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 250
7
Diseases
14
Unique genes
0.198
Avg. similarity score
Brachycephaly
Most-connected disease (5 links)
Disease
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Brachycephaly
Coronal craniosynostosis
Sweeney-cox syndrome
TCF12-related craniosynostosis
TWIST1-related craniosynostosis
Extraskeletal myxoid chondrosarcoma
Binocular vision disease
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Brachycephaly | 5 | 5 | 10 |
| Coronal craniosynostosis | 5 | 5 | 3 |
| Sweeney-cox syndrome | 3 | 3 | 1 |
| TCF12-related craniosynostosis | 3 | 3 | 1 |
| TWIST1-related craniosynostosis | 3 | 3 | 1 |
| Extraskeletal myxoid chondrosarcoma | 2 | 2 | 5 |
| Binocular vision disease | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| TCF12 | 4 / 7 | Brachycephaly, Coronal craniosynostosis, Extraskeletal myxoid chondrosarcoma, TCF12-related craniosynostosis |
| TWIST1 | 4 / 7 | Brachycephaly, Coronal craniosynostosis, Sweeney-cox syndrome, TWIST1-related craniosynostosis |
| FGFR3 | 2 / 7 | Brachycephaly, Coronal craniosynostosis |
| RPS23 | 2 / 7 | Binocular vision disease, Brachycephaly |
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 ⇵ |
|---|---|---|---|---|---|
| PI-3K cascade:FGFR3 | Reactome | 2 / 18 | 95.3× | 1.91e-4 | 3.77e-3 ✓ sig. |
| FRS-mediated FGFR3 signaling | Reactome | 2 / 20 | 85.8× | 2.37e-4 | 4.46e-3 ✓ sig. |
| Negative regulation of FGFR3 signaling | Reactome | 2 / 22 | 78.0× | 2.88e-4 | 5.19e-3 ✓ sig. |
| PI3K Cascade | Reactome | 2 / 39 | 44.0× | 9.12e-4 | 1.27e-2 ✓ sig. |
| t(4;14) translocations of FGFR3 | Reactome | 1 / 1 | 858× | 1.17e-3 | 1.52e-2 ✓ sig. |
| Transcriptional misregulation in cancer | KEGG | 3 / 198 | 13.0× | 1.40e-3 | 1.75e-2 ✓ sig. |
| Constitutive Signaling by Aberrant PI3K in Cancer | Reactome | 2 / 75 | 22.9× | 3.34e-3 | 3.32e-2 ✓ sig. |
| PIP3 activates AKT signaling | Reactome | 2 / 93 | 18.4× | 5.08e-3 | 4.42e-2 ✓ sig. |
| MET activates PTPN11 | Reactome | 1 / 5 | 172× | 5.82e-3 | 4.84e-2 ✓ sig. |
| PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling | Reactome | 2 / 103 | 16.7× | 6.20e-3 | 5.05e-2 |
| Misspliced LRP5 mutants have enhanced beta-catenin-dependent signaling | Reactome | 1 / 6 | 143× | 6.98e-3 | 5.45e-2 |
| FGFR3b ligand binding and activation | Reactome | 1 / 7 | 123× | 8.13e-3 | 6.04e-2 |
| Negative regulation of TCF-dependent signaling by WNT ligand antagonists | Reactome | 1 / 8 | 107× | 9.29e-3 | 6.56e-2 |
| RNF mutants show enhanced WNT signaling and proliferation | Reactome | 1 / 8 | 107× | 9.29e-3 | 6.56e-2 |
| MAPK1 (ERK2) activation | Reactome | 1 / 9 | 95.3× | 1.04e-2 | 7.05e-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 ⇵ |
|---|---|---|---|---|---|
| gene expression | GO:0010467 | 4 / 269 | 19.8× | 3.75e-5 | 1.45e-3 ✓ sig. |
| positive regulation of transcription by RNA polymerase II | GO:0045944 | 6 / 1,208 | 6.6× | 1.38e-4 | 3.84e-3 ✓ sig. |
| positive regulation of DNA-templated transcription | GO:0045893 | 5 / 778 | 8.6× | 1.81e-4 | 4.71e-3 ✓ sig. |
| bone morphogenesis | GO:0060349 | 2 / 32 | 83.4× | 2.55e-4 | 5.99e-3 ✓ sig. |
| platelet-derived growth factor receptor signaling pathway | GO:0048008 | 2 / 33 | 80.9× | 2.72e-4 | 6.26e-3 ✓ sig. |
| positive regulation of cell cycle | GO:0045787 | 2 / 44 | 60.7× | 4.84e-4 | 9.34e-3 ✓ sig. |
| negative regulation of developmental growth | GO:0048640 | 1 / 1 | 1,335× | 7.49e-4 | 1.25e-2 ✓ sig. |
| positive regulation of mast cell activation by Fc-epsilon receptor signaling pathway | GO:0038097 | 1 / 1 | 1,335× | 7.49e-4 | 1.25e-2 ✓ sig. |
| cell proliferation involved in heart valve development | GO:2000793 | 1 / 1 | 1,335× | 7.49e-4 | 1.25e-2 ✓ sig. |
| positive regulation of endocardial cushion to mesenchymal transition involved in heart valve formation | GO:2000802 | 1 / 1 | 1,335× | 7.49e-4 | 1.25e-2 ✓ sig. |
| negative regulation of cortisol secretion | GO:0051463 | 1 / 1 | 1,335× | 7.49e-4 | 1.25e-2 ✓ sig. |
| negative regulation of growth hormone secretion | GO:0060125 | 1 / 1 | 1,335× | 7.49e-4 | 1.25e-2 ✓ sig. |
| intestinal epithelial cell migration | GO:0061582 | 1 / 1 | 1,335× | 7.49e-4 | 1.25e-2 ✓ sig. |
| embryonic digit morphogenesis | GO:0042733 | 2 / 57 | 46.8× | 8.12e-4 | 1.31e-2 ✓ sig. |
| fibroblast growth factor receptor signaling pathway | GO:0008543 | 2 / 60 | 44.5× | 9.00e-4 | 1.41e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Brachycephaly | Coronal craniosynostosis | 0.273 | 3 | 1.97e-10 | 2.03e-9 ✓ sig. |
| Sweeney-cox syndrome | TWIST1-related craniosynostosis | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Coronal craniosynostosis | Sweeney-cox syndrome | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |
| Coronal craniosynostosis | TCF12-related craniosynostosis | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |
| Coronal craniosynostosis | TWIST1-related craniosynostosis | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |
| Extraskeletal myxoid chondrosarcoma | TCF12-related craniosynostosis | 0.167 | 1 | 3.25e-4 | 7.58e-4 ✓ sig. |
| Binocular vision disease | Brachycephaly | 0.091 | 1 | 6.49e-4 | 1.22e-3 ✓ sig. |
| Brachycephaly | Sweeney-cox syndrome | 0.091 | 1 | 6.49e-4 | 1.22e-3 ✓ sig. |
| Brachycephaly | TCF12-related craniosynostosis | 0.091 | 1 | 6.49e-4 | 1.22e-3 ✓ sig. |
| Brachycephaly | TWIST1-related craniosynostosis | 0.091 | 1 | 6.49e-4 | 1.22e-3 ✓ sig. |
| Coronal craniosynostosis | Extraskeletal myxoid chondrosarcoma | 0.125 | 1 | 9.74e-4 | 1.64e-3 ✓ sig. |