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 321
6
Diseases
5
Unique genes
0.386
Avg. similarity score
Lacrimoauriculodentodigital syndrome
Most-connected disease (5 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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Lacrimoauriculodentodigital syndrome
Ladd syndrome
Aplasia of lacrimal and salivary glands
Craniofacial dysostosis
Saethre-chotzen syndrome
Salivary gland agenesis
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Lacrimoauriculodentodigital syndrome | 5 | 5 | 3 |
| Ladd syndrome | 5 | 5 | 3 |
| Aplasia of lacrimal and salivary glands | 3 | 3 | 1 |
| Craniofacial dysostosis | 3 | 3 | 3 |
| Saethre-chotzen syndrome | 3 | 3 | 3 |
| Salivary gland agenesis | 3 | 3 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| FGF10 | 4 / 6 | Aplasia of lacrimal and salivary glands, Lacrimoauriculodentodigital syndrome, Ladd syndrome, Salivary gland agenesis |
| FGFR2 | 4 / 6 | Craniofacial dysostosis, Lacrimoauriculodentodigital syndrome, Ladd syndrome, Saethre-chotzen syndrome |
| FGFR3 | 4 / 6 | Craniofacial dysostosis, Lacrimoauriculodentodigital syndrome, Ladd syndrome, Saethre-chotzen 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 ⇵ |
|---|---|---|---|---|---|
| PI3K Cascade | Reactome | 3 / 39 | 185× | 3.15e-7 | 1.79e-5 ✓ sig. |
| Constitutive Signaling by Aberrant PI3K in Cancer | Reactome | 3 / 75 | 96.1× | 2.32e-6 | 1.00e-4 ✓ sig. |
| PIP3 activates AKT signaling | Reactome | 3 / 93 | 77.5× | 4.45e-6 | 1.73e-4 ✓ sig. |
| PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling | Reactome | 3 / 103 | 70.0× | 6.05e-6 | 2.21e-4 ✓ sig. |
| FGFR2b ligand binding and activation | Reactome | 2 / 10 | 480× | 6.23e-6 | 2.26e-4 ✓ sig. |
| RAF/MAP kinase cascade | Reactome | 3 / 124 | 58.1× | 1.06e-5 | 3.52e-4 ✓ sig. |
| Activated point mutants of FGFR2 | Reactome | 2 / 17 | 283× | 1.88e-5 | 5.70e-4 ✓ sig. |
| Phospholipase C-mediated cascade; FGFR2 | Reactome | 2 / 18 | 267× | 2.12e-5 | 6.27e-4 ✓ sig. |
| PI-3K cascade:FGFR2 | Reactome | 2 / 23 | 209× | 3.50e-5 | 9.50e-4 ✓ sig. |
| SHC-mediated cascade:FGFR2 | Reactome | 2 / 23 | 209× | 3.50e-5 | 9.50e-4 ✓ sig. |
| FRS-mediated FGFR2 signaling | Reactome | 2 / 25 | 192× | 4.14e-5 | 1.10e-3 ✓ sig. |
| Negative regulation of FGFR2 signaling | Reactome | 2 / 27 | 178× | 4.85e-5 | 1.24e-3 ✓ sig. |
| Signaling by FGFR2 in disease | Reactome | 2 / 27 | 178× | 4.85e-5 | 1.24e-3 ✓ sig. |
| Rap1 signaling pathway | KEGG | 3 / 211 | 34.2× | 5.21e-5 | 1.32e-3 ✓ sig. |
| Regulation of actin cytoskeleton | KEGG | 3 / 232 | 31.1× | 6.92e-5 | 1.66e-3 ✓ sig. |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| fibroblast growth factor receptor signaling pathway involved in mammary gland specification | GO:0060595 | 2 / 2 | 3,737× | 5.73e-8 | 7.60e-6 ✓ sig. |
| mammary gland bud formation | GO:0060615 | 2 / 2 | 3,737× | 5.73e-8 | 7.60e-6 ✓ sig. |
| branch elongation involved in salivary gland morphogenesis | GO:0060667 | 2 / 2 | 3,737× | 5.73e-8 | 7.60e-6 ✓ sig. |
| mesenchymal cell differentiation involved in lung development | GO:0060915 | 2 / 2 | 3,737× | 5.73e-8 | 7.60e-6 ✓ sig. |
| fibroblast growth factor receptor apoptotic signaling pathway | GO:1902178 | 2 / 2 | 3,737× | 5.73e-8 | 7.60e-6 ✓ sig. |
| fibroblast growth factor receptor signaling pathway | GO:0008543 | 3 / 60 | 187× | 3.13e-7 | 3.16e-5 ✓ sig. |
| positive regulation of phospholipase activity | GO:0010518 | 2 / 4 | 1,869× | 3.44e-7 | 3.40e-5 ✓ sig. |
| epithelial cell proliferation involved in salivary gland morphogenesis | GO:0060664 | 2 / 5 | 1,495× | 5.73e-7 | 5.25e-5 ✓ sig. |
| otic vesicle formation | GO:0030916 | 2 / 7 | 1,068× | 1.20e-6 | 9.61e-5 ✓ sig. |
| lacrimal gland development | GO:0032808 | 2 / 7 | 1,068× | 1.20e-6 | 9.61e-5 ✓ sig. |
| epidermis morphogenesis | GO:0048730 | 2 / 7 | 1,068× | 1.20e-6 | 9.61e-5 ✓ sig. |
| bud elongation involved in lung branching | GO:0060449 | 2 / 7 | 1,068× | 1.20e-6 | 9.61e-5 ✓ sig. |
| limb bud formation | GO:0060174 | 2 / 9 | 831× | 2.06e-6 | 1.47e-4 ✓ sig. |
| endochondral bone growth | GO:0003416 | 2 / 10 | 747× | 2.58e-6 | 1.76e-4 ✓ sig. |
| branching involved in salivary gland morphogenesis | GO:0060445 | 2 / 12 | 623× | 3.78e-6 | 2.40e-4 ✓ sig. |