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 640
5
Diseases
4
Unique genes
0.357
Avg. similarity score
Mandibuloacral dysostosis
Most-connected disease (4 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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Mandibuloacral dysostosis
Mandibuloacral dysplasia
Obsolete lethal restrictive dermopathy
Restrictive dermopathy
Tight skin contracture syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Mandibuloacral dysostosis | 4 | 4 | 3 |
| Mandibuloacral dysplasia | 4 | 4 | 4 |
| Obsolete lethal restrictive dermopathy | 4 | 4 | 1 |
| Restrictive dermopathy | 4 | 4 | 2 |
| Tight skin contracture syndrome | 4 | 4 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| ZMPSTE24 | 5 / 5 | Mandibuloacral dysostosis, Mandibuloacral dysplasia, Obsolete lethal restrictive dermopathy, Restrictive dermopathy and 1 more |
| LMNA | 3 / 5 | Mandibuloacral dysostosis, Mandibuloacral dysplasia, Restrictive dermopathy |
| MTX2 | 2 / 5 | Mandibuloacral dysostosis, Mandibuloacral dysplasia |
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 ⇵ |
|---|---|---|---|---|---|
| Breakdown of the nuclear lamina | Reactome | 1 / 3 | 1,001× | 9.99e-4 | 1.13e-2 ✓ sig. |
| Nuclear Envelope Breakdown | Reactome | 1 / 9 | 334× | 2.99e-3 | 2.54e-2 ✓ sig. |
| Depolymerisation of the Nuclear Lamina | Reactome | 1 / 15 | 200× | 4.99e-3 | 3.64e-2 ✓ sig. |
| Initiation of Nuclear Envelope (NE) Reformation | Reactome | 1 / 19 | 158× | 6.31e-3 | 4.25e-2 ✓ sig. |
| Terpenoid backbone biosynthesis | KEGG | 1 / 23 | 131× | 7.64e-3 | 4.80e-2 ✓ sig. |
| Activation of Matrix Metalloproteinases | Reactome | 1 / 33 | 91.0× | 1.09e-2 | 6.01e-2 |
| Signaling by SCF-KIT | Reactome | 1 / 37 | 81.1× | 1.23e-2 | 6.45e-2 |
| Bladder cancer | KEGG | 1 / 41 | 73.2× | 1.36e-2 | 6.85e-2 |
| XBP1(S) activates chaperone genes | Reactome | 1 / 50 | 60.1× | 1.66e-2 | 7.67e-2 |
| EPH-ephrin mediated repulsion of cells | Reactome | 1 / 50 | 60.1× | 1.66e-2 | 7.67e-2 |
| Assembly of collagen fibrils and other multimeric structures | Reactome | 1 / 51 | 58.9× | 1.69e-2 | 7.78e-2 |
| Collagen degradation | Reactome | 1 / 52 | 57.7× | 1.72e-2 | 7.87e-2 |
| Extra-nuclear estrogen signaling | Reactome | 1 / 58 | 51.8× | 1.92e-2 | 8.36e-2 |
| Signaling by BRAF and RAF fusions | Reactome | 1 / 67 | 44.8× | 2.21e-2 | 9.09e-2 |
| Degradation of the extracellular matrix | Reactome | 1 / 70 | 42.9× | 2.31e-2 | 9.31e-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 ⇵ |
|---|---|---|---|---|---|
| nuclear envelope organization | GO:0006998 | 2 / 24 | 389× | 9.47e-6 | 5.21e-4 ✓ sig. |
| nucleus organization | GO:0006997 | 2 / 34 | 275× | 1.92e-5 | 8.98e-4 ✓ sig. |
| negative regulation of cation transmembrane transport | GO:1904063 | 1 / 1 | 4,672× | 2.14e-4 | 5.31e-3 ✓ sig. |
| negative regulation of epithelial cell differentiation involved in kidney development | GO:2000697 | 1 / 1 | 4,672× | 2.14e-4 | 5.31e-3 ✓ sig. |
| regulation of stress-activated protein kinase signaling cascade | GO:0070302 | 1 / 1 | 4,672× | 2.14e-4 | 5.31e-3 ✓ sig. |
| regulation of mitotic cell cycle DNA replication | GO:1903463 | 1 / 1 | 4,672× | 2.14e-4 | 5.31e-3 ✓ sig. |
| regulation of termination of RNA polymerase I transcription | GO:2000730 | 1 / 1 | 4,672× | 2.14e-4 | 5.31e-3 ✓ sig. |
| inflammatory cell apoptotic process | GO:0006925 | 1 / 2 | 2,336× | 4.28e-4 | 8.53e-3 ✓ sig. |
| DNA double-strand break attachment to nuclear envelope | GO:1990683 | 1 / 2 | 2,336× | 4.28e-4 | 8.53e-3 ✓ sig. |
| maintenance of rDNA | GO:0043007 | 1 / 2 | 2,336× | 4.28e-4 | 8.53e-3 ✓ sig. |
| response to DNA damage checkpoint signaling | GO:0072423 | 1 / 2 | 2,336× | 4.28e-4 | 8.53e-3 ✓ sig. |
| calcium ion import into sarcoplasmic reticulum | GO:1990036 | 1 / 3 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| negative regulation of miRNA processing | GO:1903799 | 1 / 3 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| regulation of fibroblast proliferation | GO:0048145 | 1 / 3 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| CAAX-box protein processing | GO:0071586 | 1 / 3 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Mandibuloacral dysostosis | Mandibuloacral dysplasia | 0.600 | 3 | 6.46e-12 | 6.55e-11 ✓ sig. |
| Mandibuloacral dysostosis | Restrictive dermopathy | 0.500 | 2 | 2.50e-8 | 1.87e-7 ✓ sig. |
| Mandibuloacral dysplasia | Restrictive dermopathy | 0.400 | 2 | 5.00e-8 | 3.63e-7 ✓ sig. |
| Obsolete lethal restrictive dermopathy | Tight skin contracture syndrome | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Obsolete lethal restrictive dermopathy | Restrictive dermopathy | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Restrictive dermopathy | Tight skin contracture syndrome | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Mandibuloacral dysostosis | Obsolete lethal restrictive dermopathy | 0.250 | 1 | 1.94e-4 | 4.41e-4 ✓ sig. |
| Mandibuloacral dysostosis | Tight skin contracture syndrome | 0.250 | 1 | 1.94e-4 | 4.41e-4 ✓ sig. |
| Mandibuloacral dysplasia | Obsolete lethal restrictive dermopathy | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |
| Mandibuloacral dysplasia | Tight skin contracture syndrome | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |