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 319
6
Diseases
11
Unique genes
0.179
Avg. similarity score
Cleft lip with or without cleft palate
Most-connected disease (5 links)
Disease
Searched: ARHGAP29-related non-syndromic orofacial cleft
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ARHGAP29-related non-syndromic orofacial cleft
Cleft lip with or without cleft palate
Blepharocheilodontic syndrome
Hereditary diffuse gastric and lobular breast cancer syndrome
Trigeminal nerve disease
Bilateral cleft lip
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Cleft lip with or without cleft palate | 5 | 5 | 6 |
| Blepharocheilodontic syndrome | 3 | 3 | 2 |
| Hereditary diffuse gastric and lobular breast cancer syndrome | 2 | 2 | 1 |
| Trigeminal nerve disease | 2 | 2 | 6 |
| ARHGAP29-related non-syndromic orofacial cleft | 1 | 1 | 1 |
| Bilateral cleft lip | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| CDH1 | 3 / 6 | Blepharocheilodontic syndrome, Cleft lip with or without cleft palate, Hereditary diffuse gastric and lobular breast cancer syndrome |
| CTNND1 | 3 / 6 | Blepharocheilodontic syndrome, Cleft lip with or without cleft palate, Trigeminal nerve disease |
| ARHGAP29 | 2 / 6 | ARHGAP29-related non-syndromic orofacial cleft, Cleft lip with or without cleft palate |
| PLEKHA5 | 2 / 6 | Bilateral cleft lip, Cleft lip with or without cleft palate |
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 ⇵ |
|---|---|---|---|---|---|
| InlA-mediated entry of Listeria monocytogenes into host cells | Reactome | 2 / 9 | 243× | 2.74e-5 | 7.57e-4 ✓ sig. |
| Adherens junction | KEGG | 3 / 93 | 35.2× | 7.09e-5 | 1.65e-3 ✓ sig. |
| Adherens junctions interactions | Reactome | 2 / 32 | 68.2× | 3.73e-4 | 6.26e-3 ✓ sig. |
| Apoptotic cleavage of cell adhesion proteins | Reactome | 1 / 11 | 99.3× | 1.00e-2 | 6.93e-2 |
| Rap1 signaling pathway | KEGG | 2 / 211 | 10.3× | 1.52e-2 | 8.95e-2 |
| FGFR2 alternative splicing | Reactome | 1 / 26 | 42.0× | 2.36e-2 | 1.15e-1 |
| Hippo signaling pathway - multiple species | KEGG | 1 / 29 | 37.6× | 2.63e-2 | 1.22e-1 |
| VEGFR2 mediated vascular permeability | Reactome | 1 / 29 | 37.6× | 2.63e-2 | 1.22e-1 |
| RHO GTPases activate IQGAPs | Reactome | 1 / 32 | 34.1× | 2.89e-2 | 1.29e-1 |
| Detoxification of Reactive Oxygen Species | Reactome | 1 / 34 | 32.1× | 3.07e-2 | 1.34e-1 |
| Thyroid cancer | KEGG | 1 / 37 | 29.5× | 3.34e-2 | 1.40e-1 |
| Bladder cancer | KEGG | 1 / 41 | 26.6× | 3.69e-2 | 1.48e-1 |
| Synthesis of PIPs at the plasma membrane | Reactome | 1 / 51 | 21.4× | 4.58e-2 | 1.67e-1 |
| Glutathione metabolism | KEGG | 1 / 59 | 18.5× | 5.28e-2 | 1.80e-1 |
| Endometrial cancer | KEGG | 1 / 59 | 18.5× | 5.28e-2 | 1.80e-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 ⇵ |
|---|---|---|---|---|---|
| cell-cell adhesion mediated by cadherin | GO:0044331 | 4 / 42 | 162× | 7.19e-9 | 1.26e-6 ✓ sig. |
| cell-cell adhesion | GO:0098609 | 4 / 218 | 31.2× | 5.58e-6 | 3.30e-4 ✓ sig. |
| negative regulation of blood vessel branching | GO:1905554 | 1 / 1 | 1,699× | 5.89e-4 | 1.08e-2 ✓ sig. |
| negative regulation of miRNA catabolic process | GO:2000626 | 1 / 2 | 849× | 1.18e-3 | 1.67e-2 ✓ sig. |
| ureteric bud invasion | GO:0072092 | 1 / 2 | 849× | 1.18e-3 | 1.67e-2 ✓ sig. |
| positive regulation of protein localization to cell-cell junction | GO:0150107 | 1 / 3 | 566× | 1.76e-3 | 2.14e-2 ✓ sig. |
| condensed mesenchymal cell proliferation | GO:0072137 | 1 / 3 | 566× | 1.76e-3 | 2.14e-2 ✓ sig. |
| zonula adherens maintenance | GO:0045218 | 1 / 3 | 566× | 1.76e-3 | 2.14e-2 ✓ sig. |
| response to heparin | GO:0071503 | 1 / 3 | 566× | 1.76e-3 | 2.14e-2 ✓ sig. |
| regulation of protein catabolic process at postsynapse, modulating synaptic transmission | GO:0099576 | 1 / 4 | 425× | 2.35e-3 | 2.52e-2 ✓ sig. |
| target-directed miRNA degradation | GO:0140958 | 1 / 4 | 425× | 2.35e-3 | 2.52e-2 ✓ sig. |
| cellular response to indole-3-methanol | GO:0071681 | 1 / 5 | 340× | 2.94e-3 | 2.85e-2 ✓ sig. |
| response to Gram-positive bacterium | GO:0140459 | 1 / 6 | 283× | 3.53e-3 | 3.12e-2 ✓ sig. |
| negative regulation of D-glucose transmembrane transport | GO:0010829 | 1 / 7 | 243× | 4.11e-3 | 3.36e-2 ✓ sig. |
| desmosome assembly | GO:0002159 | 1 / 7 | 243× | 4.11e-3 | 3.36e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Blepharocheilodontic syndrome | Cleft lip with or without cleft palate | 0.286 | 2 | 1.27e-7 | 8.71e-7 ✓ sig. |
| Blepharocheilodontic syndrome | Hereditary diffuse gastric and lobular breast cancer syndrome | 0.333 | 1 | 1.30e-4 | 3.93e-4 ✓ sig. |
| ARHGAP29-related non-syndromic orofacial cleft | Cleft lip with or without cleft palate | 0.143 | 1 | 3.90e-4 | 8.66e-4 ✓ sig. |
| Bilateral cleft lip | Cleft lip with or without cleft palate | 0.143 | 1 | 3.90e-4 | 8.66e-4 ✓ sig. |
| Cleft lip with or without cleft palate | Hereditary diffuse gastric and lobular breast cancer syndrome | 0.143 | 1 | 3.90e-4 | 8.66e-4 ✓ sig. |
| Blepharocheilodontic syndrome | Trigeminal nerve disease | 0.125 | 1 | 7.79e-4 | 1.40e-3 ✓ sig. |
| Cleft lip with or without cleft palate | Trigeminal nerve disease | 0.083 | 1 | 2.34e-3 | 3.24e-3 ✓ sig. |