A1
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Congenital hemihypertrophy | 4 | 4 | 4 |
| Congenital joint contractures | 4 | 4 | 9 |
| Charcot-Marie-Tooth disease type 4C | 3 | 3 | 1 |
| Mononeuropathy of the median nerve, mild | 3 | 3 | 1 |
| Charcot-Marie-Tooth disease type 2A1 | 2 | 2 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| SH3TC2 | 4 / 5 | Charcot-Marie-Tooth disease type 4C, Congenital hemihypertrophy, Congenital joint contractures, Mononeuropathy of the median nerve, mild |
| KIF1B | 3 / 5 | Charcot-Marie-Tooth disease type 2A1, Congenital hemihypertrophy, Congenital joint contractures |
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 ⇵ |
|---|---|---|---|---|---|
| PI3K/AKT activation | Reactome | 2 / 9 | 243× | 2.74e-5 | 6.73e-4 ✓ sig. |
| GPVI-mediated activation cascade | Reactome | 2 / 34 | 64.2× | 4.21e-4 | 5.85e-3 ✓ sig. |
| Focal adhesion | KEGG | 3 / 203 | 16.1× | 7.10e-4 | 8.74e-3 ✓ sig. |
| Assembly of collagen fibrils and other multimeric structures | Reactome | 2 / 51 | 42.8× | 9.49e-4 | 1.09e-2 ✓ sig. |
| VEGFA-VEGFR2 Pathway | Reactome | 2 / 62 | 35.2× | 1.40e-3 | 1.46e-2 ✓ sig. |
| Bacterial invasion of epithelial cells | KEGG | 2 / 78 | 28.0× | 2.20e-3 | 2.05e-2 ✓ sig. |
| Colorectal cancer | KEGG | 2 / 87 | 25.1× | 2.73e-3 | 2.39e-2 ✓ sig. |
| Axonal growth stimulation | Reactome | 1 / 4 | 273× | 3.66e-3 | 2.93e-2 ✓ sig. |
| SLIT2:ROBO1 increases RHOA activity | Reactome | 1 / 4 | 273× | 3.66e-3 | 2.93e-2 ✓ sig. |
| C-type lectin receptor signaling pathway | KEGG | 2 / 105 | 20.8× | 3.96e-3 | 3.11e-2 ✓ sig. |
| RHO GTPases Activate ROCKs | Reactome | 1 / 5 | 218× | 4.57e-3 | 3.44e-2 ✓ sig. |
| Leukocyte transendothelial migration | KEGG | 2 / 116 | 18.8× | 4.81e-3 | 3.56e-2 ✓ sig. |
| Neurotrophin signaling pathway | KEGG | 2 / 120 | 18.2× | 5.13e-3 | 3.72e-2 ✓ sig. |
| Sphingolipid signaling pathway | KEGG | 2 / 122 | 17.9× | 5.30e-3 | 3.79e-2 ✓ sig. |
| T cell receptor signaling pathway | KEGG | 2 / 122 | 17.9× | 5.30e-3 | 3.79e-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 ⇵ |
|---|---|---|---|---|---|
| ossification involved in bone maturation | GO:0043931 | 2 / 12 | 283× | 2.07e-5 | 9.51e-4 ✓ sig. |
| endothelial cell migration | GO:0043542 | 2 / 48 | 70.8× | 3.50e-4 | 7.49e-3 ✓ sig. |
| angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure | GO:0001998 | 1 / 1 | 1,699× | 5.89e-4 | 1.06e-2 ✓ sig. |
| alpha-beta T cell lineage commitment | GO:0002363 | 1 / 1 | 1,699× | 5.89e-4 | 1.06e-2 ✓ sig. |
| mitotic cleavage furrow formation | GO:1903673 | 1 / 1 | 1,699× | 5.89e-4 | 1.06e-2 ✓ sig. |
| regulation of ERBB signaling pathway | GO:1901184 | 1 / 1 | 1,699× | 5.89e-4 | 1.06e-2 ✓ sig. |
| response to butyrate | GO:1903544 | 1 / 1 | 1,699× | 5.89e-4 | 1.06e-2 ✓ sig. |
| regulation of membrane potential | GO:0042391 | 2 / 85 | 40.0× | 1.10e-3 | 1.54e-2 ✓ sig. |
| aortic valve formation | GO:0003189 | 1 / 2 | 849× | 1.18e-3 | 1.59e-2 ✓ sig. |
| endothelial tube lumen extension | GO:0097498 | 1 / 2 | 849× | 1.18e-3 | 1.59e-2 ✓ sig. |
| skeletal muscle satellite cell migration | GO:1902766 | 1 / 2 | 849× | 1.18e-3 | 1.59e-2 ✓ sig. |
| positive regulation of vascular associated smooth muscle contraction | GO:1904695 | 1 / 2 | 849× | 1.18e-3 | 1.59e-2 ✓ sig. |
| microvillus organization | GO:0032528 | 1 / 2 | 849× | 1.18e-3 | 1.59e-2 ✓ sig. |
| response to muscle inactivity | GO:0014870 | 1 / 2 | 849× | 1.18e-3 | 1.59e-2 ✓ sig. |
| phosphatidylinositol 3-kinase/protein kinase B signal transduction | GO:0043491 | 2 / 92 | 36.9× | 1.28e-3 | 1.67e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Congenital hemihypertrophy | Congenital joint contractures | 0.182 | 2 | 9.00e-7 | 5.50e-6 ✓ sig. |
| Charcot-Marie-Tooth disease type 4C | Mononeuropathy of the median nerve, mild | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Charcot-Marie-Tooth disease type 2A1 | Congenital hemihypertrophy | 0.250 | 1 | 1.94e-4 | 4.41e-4 ✓ sig. |
| Charcot-Marie-Tooth disease type 4C | Congenital hemihypertrophy | 0.250 | 1 | 1.94e-4 | 4.41e-4 ✓ sig. |
| Congenital hemihypertrophy | Mononeuropathy of the median nerve, mild | 0.250 | 1 | 1.94e-4 | 4.41e-4 ✓ sig. |
| Charcot-Marie-Tooth disease type 2A1 | Congenital joint contractures | 0.100 | 1 | 5.81e-4 | 1.00e-3 ✓ sig. |
| Charcot-Marie-Tooth disease type 4C | Congenital joint contractures | 0.100 | 1 | 5.81e-4 | 1.00e-3 ✓ sig. |
| Congenital joint contractures | Mononeuropathy of the median nerve, mild | 0.100 | 1 | 5.81e-4 | 1.00e-3 ✓ sig. |