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 350
5
Diseases
15
Unique genes
0.194
Avg. similarity score
1p36 deletion syndrome
Most-connected disease (4 links)
Disease
Searched: radio-tartaglia syndrome
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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radio-tartaglia syndrome
1p36 deletion syndrome
Dyssegmental dysplasia
Schwartz-jampel syndrome
Silverman-Handmaker type dyssegmental dysplasia
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| 1p36 deletion syndrome | 4 | 4 | 13 |
| Dyssegmental dysplasia | 3 | 3 | 2 |
| Schwartz-jampel syndrome | 3 | 3 | 3 |
| Silverman-Handmaker type dyssegmental dysplasia | 3 | 3 | 1 |
| radio-tartaglia syndrome | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| HSPG2 | 4 / 5 | 1p36 deletion syndrome, Dyssegmental dysplasia, Schwartz-jampel syndrome, Silverman-Handmaker type dyssegmental dysplasia |
| LDLRAD2 | 2 / 5 | Dyssegmental dysplasia, Schwartz-jampel syndrome |
| SPEN | 2 / 5 | 1p36 deletion syndrome, radio-tartaglia 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)
None of these pathways reaches significance (all FDR q ≥ 0.05). They’re the best candidates found, but treat them as weak evidence for why this cluster groups together.
| Pathway ⇵ | Source ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Estrogen-stimulated signaling through PRKCZ | Reactome | 1 / 6 | 133× | 7.47e-3 | 5.89e-2 |
| Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion | Reactome | 1 / 8 | 100× | 9.95e-3 | 7.05e-2 |
| Acetylcholine regulates insulin secretion | Reactome | 1 / 9 | 89.0× | 1.12e-2 | 7.60e-2 |
| Defective EXT2 causes exostoses 2 | Reactome | 1 / 14 | 57.2× | 1.74e-2 | 9.88e-2 |
| Defective EXT1 causes exostoses 1, TRPS2 and CHDS | Reactome | 1 / 14 | 57.2× | 1.74e-2 | 9.88e-2 |
| VEGFR2 mediated cell proliferation | Reactome | 1 / 14 | 57.2× | 1.74e-2 | 9.88e-2 |
| TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) | Reactome | 1 / 15 | 53.4× | 1.86e-2 | 1.03e-1 |
| Defective B4GALT7 causes EDS, progeroid type | Reactome | 1 / 20 | 40.0× | 2.47e-2 | 1.21e-1 |
| Defective B3GAT3 causes JDSSDHD | Reactome | 1 / 20 | 40.0× | 2.47e-2 | 1.21e-1 |
| Defective B3GALT6 causes EDSP2 and SEMDJL1 | Reactome | 1 / 20 | 40.0× | 2.47e-2 | 1.21e-1 |
| HS-GAG degradation | Reactome | 1 / 22 | 36.4× | 2.71e-2 | 1.27e-1 |
| Downregulation of SMAD2/3:SMAD4 transcriptional activity | Reactome | 1 / 22 | 36.4× | 2.71e-2 | 1.27e-1 |
| Thromboxane signalling through TP receptor | Reactome | 1 / 24 | 33.4× | 2.96e-2 | 1.33e-1 |
| RHO GTPases Activate NADPH Oxidases | Reactome | 1 / 24 | 33.4× | 2.96e-2 | 1.33e-1 |
| Non-integrin membrane-ECM interactions | Reactome | 1 / 24 | 33.4× | 2.96e-2 | 1.33e-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 ⇵ |
|---|---|---|---|---|---|
| neural fold bending | GO:0021503 | 1 / 1 | 1,246× | 8.03e-4 | 1.35e-2 ✓ sig. |
| contractile ring contraction | GO:0036213 | 1 / 1 | 1,246× | 8.03e-4 | 1.35e-2 ✓ sig. |
| regulation of myofibroblast contraction | GO:1904328 | 1 / 1 | 1,246× | 8.03e-4 | 1.35e-2 ✓ sig. |
| granzyme-mediated apoptotic signaling pathway | GO:0008626 | 1 / 1 | 1,246× | 8.03e-4 | 1.35e-2 ✓ sig. |
| regulation of melanocyte differentiation | GO:0045634 | 1 / 1 | 1,246× | 8.03e-4 | 1.35e-2 ✓ sig. |
| cerebellar Purkinje cell layer maturation | GO:0021691 | 1 / 2 | 623× | 1.60e-3 | 2.06e-2 ✓ sig. |
| radial glia guided migration of Purkinje cell | GO:0021942 | 1 / 3 | 415× | 2.41e-3 | 2.59e-2 ✓ sig. |
| nose morphogenesis | GO:0043585 | 1 / 3 | 415× | 2.41e-3 | 2.59e-2 ✓ sig. |
| lymphatic endothelial cell fate commitment | GO:0060838 | 1 / 3 | 415× | 2.41e-3 | 2.59e-2 ✓ sig. |
| actin-mediated cell contraction | GO:0070252 | 1 / 3 | 415× | 2.41e-3 | 2.59e-2 ✓ sig. |
| regulation of lamellipodium morphogenesis | GO:2000392 | 1 / 3 | 415× | 2.41e-3 | 2.59e-2 ✓ sig. |
| apical constriction | GO:0003383 | 1 / 5 | 249× | 4.01e-3 | 3.37e-2 ✓ sig. |
| protein localization to actin cytoskeleton | GO:1903119 | 1 / 5 | 249× | 4.01e-3 | 3.37e-2 ✓ sig. |
| regulation of substrate adhesion-dependent cell spreading | GO:1900024 | 1 / 5 | 249× | 4.01e-3 | 3.37e-2 ✓ sig. |
| negative regulation of transforming growth factor beta receptor signaling pathway | GO:0030512 | 2 / 128 | 19.5× | 4.61e-3 | 3.65e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Dyssegmental dysplasia | Schwartz-jampel syndrome | 0.500 | 2 | 2.53e-8 | 1.93e-7 ✓ sig. |
| Dyssegmental dysplasia | Silverman-Handmaker type dyssegmental dysplasia | 0.333 | 1 | 1.30e-4 | 3.93e-4 ✓ sig. |
| Schwartz-jampel syndrome | Silverman-Handmaker type dyssegmental dysplasia | 0.250 | 1 | 1.95e-4 | 5.35e-4 ✓ sig. |
| 1p36 deletion syndrome | Silverman-Handmaker type dyssegmental dysplasia | 0.071 | 1 | 8.44e-4 | 1.50e-3 ✓ sig. |
| 1p36 deletion syndrome | radio-tartaglia syndrome | 0.071 | 1 | 8.44e-4 | 1.50e-3 ✓ sig. |
| 1p36 deletion syndrome | Dyssegmental dysplasia | 0.067 | 1 | 1.69e-3 | 2.53e-3 ✓ sig. |
| 1p36 deletion syndrome | Schwartz-jampel syndrome | 0.063 | 1 | 2.53e-3 | 3.45e-3 ✓ sig. |