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 386
5
Diseases
3
Unique genes
0.344
Avg. similarity score
Alopecia-intellectual disability syndrome
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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Alopecia-intellectual disability syndrome
Perniola krajewska carnevale syndrome
Cataract-alopecia-sclerodactyly syndrome
Palmoplantar keratoderma and congenital alopecia
Amr syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Alopecia-intellectual disability syndrome | 4 | 4 | 2 |
| Perniola krajewska carnevale syndrome | 4 | 4 | 3 |
| Cataract-alopecia-sclerodactyly syndrome | 3 | 3 | 1 |
| Palmoplantar keratoderma and congenital alopecia | 3 | 3 | 1 |
| Amr syndrome | 2 | 2 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| LSS | 4 / 5 | Alopecia-intellectual disability syndrome, Cataract-alopecia-sclerodactyly syndrome, Palmoplantar keratoderma and congenital alopecia, Perniola krajewska carnevale syndrome |
| AHSG | 3 / 5 | Alopecia-intellectual disability syndrome, Amr syndrome, Perniola krajewska carnevale 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 ⇵ |
|---|---|---|---|---|---|
| Elastic fibre formation | Reactome | 1 / 18 | 222× | 4.49e-3 | 4.08e-2 ✓ sig. |
| Steroid biosynthesis | KEGG | 1 / 20 | 200× | 4.99e-3 | 4.37e-2 ✓ sig. |
| Cholesterol biosynthesis | Reactome | 1 / 21 | 191× | 5.24e-3 | 4.50e-2 ✓ sig. |
| Molecules associated with elastic fibres | Reactome | 1 / 38 | 105× | 9.46e-3 | 6.63e-2 |
| Activation of gene expression by SREBF (SREBP) | Reactome | 1 / 42 | 95.3× | 1.05e-2 | 7.05e-2 |
| ECM proteoglycans | Reactome | 1 / 51 | 78.5× | 1.27e-2 | 7.88e-2 |
| Integrin cell surface interactions | Reactome | 1 / 81 | 49.4× | 2.01e-2 | 1.03e-1 |
| Arrhythmogenic right ventricular cardiomyopathy | KEGG | 1 / 86 | 46.6× | 2.13e-2 | 1.07e-1 |
| ECM-receptor interaction | KEGG | 1 / 89 | 45.0× | 2.21e-2 | 1.09e-1 |
| Hypertrophic cardiomyopathy | KEGG | 1 / 99 | 40.4× | 2.45e-2 | 1.15e-1 |
| Dilated cardiomyopathy | KEGG | 1 / 105 | 38.1× | 2.60e-2 | 1.19e-1 |
| Post-translational protein phosphorylation | Reactome | 1 / 108 | 37.1× | 2.67e-2 | 1.21e-1 |
| Platelet degranulation | Reactome | 1 / 123 | 32.5× | 3.04e-2 | 1.30e-1 |
| Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) | Reactome | 1 / 125 | 32.0× | 3.09e-2 | 1.31e-1 |
| Focal adhesion | KEGG | 1 / 203 | 19.7× | 4.99e-2 | 1.71e-1 |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| triterpenoid biosynthetic process | GO:0016104 | 1 / 1 | 6,229× | 1.61e-4 | 4.31e-3 ✓ sig. |
| transforming growth factor beta production | GO:0071604 | 1 / 2 | 3,115× | 3.21e-4 | 7.03e-3 ✓ sig. |
| pinocytosis | GO:0006907 | 1 / 4 | 1,557× | 6.42e-4 | 1.13e-2 ✓ sig. |
| Langerhans cell differentiation | GO:0061520 | 1 / 4 | 1,557× | 6.42e-4 | 1.13e-2 ✓ sig. |
| bronchiole development | GO:0060435 | 1 / 5 | 1,246× | 8.03e-4 | 1.30e-2 ✓ sig. |
| hard palate development | GO:0060022 | 1 / 9 | 692× | 1.44e-3 | 1.87e-2 ✓ sig. |
| enamel mineralization | GO:0070166 | 1 / 14 | 445× | 2.25e-3 | 2.41e-2 ✓ sig. |
| phospholipid homeostasis | GO:0055091 | 1 / 17 | 366× | 2.73e-3 | 2.68e-2 ✓ sig. |
| negative regulation of bone mineralization | GO:0030502 | 1 / 17 | 366× | 2.73e-3 | 2.68e-2 ✓ sig. |
| surfactant homeostasis | GO:0043129 | 1 / 18 | 346× | 2.89e-3 | 2.76e-2 ✓ sig. |
| regulation of bone mineralization | GO:0030500 | 1 / 24 | 260× | 3.85e-3 | 3.22e-2 ✓ sig. |
| cell adhesion mediated by integrin | GO:0033627 | 1 / 25 | 249× | 4.01e-3 | 3.28e-2 ✓ sig. |
| acute-phase response | GO:0006953 | 1 / 37 | 168× | 5.93e-3 | 4.00e-2 ✓ sig. |
| cholesterol biosynthetic process | GO:0006695 | 1 / 39 | 160× | 6.25e-3 | 4.10e-2 ✓ sig. |
| cellular response to ionizing radiation | GO:0071479 | 1 / 41 | 152× | 6.57e-3 | 4.22e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Alopecia-intellectual disability syndrome | Perniola krajewska carnevale syndrome | 0.500 | 2 | 2.53e-8 | 2.03e-7 ✓ sig. |
| Cataract-alopecia-sclerodactyly syndrome | Palmoplantar keratoderma and congenital alopecia | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Alopecia-intellectual disability syndrome | Amr syndrome | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Alopecia-intellectual disability syndrome | Palmoplantar keratoderma and congenital alopecia | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Alopecia-intellectual disability syndrome | Cataract-alopecia-sclerodactyly syndrome | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Amr syndrome | Perniola krajewska carnevale syndrome | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |
| Cataract-alopecia-sclerodactyly syndrome | Perniola krajewska carnevale syndrome | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |
| Palmoplantar keratoderma and congenital alopecia | Perniola krajewska carnevale syndrome | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |