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 393

5 diseases · 10 shared-gene connections
5 Diseases
6 Unique genes
0.422 Avg. similarity score
Bethlem myopathy Most-connected disease (4 links)
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Disease Searched: dystonia 27 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.

Member diseases (most connected first ‐ the cluster's core)

Disease ⇵ Connections in cluster ⇵ Significant partners ⇵ Curated genes ⇵
Bethlem myopathy 4 4 6
Collagen vi muscular dystrophy 4 4 3
Ullrich congenital muscular dystrophy 4 4 4
collagen 6-related myopathy 4 4 3
dystonia 27 4 4 1

Top shared genes (genes linked to 2+ member diseases)

Gene ⇵ Member diseases ⇵ Linked diseases
COL6A3 5 / 5 Bethlem myopathy, collagen 6-related myopathy, Collagen vi muscular dystrophy, dystonia 27 and 1 more
COL6A1 4 / 5 Bethlem myopathy, collagen 6-related myopathy, Collagen vi muscular dystrophy, Ullrich congenital muscular dystrophy
COL6A2 4 / 5 Bethlem myopathy, collagen 6-related myopathy, Collagen vi muscular dystrophy, Ullrich congenital muscular dystrophy
COL12A1 2 / 5 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
COL12A1, COL6A1, COL6A2, COL6A3
 Reactome 4 / 44 182× 2.34e-9 2.50e-7 ✓ sig.
Assembly of collagen fibrils and other multimeric structures
COL12A1, COL6A1, COL6A2, COL6A3
 Reactome 4 / 51 157× 4.30e-9 4.36e-7 ✓ sig.
Collagen degradation
COL12A1, COL6A1, COL6A2, COL6A3
 Reactome 4 / 52 154× 4.66e-9 4.69e-7 ✓ sig.
Collagen biosynthesis and modifying enzymes
COL12A1, COL6A1, COL6A2, COL6A3
 Reactome 4 / 67 120× 1.32e-8 1.16e-6 ✓ sig.
Protein digestion and absorption
COL12A1, COL6A1, COL6A2, COL6A3
 KEGG 4 / 103 77.7× 7.55e-8 5.47e-6 ✓ sig.
NCAM1 interactions
COL6A1, COL6A2, COL6A3
 Reactome 3 / 21 286× 9.18e-8 6.55e-6 ✓ sig.
Signaling by PDGF
COL6A1, COL6A2, COL6A3
 Reactome 3 / 33 182× 3.76e-7 2.23e-5 ✓ sig.
ECM proteoglycans
COL6A1, COL6A2, COL6A3
 Reactome 3 / 51 118× 1.43e-6 7.17e-5 ✓ sig.
Cytoskeleton in muscle cells
COL6A1, COL6A2, COL6A3, LMNA
 KEGG 4 / 232 34.5× 1.97e-6 9.37e-5 ✓ sig.
Integrin cell surface interactions
COL6A1, COL6A2, COL6A3
 Reactome 3 / 81 74.1× 5.83e-6 2.29e-4 ✓ sig.
ECM-receptor interaction
COL6A1, COL6A2, COL6A3
 KEGG 3 / 89 67.5× 7.74e-6 2.89e-4 ✓ sig.
Focal adhesion
COL6A1, COL6A2, COL6A3
 KEGG 3 / 203 29.6× 9.17e-5 2.16e-3 ✓ sig.
Human papillomavirus infection
COL6A1, COL6A2, COL6A3
 KEGG 3 / 333 18.0× 3.97e-4 6.91e-3 ✓ sig.
PI3K-Akt signaling pathway
COL6A1, COL6A2, COL6A3
 KEGG 3 / 361 16.6× 5.03e-4 8.31e-3 ✓ sig.
Breakdown of the nuclear lamina
LMNA
 Reactome 1 / 3 667× 1.50e-3 1.92e-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 ⇵
muscle cell apoptotic process
COL6A1, DMPK
 GO:0010657 2 / 2 3,115× 8.59e-8 1.08e-5 ✓ sig.
response to UV
COL6A1, COL6A2, COL6A3
 GO:0009411 3 / 54 173× 4.53e-7 4.42e-5 ✓ sig.
phosphatidylinositol 3-kinase/protein kinase B signal transduction
COL6A1, COL6A2, COL6A3
 GO:0043491 3 / 92 102× 2.29e-6 1.66e-4 ✓ sig.
neuron apoptotic process
COL6A1, COL6A2, COL6A3
 GO:0051402 3 / 98 95.3× 2.77e-6 1.93e-4 ✓ sig.
muscle organ development
COL6A1, COL6A3, LMNA
 GO:0007517 3 / 114 82.0× 4.36e-6 2.77e-4 ✓ sig.
cell adhesion
COL12A1, COL6A1, COL6A2, COL6A3
 GO:0007155 4 / 665 18.7× 2.25e-5 1.02e-3 ✓ sig.
nuclear envelope organization
DMPK, LMNA
 GO:0006998 2 / 24 260× 2.36e-5 1.05e-3 ✓ sig.
endodermal cell differentiation
COL12A1, COL6A1
 GO:0035987 2 / 36 173× 5.39e-5 1.97e-3 ✓ sig.
tissue development
COL12A1, COL6A1
 GO:0009888 2 / 51 122× 1.09e-4 3.33e-3 ✓ sig.
collagen fibril organization
COL12A1, COL6A1
 GO:0030199 2 / 65 95.8× 1.77e-4 4.78e-3 ✓ sig.
response to glucose
COL6A2, COL6A3
 GO:0009749 2 / 68 91.6× 1.94e-4 5.11e-3 ✓ sig.
response to polyamine macromolecule
COL6A1
 GO:1904583 1 / 1 3,115× 3.21e-4 7.28e-3 ✓ sig.
regulation of excitatory postsynaptic membrane potential involved in skeletal muscle contraction
DMPK
 GO:0014853 1 / 1 3,115× 3.21e-4 7.28e-3 ✓ sig.
DNA double-strand break attachment to nuclear envelope
LMNA
 GO:1990683 1 / 2 1,557× 6.42e-4 1.16e-2 ✓ sig.
multicellular organismal locomotion
COL6A1
 GO:0071965 1 / 2 1,557× 6.42e-4 1.16e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Bethlem myopathy Ullrich congenital muscular dystrophy 0.571 4 6.41e-15 9.10e-14 ✓ sig.
collagen 6-related myopathy Collagen vi muscular dystrophy 0.750 3 1.64e-12 1.92e-11 ✓ sig.
collagen 6-related myopathy Ullrich congenital muscular dystrophy 0.600 3 6.58e-12 7.30e-11 ✓ sig.
Collagen vi muscular dystrophy Ullrich congenital muscular dystrophy 0.600 3 6.58e-12 7.30e-11 ✓ sig.
Bethlem myopathy Collagen vi muscular dystrophy 0.429 3 3.29e-11 3.41e-10 ✓ sig.
Bethlem myopathy collagen 6-related myopathy 0.429 3 3.29e-11 3.41e-10 ✓ sig.
collagen 6-related myopathy dystonia 27 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Collagen vi muscular dystrophy dystonia 27 0.250 1 1.95e-4 5.35e-4 ✓ sig.
dystonia 27 Ullrich congenital muscular dystrophy 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Bethlem myopathy dystonia 27 0.143 1 3.90e-4 8.67e-4 ✓ sig.