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 344
6
Diseases
11
Unique genes
0.219
Avg. similarity score
Tooth abnormalities
Most-connected disease (4 links)
Disease
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
click a node to select it and show its pairs below (double-click or Ctrl/⌘-click opens the disease page) ·
drag a node to pin it in place · scroll/pinch to zoom.
Tooth abnormalities
cenani-lenz syndactyly syndrome
congenital myasthenic syndrome 17
Sclerosteosis
Ehlers-Danlos syndrome, spondylocheirodysplastic type
Ulnar-mammary syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Tooth abnormalities | 4 | 4 | 10 |
| cenani-lenz syndactyly syndrome | 3 | 3 | 1 |
| congenital myasthenic syndrome 17 | 3 | 3 | 1 |
| Sclerosteosis | 2 | 2 | 2 |
| Ehlers-Danlos syndrome, spondylocheirodysplastic type | 1 | 1 | 1 |
| Ulnar-mammary syndrome | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| LRP4 | 4 / 6 | cenani-lenz syndactyly syndrome, congenital myasthenic syndrome 17, Sclerosteosis, Tooth abnormalities |
| SLC39A13 | 2 / 6 | Ehlers-Danlos syndrome, spondylocheirodysplastic type, Tooth abnormalities |
| TBX3 | 2 / 6 | Tooth abnormalities, Ulnar-mammary 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)
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| animal organ morphogenesis | GO:0009887 | 5 / 130 | 65.3× | 6.74e-9 | 1.22e-6 ✓ sig. |
| embryonic hindlimb morphogenesis | GO:0035116 | 3 / 29 | 176× | 5.50e-7 | 5.07e-5 ✓ sig. |
| pituitary gland development | GO:0021983 | 3 / 30 | 170× | 6.11e-7 | 5.54e-5 ✓ sig. |
| embryonic forelimb morphogenesis | GO:0035115 | 3 / 33 | 154× | 8.20e-7 | 7.06e-5 ✓ sig. |
| odontogenesis | GO:0042476 | 3 / 36 | 142× | 1.07e-6 | 8.76e-5 ✓ sig. |
| positive regulation of cell cycle | GO:0045787 | 3 / 44 | 116× | 1.98e-6 | 1.43e-4 ✓ sig. |
| bone mineralization | GO:0030282 | 3 / 56 | 91.0× | 4.14e-6 | 2.58e-4 ✓ sig. |
| odontogenesis of dentin-containing tooth | GO:0042475 | 3 / 56 | 91.0× | 4.14e-6 | 2.58e-4 ✓ sig. |
| embryonic digit morphogenesis | GO:0042733 | 3 / 57 | 89.4× | 4.36e-6 | 2.69e-4 ✓ sig. |
| lacrimal gland development | GO:0032808 | 2 / 7 | 485× | 6.60e-6 | 3.74e-4 ✓ sig. |
| in utero embryonic development | GO:0001701 | 4 / 252 | 27.0× | 9.89e-6 | 5.18e-4 ✓ sig. |
| response to sodium phosphate | GO:1904383 | 2 / 9 | 378× | 1.13e-5 | 5.73e-4 ✓ sig. |
| iris morphogenesis | GO:0061072 | 2 / 9 | 378× | 1.13e-5 | 5.73e-4 ✓ sig. |
| BMP signaling pathway | GO:0030509 | 3 / 88 | 57.9× | 1.62e-5 | 7.64e-4 ✓ sig. |
| positive regulation of transcription by RNA polymerase II | GO:0045944 | 6 / 1,208 | 8.4× | 2.51e-5 | 1.07e-3 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| cenani-lenz syndactyly syndrome | congenital myasthenic syndrome 17 | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| cenani-lenz syndactyly syndrome | Sclerosteosis | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| congenital myasthenic syndrome 17 | Sclerosteosis | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| cenani-lenz syndactyly syndrome | Tooth abnormalities | 0.091 | 1 | 6.49e-4 | 1.22e-3 ✓ sig. |
| congenital myasthenic syndrome 17 | Tooth abnormalities | 0.091 | 1 | 6.49e-4 | 1.22e-3 ✓ sig. |
| Ehlers-Danlos syndrome, spondylocheirodysplastic type | Tooth abnormalities | 0.091 | 1 | 6.49e-4 | 1.22e-3 ✓ sig. |
| Tooth abnormalities | Ulnar-mammary syndrome | 0.091 | 1 | 6.49e-4 | 1.22e-3 ✓ sig. |