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 458
6
Diseases
17
Unique genes
0.205
Avg. similarity score
Genetic peripheral neuropathy
Most-connected disease (4 links)
Disease
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Genetic peripheral neuropathy
Benign fasciculation-cramp syndrome
Cramp-fasciculation syndrome
Bronchial hyperreactivity
Charcot-Marie-Tooth disease axonal type 2F
Slowed nerve conduction velocity
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Genetic peripheral neuropathy | 4 | 4 | 4 |
| Benign fasciculation-cramp syndrome | 3 | 3 | 1 |
| Cramp-fasciculation syndrome | 3 | 3 | 1 |
| Bronchial hyperreactivity | 2 | 2 | 14 |
| Charcot-Marie-Tooth disease axonal type 2F | 1 | 1 | 1 |
| Slowed nerve conduction velocity | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| TRPA1 | 4 / 6 | Benign fasciculation-cramp syndrome, Bronchial hyperreactivity, Cramp-fasciculation syndrome, Genetic peripheral neuropathy |
| ARHGEF10 | 2 / 6 | Genetic peripheral neuropathy, Slowed nerve conduction velocity |
| HSPB1 | 2 / 6 | Charcot-Marie-Tooth disease axonal type 2F, Genetic peripheral neuropathy |
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 ⇵ |
|---|---|---|---|---|---|
| Cytokine-cytokine receptor interaction | KEGG | 7 / 298 | 16.6× | 8.48e-8 | 4.83e-6 ✓ sig. |
| Interleukin-10 signaling | Reactome | 4 / 47 | 60.1× | 4.72e-7 | 2.17e-5 ✓ sig. |
| Chemokine receptors bind chemokines | Reactome | 3 / 59 | 35.9× | 7.29e-5 | 1.48e-3 ✓ sig. |
| IL-17 signaling pathway | KEGG | 3 / 94 | 22.5× | 2.92e-4 | 4.41e-3 ✓ sig. |
| Rheumatoid arthritis | KEGG | 3 / 95 | 22.3× | 3.01e-4 | 4.52e-3 ✓ sig. |
| Viral protein interaction with cytokine and cytokine receptor | KEGG | 3 / 100 | 21.2× | 3.50e-4 | 5.07e-3 ✓ sig. |
| NF-kappa B signaling pathway | KEGG | 3 / 105 | 20.2× | 4.04e-4 | 5.66e-3 ✓ sig. |
| Interleukin-4 and Interleukin-13 signaling | Reactome | 3 / 108 | 19.6× | 4.39e-4 | 6.03e-3 ✓ sig. |
| TNF signaling pathway | KEGG | 3 / 119 | 17.8× | 5.83e-4 | 7.52e-3 ✓ sig. |
| COX reactions | Reactome | 1 / 1 | 706× | 1.42e-3 | 1.47e-2 ✓ sig. |
| Malaria | KEGG | 2 / 50 | 28.3× | 2.22e-3 | 2.06e-2 ✓ sig. |
| Chemokine signaling pathway | KEGG | 3 / 193 | 11.0× | 2.35e-3 | 2.15e-2 ✓ sig. |
| TRKA activation by NGF | Reactome | 1 / 2 | 353× | 2.83e-3 | 2.44e-2 ✓ sig. |
| NFG and proNGF binds to p75NTR | Reactome | 1 / 2 | 353× | 2.83e-3 | 2.44e-2 ✓ sig. |
| Lipid and atherosclerosis | KEGG | 3 / 216 | 9.8× | 3.24e-3 | 2.69e-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 ⇵ |
|---|---|---|---|---|---|
| antimicrobial humoral immune response mediated by antimicrobial peptide | GO:0061844 | 6 / 124 | 53.2× | 8.81e-10 | 2.08e-7 ✓ sig. |
| sensory perception of pain | GO:0019233 | 4 / 44 | 99.9× | 6.22e-8 | 8.53e-6 ✓ sig. |
| inflammatory response | GO:0006954 | 7 / 467 | 16.5× | 9.11e-8 | 1.17e-5 ✓ sig. |
| antifungal humoral response | GO:0019732 | 3 / 13 | 254× | 1.78e-7 | 2.05e-5 ✓ sig. |
| immune response | GO:0006955 | 7 / 543 | 14.2× | 2.54e-7 | 2.77e-5 ✓ sig. |
| response to yeast | GO:0001878 | 3 / 16 | 206× | 3.48e-7 | 3.60e-5 ✓ sig. |
| antibacterial humoral response | GO:0019731 | 3 / 65 | 50.7× | 2.64e-5 | 1.13e-3 ✓ sig. |
| regulation of blood pressure | GO:0008217 | 3 / 83 | 39.7× | 5.49e-5 | 1.98e-3 ✓ sig. |
| cellular response to oxygen-containing compound | GO:1901701 | 2 / 16 | 137× | 9.28e-5 | 2.92e-3 ✓ sig. |
| killing of cells of another organism | GO:0031640 | 3 / 104 | 31.7× | 1.08e-4 | 3.26e-3 ✓ sig. |
| defense response to Gram-negative bacterium | GO:0050829 | 3 / 106 | 31.1× | 1.14e-4 | 3.40e-3 ✓ sig. |
| response to pain | GO:0048265 | 2 / 19 | 116× | 1.32e-4 | 3.77e-3 ✓ sig. |
| eosinophil chemotaxis | GO:0048245 | 2 / 20 | 110× | 1.47e-4 | 4.07e-3 ✓ sig. |
| positive regulation of macrophage activation | GO:0043032 | 2 / 21 | 105× | 1.62e-4 | 4.37e-3 ✓ sig. |
| defense response to Gram-positive bacterium | GO:0050830 | 3 / 135 | 24.4× | 2.33e-4 | 5.65e-3 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Benign fasciculation-cramp syndrome | Cramp-fasciculation syndrome | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Benign fasciculation-cramp syndrome | Genetic peripheral neuropathy | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |
| Charcot-Marie-Tooth disease axonal type 2F | Genetic peripheral neuropathy | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |
| Cramp-fasciculation syndrome | Genetic peripheral neuropathy | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |
| Genetic peripheral neuropathy | Slowed nerve conduction velocity | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |
| Benign fasciculation-cramp syndrome | Bronchial hyperreactivity | 0.067 | 1 | 9.04e-4 | 1.41e-3 ✓ sig. |
| Bronchial hyperreactivity | Cramp-fasciculation syndrome | 0.067 | 1 | 9.04e-4 | 1.41e-3 ✓ sig. |