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 310
6
Diseases
3
Unique genes
0.386
Avg. similarity score
Bent bone dysplasia
Most-connected disease (5 links)
Disease
Searched: isolated Pierre-Robin syndrome
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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isolated Pierre-Robin syndrome
Bent bone dysplasia
Campomelic dysplasia
Camptomelic dysplasia
Cooks syndrome
LAMA5-related multisystemic syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Bent bone dysplasia | 5 | 5 | 3 |
| Campomelic dysplasia | 4 | 4 | 1 |
| Camptomelic dysplasia | 4 | 4 | 1 |
| Cooks syndrome | 4 | 4 | 1 |
| isolated Pierre-Robin syndrome | 4 | 4 | 1 |
| LAMA5-related multisystemic syndrome | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| SOX9 | 5 / 6 | Bent bone dysplasia, Campomelic dysplasia, Camptomelic dysplasia, Cooks syndrome and 1 more |
| LAMA5 | 2 / 6 | Bent bone dysplasia, LAMA5-related multisystemic 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 ⇵ |
|---|---|---|---|---|---|
| Signaling by FGFR2 amplification mutants | Reactome | 1 / 1 | 4,003× | 2.50e-4 | 4.76e-3 ✓ sig. |
| Signaling by FGFR2 fusions | Reactome | 1 / 1 | 4,003× | 2.50e-4 | 4.76e-3 ✓ sig. |
| FGFR2b ligand binding and activation | Reactome | 1 / 10 | 400× | 2.50e-3 | 2.77e-2 ✓ sig. |
| PI3K-Akt signaling pathway | KEGG | 2 / 361 | 22.2× | 2.65e-3 | 2.90e-2 ✓ sig. |
| Transcriptional regulation by RUNX2 | Reactome | 1 / 12 | 334× | 2.99e-3 | 3.15e-2 ✓ sig. |
| FGFR2c ligand binding and activation | Reactome | 1 / 13 | 308× | 3.24e-3 | 3.33e-2 ✓ sig. |
| Activated point mutants of FGFR2 | Reactome | 1 / 17 | 235× | 4.24e-3 | 4.04e-2 ✓ sig. |
| Phospholipase C-mediated cascade; FGFR2 | Reactome | 1 / 18 | 222× | 4.49e-3 | 4.21e-2 ✓ sig. |
| Pathways in cancer | KEGG | 2 / 533 | 15.0× | 5.72e-3 | 4.96e-2 ✓ sig. |
| PI-3K cascade:FGFR2 | Reactome | 1 / 23 | 174× | 5.73e-3 | 4.97e-2 ✓ sig. |
| SHC-mediated cascade:FGFR2 | Reactome | 1 / 23 | 174× | 5.73e-3 | 4.97e-2 ✓ sig. |
| FRS-mediated FGFR2 signaling | Reactome | 1 / 25 | 160× | 6.23e-3 | 5.25e-2 |
| Negative regulation of FGFR2 signaling | Reactome | 1 / 27 | 148× | 6.73e-3 | 5.51e-2 |
| Signaling by FGFR2 in disease | Reactome | 1 / 27 | 148× | 6.73e-3 | 5.51e-2 |
| Laminin interactions | Reactome | 1 / 28 | 143× | 6.98e-3 | 5.64e-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 ⇵ |
|---|---|---|---|---|---|
| prostate gland morphogenesis | GO:0060512 | 2 / 5 | 2,492× | 1.72e-7 | 1.95e-5 ✓ sig. |
| otic vesicle formation | GO:0030916 | 2 / 7 | 1,780× | 3.61e-7 | 3.64e-5 ✓ sig. |
| lacrimal gland development | GO:0032808 | 2 / 7 | 1,780× | 3.61e-7 | 3.64e-5 ✓ sig. |
| limb bud formation | GO:0060174 | 2 / 9 | 1,384× | 6.18e-7 | 5.71e-5 ✓ sig. |
| branching involved in salivary gland morphogenesis | GO:0060445 | 2 / 12 | 1,038× | 1.13e-6 | 9.38e-5 ✓ sig. |
| morphogenesis of embryonic epithelium | GO:0016331 | 2 / 13 | 958× | 1.34e-6 | 1.07e-4 ✓ sig. |
| positive regulation of mesenchymal cell proliferation | GO:0002053 | 2 / 26 | 479× | 5.58e-6 | 3.39e-4 ✓ sig. |
| skeletal system morphogenesis | GO:0048705 | 2 / 45 | 277× | 1.70e-5 | 8.15e-4 ✓ sig. |
| branching involved in ureteric bud morphogenesis | GO:0001658 | 2 / 45 | 277× | 1.70e-5 | 8.15e-4 ✓ sig. |
| hair follicle development | GO:0001942 | 2 / 48 | 260× | 1.94e-5 | 9.05e-4 ✓ sig. |
| regulation of cell differentiation | GO:0045595 | 2 / 54 | 231× | 2.45e-5 | 1.08e-3 ✓ sig. |
| bone mineralization | GO:0030282 | 2 / 56 | 222× | 2.64e-5 | 1.14e-3 ✓ sig. |
| epithelial to mesenchymal transition | GO:0001837 | 2 / 61 | 204× | 3.14e-5 | 1.30e-3 ✓ sig. |
| regulation of cell adhesion | GO:0030155 | 2 / 61 | 204× | 3.14e-5 | 1.30e-3 ✓ sig. |
| negative regulation of epithelial cell proliferation | GO:0050680 | 2 / 62 | 201× | 3.24e-5 | 1.34e-3 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Campomelic dysplasia | Camptomelic dysplasia | 0.500 | 1 | 6.49e-5 | 2.33e-4 ✓ sig. |
| Campomelic dysplasia | Cooks syndrome | 0.500 | 1 | 6.49e-5 | 2.33e-4 ✓ sig. |
| Campomelic dysplasia | isolated Pierre-Robin syndrome | 0.500 | 1 | 6.49e-5 | 2.33e-4 ✓ sig. |
| Camptomelic dysplasia | Cooks syndrome | 0.500 | 1 | 6.49e-5 | 2.33e-4 ✓ sig. |
| Camptomelic dysplasia | isolated Pierre-Robin syndrome | 0.500 | 1 | 6.49e-5 | 2.33e-4 ✓ sig. |
| Cooks syndrome | isolated Pierre-Robin syndrome | 0.500 | 1 | 6.49e-5 | 2.33e-4 ✓ sig. |
| Bent bone dysplasia | Campomelic dysplasia | 0.250 | 1 | 1.95e-4 | 5.35e-4 ✓ sig. |
| Bent bone dysplasia | Camptomelic dysplasia | 0.250 | 1 | 1.95e-4 | 5.35e-4 ✓ sig. |
| Bent bone dysplasia | Cooks syndrome | 0.250 | 1 | 1.95e-4 | 5.35e-4 ✓ sig. |
| Bent bone dysplasia | isolated Pierre-Robin syndrome | 0.250 | 1 | 1.95e-4 | 5.35e-4 ✓ sig. |
| Bent bone dysplasia | LAMA5-related multisystemic syndrome | 0.250 | 1 | 1.95e-4 | 5.35e-4 ✓ sig. |