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 330
6
Diseases
17
Unique genes
0.117
Avg. similarity score
Skin ulcer
Most-connected disease (5 links)
Disease
Searched: Tonic-clonic epilepsy
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Tonic-clonic epilepsy
Skin ulcer
Congenital sensory neuropathy
Periapical periodontitis
Laryngo-onycho-cutaneous syndrome
Prolidase deficiency
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Skin ulcer | 5 | 5 | 6 |
| Tonic-clonic epilepsy | 3 | 3 | 12 |
| Congenital sensory neuropathy | 2 | 2 | 1 |
| Periapical periodontitis | 2 | 2 | 2 |
| Laryngo-onycho-cutaneous syndrome | 1 | 1 | 1 |
| Prolidase deficiency | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| FGF2 | 3 / 6 | Periapical periodontitis, Skin ulcer, Tonic-clonic epilepsy |
| NGF | 3 / 6 | Congenital sensory neuropathy, Skin ulcer, Tonic-clonic epilepsy |
| LAMA3 | 2 / 6 | Laryngo-onycho-cutaneous syndrome, Skin ulcer |
| PEPD | 2 / 6 | Prolidase deficiency, Skin ulcer |
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 ⇵ |
|---|---|---|---|---|---|
| Interleukin-4 and Interleukin-13 signaling | Reactome | 4 / 108 | 26.2× | 1.34e-5 | 4.53e-4 ✓ sig. |
| PI3K-Akt signaling pathway | KEGG | 5 / 361 | 9.8× | 1.10e-4 | 2.50e-3 ✓ sig. |
| Ras signaling pathway | KEGG | 4 / 237 | 11.9× | 2.87e-4 | 5.34e-3 ✓ sig. |
| Endocrine resistance | KEGG | 3 / 99 | 21.4× | 3.40e-4 | 6.11e-3 ✓ sig. |
| Neurotrophin signaling pathway | KEGG | 3 / 120 | 17.7× | 5.97e-4 | 9.48e-3 ✓ sig. |
| MAPK signaling pathway | KEGG | 4 / 299 | 9.5× | 6.93e-4 | 1.06e-2 ✓ sig. |
| Estrogen signaling pathway | KEGG | 3 / 139 | 15.2× | 9.16e-4 | 1.31e-2 ✓ sig. |
| Bladder cancer | KEGG | 2 / 41 | 34.5× | 1.50e-3 | 1.92e-2 ✓ sig. |
| Assembly of collagen fibrils and other multimeric structures | Reactome | 2 / 51 | 27.7× | 2.31e-3 | 2.63e-2 ✓ sig. |
| Proteoglycans in cancer | KEGG | 3 / 204 | 10.4× | 2.75e-3 | 2.97e-2 ✓ sig. |
| Defective ACTH causes Obesity and Pro-opiomelanocortinin deficiency (POMCD) | Reactome | 1 / 2 | 353× | 2.83e-3 | 3.03e-2 ✓ sig. |
| TRKA activation by NGF | Reactome | 1 / 2 | 353× | 2.83e-3 | 3.03e-2 ✓ sig. |
| NFG and proNGF binds to p75NTR | Reactome | 1 / 2 | 353× | 2.83e-3 | 3.03e-2 ✓ sig. |
| NTF3 activates NTRK3 signaling | Reactome | 1 / 2 | 353× | 2.83e-3 | 3.03e-2 ✓ sig. |
| Peptide hormone biosynthesis | Reactome | 1 / 2 | 353× | 2.83e-3 | 3.03e-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 ⇵ |
|---|---|---|---|---|---|
| nerve growth factor signaling pathway | GO:0038180 | 3 / 14 | 236× | 2.26e-7 | 2.48e-5 ✓ sig. |
| nerve development | GO:0021675 | 3 / 19 | 174× | 6.01e-7 | 5.57e-5 ✓ sig. |
| endodermal cell differentiation | GO:0035987 | 3 / 36 | 91.6× | 4.38e-6 | 2.78e-4 ✓ sig. |
| negative regulation of neuron apoptotic process | GO:0043524 | 4 / 160 | 27.5× | 1.13e-5 | 5.94e-4 ✓ sig. |
| positive regulation of collateral sprouting | GO:0048672 | 2 / 9 | 244× | 2.79e-5 | 1.19e-3 ✓ sig. |
| neuron projection morphogenesis | GO:0048812 | 3 / 70 | 47.1× | 3.30e-5 | 1.36e-3 ✓ sig. |
| positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction | GO:0051897 | 4 / 217 | 20.3× | 3.74e-5 | 1.49e-3 ✓ sig. |
| positive regulation of keratinocyte migration | GO:0051549 | 2 / 12 | 183× | 5.11e-5 | 1.90e-3 ✓ sig. |
| cell surface receptor protein tyrosine kinase signaling pathway | GO:0007169 | 3 / 120 | 27.5× | 1.64e-4 | 4.52e-3 ✓ sig. |
| modulation of chemical synaptic transmission | GO:0050804 | 3 / 121 | 27.3× | 1.69e-4 | 4.60e-3 ✓ sig. |
| regulation of heart rate | GO:0002027 | 2 / 39 | 56.4× | 5.66e-4 | 1.07e-2 ✓ sig. |
| collagen catabolic process | GO:0030574 | 2 / 41 | 53.6× | 6.26e-4 | 1.15e-2 ✓ sig. |
| endothelial cell migration | GO:0043542 | 2 / 48 | 45.8× | 8.57e-4 | 1.41e-2 ✓ sig. |
| cocaine metabolic process | GO:0050783 | 1 / 1 | 1,099× | 9.10e-4 | 1.47e-2 ✓ sig. |
| isoquinoline alkaloid metabolic process | GO:0033076 | 1 / 1 | 1,099× | 9.10e-4 | 1.47e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Skin ulcer | Tonic-clonic epilepsy | 0.118 | 2 | 8.34e-6 | 4.16e-5 ✓ sig. |
| Congenital sensory neuropathy | Skin ulcer | 0.143 | 1 | 3.90e-4 | 8.67e-4 ✓ sig. |
| Laryngo-onycho-cutaneous syndrome | Skin ulcer | 0.143 | 1 | 3.90e-4 | 8.67e-4 ✓ sig. |
| Prolidase deficiency | Skin ulcer | 0.143 | 1 | 3.90e-4 | 8.67e-4 ✓ sig. |
| Periapical periodontitis | Skin ulcer | 0.125 | 1 | 7.79e-4 | 1.41e-3 ✓ sig. |
| Congenital sensory neuropathy | Tonic-clonic epilepsy | 0.077 | 1 | 7.79e-4 | 1.41e-3 ✓ sig. |
| Periapical periodontitis | Tonic-clonic epilepsy | 0.071 | 1 | 1.56e-3 | 2.38e-3 ✓ sig. |