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 307
6
Diseases
9
Unique genes
0.393
Avg. similarity score
Bethlem myopathy
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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Bethlem myopathy
Collagen vi muscular dystrophy
Collagen vi-related myopathy
Ullrich congenital muscular dystrophy
collagen 6-related myopathy
dystonia 27
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Bethlem myopathy | 5 | 5 | 6 |
| Collagen vi muscular dystrophy | 5 | 5 | 3 |
| Collagen vi-related myopathy | 5 | 5 | 6 |
| Ullrich congenital muscular dystrophy | 5 | 5 | 4 |
| collagen 6-related myopathy | 5 | 5 | 3 |
| dystonia 27 | 5 | 5 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| COL6A3 | 6 / 6 | Bethlem myopathy, collagen 6-related myopathy, Collagen vi muscular dystrophy, Collagen vi-related myopathy and 2 more |
| COL6A1 | 5 / 6 | Bethlem myopathy, collagen 6-related myopathy, Collagen vi muscular dystrophy, Collagen vi-related myopathy and 1 more |
| COL6A2 | 5 / 6 | Bethlem myopathy, collagen 6-related myopathy, Collagen vi muscular dystrophy, Collagen vi-related myopathy and 1 more |
| COL12A1 | 2 / 6 | Bethlem myopathy, Ullrich congenital muscular dystrophy |
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 ⇵ |
|---|---|---|---|---|---|
| Collagen chain trimerization | Reactome | 7 / 44 | 212× | 1.92e-16 | 8.42e-14 ✓ sig. |
| Assembly of collagen fibrils and other multimeric structures | Reactome | 7 / 51 | 183× | 5.80e-16 | 2.34e-13 ✓ sig. |
| Collagen degradation | Reactome | 7 / 52 | 180× | 6.70e-16 | 2.66e-13 ✓ sig. |
| NCAM1 interactions | Reactome | 6 / 21 | 381× | 1.09e-15 | 4.21e-13 ✓ sig. |
| Collagen biosynthesis and modifying enzymes | Reactome | 7 / 67 | 139× | 4.35e-15 | 1.49e-12 ✓ sig. |
| Signaling by PDGF | Reactome | 6 / 33 | 243× | 2.22e-14 | 6.44e-12 ✓ sig. |
| Protein digestion and absorption | KEGG | 7 / 103 | 90.7× | 9.85e-14 | 2.53e-11 ✓ sig. |
| Integrin cell surface interactions | Reactome | 6 / 81 | 98.8× | 6.44e-12 | 1.20e-9 ✓ sig. |
| ECM-receptor interaction | KEGG | 6 / 89 | 90.0× | 1.15e-11 | 2.03e-9 ✓ sig. |
| Cytoskeleton in muscle cells | KEGG | 7 / 232 | 40.3× | 3.20e-11 | 5.15e-9 ✓ sig. |
| Focal adhesion | KEGG | 6 / 203 | 39.4× | 1.74e-9 | 1.82e-7 ✓ sig. |
| Human papillomavirus infection | KEGG | 6 / 333 | 24.0× | 3.40e-8 | 2.55e-6 ✓ sig. |
| PI3K-Akt signaling pathway | KEGG | 6 / 361 | 22.2× | 5.51e-8 | 3.89e-6 ✓ sig. |
| Extracellular matrix organization | Reactome | 3 / 15 | 267× | 1.32e-7 | 8.31e-6 ✓ sig. |
| Anchoring fibril formation | Reactome | 3 / 15 | 267× | 1.32e-7 | 8.31e-6 ✓ 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 ⇵ |
|---|---|---|---|---|---|
| muscle cell apoptotic process | GO:0010657 | 2 / 2 | 2,076× | 2.06e-7 | 2.23e-5 ✓ sig. |
| response to UV | GO:0009411 | 3 / 54 | 115× | 1.89e-6 | 1.38e-4 ✓ sig. |
| cell adhesion | GO:0007155 | 5 / 665 | 15.6× | 6.29e-6 | 3.60e-4 ✓ sig. |
| glomerular basement membrane development | GO:0032836 | 2 / 10 | 415× | 9.26e-6 | 4.92e-4 ✓ sig. |
| phosphatidylinositol 3-kinase/protein kinase B signal transduction | GO:0043491 | 3 / 92 | 67.7× | 9.49e-6 | 5.02e-4 ✓ sig. |
| neuron apoptotic process | GO:0051402 | 3 / 98 | 63.6× | 1.15e-5 | 5.80e-4 ✓ sig. |
| collagen-activated tyrosine kinase receptor signaling pathway | GO:0038063 | 2 / 12 | 346× | 1.36e-5 | 6.62e-4 ✓ sig. |
| muscle organ development | GO:0007517 | 3 / 114 | 54.6× | 1.81e-5 | 8.29e-4 ✓ sig. |
| nuclear envelope organization | GO:0006998 | 2 / 24 | 173× | 5.66e-5 | 1.97e-3 ✓ sig. |
| endodermal cell differentiation | GO:0035987 | 2 / 36 | 115× | 1.29e-4 | 3.66e-3 ✓ sig. |
| tissue development | GO:0009888 | 2 / 51 | 81.4× | 2.60e-4 | 6.08e-3 ✓ sig. |
| collagen fibril organization | GO:0030199 | 2 / 65 | 63.9× | 4.22e-4 | 8.54e-3 ✓ sig. |
| response to glucose | GO:0009749 | 2 / 68 | 61.1× | 4.62e-4 | 9.07e-3 ✓ sig. |
| response to polyamine macromolecule | GO:1904583 | 1 / 1 | 2,076× | 4.82e-4 | 9.31e-3 ✓ sig. |
| regulation of excitatory postsynaptic membrane potential involved in skeletal muscle contraction | GO:0014853 | 1 / 1 | 2,076× | 4.82e-4 | 9.31e-3 ✓ sig. |