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 398
5
Diseases
17
Unique genes
0.197
Avg. similarity score
Arachnodactyly
Most-connected disease (4 links)
Disease
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Arachnodactyly
Byzanthine arch palate
Ck syndrome
Congenital hemidysplasia with ichthyosiform erythroderma and limb defects
Perisylvian polymicrogyria
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Arachnodactyly | 4 | 4 | 5 |
| Byzanthine arch palate | 4 | 4 | 13 |
| Ck syndrome | 4 | 4 | 1 |
| Congenital hemidysplasia with ichthyosiform erythroderma and limb defects | 4 | 4 | 1 |
| Perisylvian polymicrogyria | 4 | 4 | 2 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| NSDHL | 5 / 5 | Arachnodactyly, Byzanthine arch palate, Ck syndrome, Congenital hemidysplasia with ichthyosiform erythroderma and limb defects and 1 more |
| FBN1 | 2 / 5 | Arachnodactyly, Byzanthine arch 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 ⇵ |
|---|---|---|---|---|---|
| Gastric cancer | KEGG | 4 / 150 | 18.8× | 4.90e-5 | 1.26e-3 ✓ sig. |
| Proteoglycans in cancer | KEGG | 4 / 204 | 13.9× | 1.62e-4 | 3.31e-3 ✓ sig. |
| Pathways in cancer | KEGG | 5 / 533 | 6.6× | 6.70e-4 | 1.00e-2 ✓ sig. |
| Yersinia infection | KEGG | 3 / 138 | 15.4× | 8.97e-4 | 1.25e-2 ✓ sig. |
| Signaling pathways regulating pluripotency of stem cells | KEGG | 3 / 144 | 14.7× | 1.01e-3 | 1.37e-2 ✓ sig. |
| Molecules associated with elastic fibres | Reactome | 2 / 38 | 37.2× | 1.29e-3 | 1.64e-2 ✓ sig. |
| Signaling by FGFR2 amplification mutants | Reactome | 1 / 1 | 706× | 1.42e-3 | 1.76e-2 ✓ sig. |
| Signaling by FGFR2 fusions | Reactome | 1 / 1 | 706× | 1.42e-3 | 1.76e-2 ✓ sig. |
| Human immunodeficiency virus 1 infection | KEGG | 3 / 213 | 10.0× | 3.11e-3 | 3.16e-2 ✓ sig. |
| VEGF signaling pathway | KEGG | 2 / 60 | 23.5× | 3.18e-3 | 3.21e-2 ✓ sig. |
| Basal cell carcinoma | KEGG | 2 / 63 | 22.4× | 3.50e-3 | 3.43e-2 ✓ sig. |
| Regulation of actin cytoskeleton | KEGG | 3 / 232 | 9.1× | 3.96e-3 | 3.75e-2 ✓ sig. |
| Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors | Reactome | 1 / 3 | 235× | 4.24e-3 | 3.93e-2 ✓ sig. |
| Central carbon metabolism in cancer | KEGG | 2 / 71 | 19.9× | 4.43e-3 | 4.04e-2 ✓ sig. |
| EGFR tyrosine kinase inhibitor resistance | KEGG | 2 / 80 | 17.7× | 5.59e-3 | 4.71e-2 ✓ 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 ⇵ |
|---|---|---|---|---|---|
| post-embryonic eye morphogenesis | GO:0048050 | 2 / 3 | 733× | 2.34e-6 | 1.63e-4 ✓ sig. |
| prostate epithelial cord elongation | GO:0060523 | 2 / 3 | 733× | 2.34e-6 | 1.63e-4 ✓ sig. |
| peptidyl-tyrosine phosphorylation | GO:0018108 | 3 / 39 | 84.6× | 5.60e-6 | 3.28e-4 ✓ sig. |
| epithelial cell proliferation involved in salivary gland morphogenesis | GO:0060664 | 2 / 5 | 440× | 7.78e-6 | 4.28e-4 ✓ sig. |
| mesenchymal cell proliferation involved in lung development | GO:0060916 | 2 / 5 | 440× | 7.78e-6 | 4.28e-4 ✓ sig. |
| branching involved in prostate gland morphogenesis | GO:0060442 | 2 / 6 | 366× | 1.17e-5 | 5.87e-4 ✓ sig. |
| regulation of cell differentiation | GO:0045595 | 3 / 54 | 61.1× | 1.51e-5 | 7.21e-4 ✓ sig. |
| lung lobe morphogenesis | GO:0060463 | 2 / 8 | 275× | 2.17e-5 | 9.59e-4 ✓ sig. |
| limb bud formation | GO:0060174 | 2 / 9 | 244× | 2.79e-5 | 1.16e-3 ✓ sig. |
| lung-associated mesenchyme development | GO:0060484 | 2 / 9 | 244× | 2.79e-5 | 1.16e-3 ✓ sig. |
| camera-type eye development | GO:0043010 | 3 / 74 | 44.6× | 3.90e-5 | 1.49e-3 ✓ sig. |
| embryonic eye morphogenesis | GO:0048048 | 2 / 11 | 200× | 4.26e-5 | 1.60e-3 ✓ sig. |
| branching involved in salivary gland morphogenesis | GO:0060445 | 2 / 12 | 183× | 5.11e-5 | 1.83e-3 ✓ sig. |
| regulation of osteoblast differentiation | GO:0045667 | 2 / 17 | 129× | 1.05e-4 | 3.14e-3 ✓ sig. |
| angiogenesis | GO:0001525 | 4 / 284 | 15.5× | 1.06e-4 | 3.17e-3 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Arachnodactyly | Byzanthine arch palate | 0.118 | 2 | 6.57e-6 | 3.53e-5 ✓ sig. |
| Ck syndrome | Congenital hemidysplasia with ichthyosiform erythroderma and limb defects | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Ck syndrome | Perisylvian polymicrogyria | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Congenital hemidysplasia with ichthyosiform erythroderma and limb defects | Perisylvian polymicrogyria | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Arachnodactyly | Ck syndrome | 0.167 | 1 | 3.25e-4 | 7.58e-4 ✓ sig. |
| Arachnodactyly | Congenital hemidysplasia with ichthyosiform erythroderma and limb defects | 0.167 | 1 | 3.25e-4 | 7.58e-4 ✓ sig. |
| Arachnodactyly | Perisylvian polymicrogyria | 0.143 | 1 | 6.49e-4 | 1.22e-3 ✓ sig. |
| Byzanthine arch palate | Ck syndrome | 0.071 | 1 | 8.44e-4 | 1.48e-3 ✓ sig. |
| Byzanthine arch palate | Congenital hemidysplasia with ichthyosiform erythroderma and limb defects | 0.071 | 1 | 8.44e-4 | 1.48e-3 ✓ sig. |
| Byzanthine arch palate | Perisylvian polymicrogyria | 0.067 | 1 | 1.69e-3 | 2.51e-3 ✓ sig. |