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 381
5
Diseases
51
Unique genes
0.225
Avg. similarity score
Otosclerosis
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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Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Otosclerosis | 4 | 4 | 51 |
| Agnathia-otocephaly | 3 | 3 | 1 |
| Dysgnathia complex | 3 | 3 | 1 |
| Retrognathia | 3 | 3 | 1 |
| Mak-related retinopathy | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| PRRX1 | 4 / 5 | Agnathia-otocephaly, Dysgnathia complex, Otosclerosis, Retrognathia |
| MAK | 2 / 5 | Mak-related retinopathy, Otosclerosis |
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 ⇵ |
|---|---|---|---|---|---|
| SMAD2/3 Phosphorylation Motif Mutants in Cancer | Reactome | 2 / 6 | 78.5× | 2.62e-4 | 4.83e-3 ✓ sig. |
| TGFBR1 KD Mutants in Cancer | Reactome | 2 / 6 | 78.5× | 2.62e-4 | 4.83e-3 ✓ sig. |
| RUNX3 regulates CDKN1A transcription | Reactome | 2 / 7 | 67.3× | 3.66e-4 | 6.27e-3 ✓ sig. |
| TGF-beta receptor signaling activates SMADs | Reactome | 2 / 12 | 39.2× | 1.14e-3 | 1.49e-2 ✓ sig. |
| Downregulation of TGF-beta receptor signaling | Reactome | 2 / 16 | 29.4× | 2.04e-3 | 2.32e-2 ✓ sig. |
| Integrin cell surface interactions | Reactome | 3 / 81 | 8.7× | 4.88e-3 | 4.32e-2 ✓ sig. |
| ECM-receptor interaction | KEGG | 3 / 89 | 7.9× | 6.34e-3 | 5.11e-2 |
| Rheumatoid arthritis | KEGG | 3 / 95 | 7.4× | 7.59e-3 | 5.76e-2 |
| Influenza Virus Induced Apoptosis | Reactome | 1 / 2 | 118× | 8.48e-3 | 6.20e-2 |
| TGFBR2 MSI Frameshift Mutants in Cancer | Reactome | 1 / 2 | 118× | 8.48e-3 | 6.20e-2 |
| Signaling by PDGF | Reactome | 2 / 33 | 14.3× | 8.58e-3 | 6.26e-2 |
| AGE-RAGE signaling pathway in diabetic complications | KEGG | 3 / 101 | 7.0× | 8.98e-3 | 6.42e-2 |
| Focal adhesion | KEGG | 4 / 203 | 4.6× | 1.07e-2 | 7.14e-2 |
| Post-translational protein phosphorylation | Reactome | 3 / 108 | 6.5× | 1.08e-2 | 7.19e-2 |
| Molecules associated with elastic fibres | Reactome | 2 / 38 | 12.4× | 1.13e-2 | 7.36e-2 |
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 bone resorption | GO:0045780 | 3 / 15 | 73.3× | 8.51e-6 | 4.60e-4 ✓ sig. |
| stem cell proliferation | GO:0072089 | 4 / 54 | 27.1× | 1.41e-5 | 6.82e-4 ✓ sig. |
| positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction | GO:0051897 | 6 / 217 | 10.1× | 2.66e-5 | 1.12e-3 ✓ sig. |
| regulation of miRNA transcription | GO:1902893 | 2 / 4 | 183× | 4.37e-5 | 1.63e-3 ✓ sig. |
| osteoclast proliferation | GO:0002158 | 2 / 5 | 147× | 7.26e-5 | 2.38e-3 ✓ sig. |
| embryonic cranial skeleton morphogenesis | GO:0048701 | 3 / 31 | 35.5× | 8.16e-5 | 2.60e-3 ✓ sig. |
| regulation of striated muscle tissue development | GO:0016202 | 2 / 6 | 122× | 1.09e-4 | 3.22e-3 ✓ sig. |
| positive regulation of cell migration | GO:0030335 | 6 / 292 | 7.5× | 1.38e-4 | 3.84e-3 ✓ sig. |
| positive regulation of mesenchymal stem cell proliferation | GO:1902462 | 2 / 7 | 105× | 1.52e-4 | 4.14e-3 ✓ sig. |
| positive regulation of stem cell proliferation | GO:2000648 | 3 / 41 | 26.8× | 1.90e-4 | 4.88e-3 ✓ sig. |
| protein autophosphorylation | GO:0046777 | 4 / 113 | 13.0× | 2.54e-4 | 5.99e-3 ✓ sig. |
| positive regulation of extracellular matrix assembly | GO:1901203 | 2 / 9 | 81.4× | 2.60e-4 | 6.08e-3 ✓ sig. |
| osteoclast differentiation | GO:0030316 | 3 / 49 | 22.4× | 3.23e-4 | 7.06e-3 ✓ sig. |
| positive regulation of positive chemotaxis | GO:0050927 | 2 / 11 | 66.6× | 3.95e-4 | 8.14e-3 ✓ sig. |
| transforming growth factor beta receptor superfamily signaling pathway | GO:0141091 | 2 / 11 | 66.6× | 3.95e-4 | 8.14e-3 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Agnathia-otocephaly | Dysgnathia complex | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Agnathia-otocephaly | Retrognathia | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Dysgnathia complex | Retrognathia | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Agnathia-otocephaly | Otosclerosis | 0.019 | 1 | 3.31e-3 | 4.30e-3 ✓ sig. |
| Dysgnathia complex | Otosclerosis | 0.019 | 1 | 3.31e-3 | 4.30e-3 ✓ sig. |
| Mak-related retinopathy | Otosclerosis | 0.019 | 1 | 3.31e-3 | 4.30e-3 ✓ sig. |
| Otosclerosis | Retrognathia | 0.019 | 1 | 3.31e-3 | 4.30e-3 ✓ sig. |