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 394
5
Diseases
15
Unique genes
0.202
Avg. similarity score
Intellectual developmental disorder dysmorphic brain
Most-connected disease (3 links)
Disease
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Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Intellectual developmental disorder dysmorphic brain
Malunion fracture
intellectual disability-obesity-brain malformations-facial dysmorphism syndrome
Bile duct cancer
Antecubital pterygium syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Intellectual developmental disorder dysmorphic brain | 3 | 3 | 1 |
| Malunion fracture | 3 | 3 | 13 |
| intellectual disability-obesity-brain malformations-facial dysmorphism syndrome | 3 | 3 | 1 |
| Bile duct cancer | 2 | 2 | 3 |
| Antecubital pterygium syndrome | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| TRAPPC9 | 4 / 5 | Bile duct cancer, Intellectual developmental disorder dysmorphic brain, intellectual disability-obesity-brain malformations-facial dysmorphism syndrome, Malunion fracture |
| PSD3 | 2 / 5 | Antecubital pterygium syndrome, Malunion fracture |
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 ⇵ |
|---|---|---|---|---|---|
| phospho-PLA2 pathway | Reactome | 1 / 2 | 400× | 2.50e-3 | 2.69e-2 ✓ sig. |
| GnRH secretion | KEGG | 2 / 65 | 24.6× | 2.89e-3 | 3.00e-2 ✓ sig. |
| Acute myeloid leukemia | KEGG | 2 / 68 | 23.5× | 3.16e-3 | 3.20e-2 ✓ sig. |
| HDL clearance | Reactome | 1 / 5 | 160× | 6.23e-3 | 5.06e-2 |
| Scavenging by Class B Receptors | Reactome | 1 / 5 | 160× | 6.23e-3 | 5.06e-2 |
| Circadian entrainment | KEGG | 2 / 97 | 16.5× | 6.33e-3 | 5.11e-2 |
| Estrogen-stimulated signaling through PRKCZ | Reactome | 1 / 6 | 133× | 7.47e-3 | 5.69e-2 |
| Negative feedback regulation of MAPK pathway | Reactome | 1 / 6 | 133× | 7.47e-3 | 5.69e-2 |
| Suppression of apoptosis | Reactome | 1 / 7 | 114× | 8.71e-3 | 6.31e-2 |
| Cholinergic synapse | KEGG | 2 / 115 | 13.9× | 8.80e-3 | 6.35e-2 |
| Serotonergic synapse | KEGG | 2 / 115 | 13.9× | 8.80e-3 | 6.35e-2 |
| Glutamatergic synapse | KEGG | 2 / 116 | 13.8× | 8.95e-3 | 6.42e-2 |
| NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis | Reactome | 1 / 9 | 89.0× | 1.12e-2 | 7.34e-2 |
| Gastrin-CREB signalling pathway via PKC and MAPK | Reactome | 1 / 9 | 89.0× | 1.12e-2 | 7.34e-2 |
| MAPK1 (ERK2) activation | Reactome | 1 / 9 | 89.0× | 1.12e-2 | 7.34e-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 ⇵ |
|---|---|---|---|---|---|
| lipopolysaccharide-mediated signaling pathway | GO:0031663 | 2 / 38 | 65.6× | 4.16e-4 | 8.44e-3 ✓ sig. |
| high density lipoprotein particle mediated signaling | GO:0055097 | 1 / 1 | 1,246× | 8.03e-4 | 1.30e-2 ✓ sig. |
| positive regulation of endothelial cell migration | GO:0010595 | 2 / 66 | 37.8× | 1.25e-3 | 1.73e-2 ✓ sig. |
| regulation of phosphatidylcholine catabolic process | GO:0010899 | 1 / 2 | 623× | 1.60e-3 | 1.98e-2 ✓ sig. |
| lipopolysaccharide transport | GO:0015920 | 1 / 2 | 623× | 1.60e-3 | 1.98e-2 ✓ sig. |
| positive regulation of sphingolipid mediated signaling pathway | GO:1902070 | 1 / 2 | 623× | 1.60e-3 | 1.98e-2 ✓ sig. |
| cytosine metabolic process | GO:0019858 | 1 / 2 | 623× | 1.60e-3 | 1.98e-2 ✓ sig. |
| positive regulation of peptidase activity | GO:0010952 | 1 / 2 | 623× | 1.60e-3 | 1.98e-2 ✓ sig. |
| interleukin-34-mediated signaling pathway | GO:0061514 | 1 / 3 | 415× | 2.41e-3 | 2.50e-2 ✓ sig. |
| ventricular cardiac muscle cell membrane repolarization | GO:0099625 | 1 / 3 | 415× | 2.41e-3 | 2.50e-2 ✓ sig. |
| vitamin transmembrane transport | GO:0035461 | 1 / 3 | 415× | 2.41e-3 | 2.50e-2 ✓ sig. |
| intestinal lipid absorption | GO:0098856 | 1 / 3 | 415× | 2.41e-3 | 2.50e-2 ✓ sig. |
| cardiac neural crest cell development involved in heart development | GO:0061308 | 1 / 3 | 415× | 2.41e-3 | 2.50e-2 ✓ sig. |
| positive regulation of nitric oxide mediated signal transduction | GO:0010750 | 1 / 4 | 311× | 3.21e-3 | 2.91e-2 ✓ sig. |
| plasma lipoprotein particle clearance | GO:0034381 | 1 / 4 | 311× | 3.21e-3 | 2.91e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Intellectual developmental disorder dysmorphic brain | intellectual disability-obesity-brain malformations-facial dysmorphism syndrome | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Bile duct cancer | Intellectual developmental disorder dysmorphic brain | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |
| Bile duct cancer | intellectual disability-obesity-brain malformations-facial dysmorphism syndrome | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |
| Antecubital pterygium syndrome | Malunion fracture | 0.071 | 1 | 8.44e-4 | 1.48e-3 ✓ sig. |
| Intellectual developmental disorder dysmorphic brain | Malunion fracture | 0.071 | 1 | 8.44e-4 | 1.48e-3 ✓ sig. |
| intellectual disability-obesity-brain malformations-facial dysmorphism syndrome | Malunion fracture | 0.071 | 1 | 8.44e-4 | 1.48e-3 ✓ sig. |