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 310

6 diseases · 12 shared-gene connections
6 Diseases
15 Unique genes
0.224 Avg. similarity score
Distal myopathy Most-connected disease (5 links)
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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.

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

Disease ⇵ Connections in cluster ⇵ Significant partners ⇵ Curated genes ⇵
Distal myopathy 5 5 14
Vitelliform macular dystrophy 5 5 5
Benign concentric annular macular dystrophy 4 4 1
IMPG1-related dominant retinopathy 4 4 1
IMPG1-related recessive retinopathy 4 4 1
IMPG2-related recessive retinopathy 2 2 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
IMPG1 5 / 6 Benign concentric annular macular dystrophy, Distal myopathy, IMPG1-related dominant retinopathy, IMPG1-related recessive retinopathy and 1 more
IMPG2 3 / 6 Distal myopathy, IMPG2-related recessive retinopathy, Vitelliform macular dystrophy
BEST1 2 / 6 Distal myopathy, Vitelliform macular dystrophy
PRPH2 2 / 6 Distal myopathy, Vitelliform macular 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 ⇵
Hypertrophic cardiomyopathy
MYH7, TTN, CAV3
 KEGG 3 / 99 24.3× 2.30e-4 4.37e-3 ✓ sig.
Dilated cardiomyopathy
MYH7, TTN, CAV3
 KEGG 3 / 105 22.9× 2.74e-4 4.99e-3 ✓ sig.
Smooth Muscle Contraction
DYSF, CAV3
 Reactome 2 / 34 47.1× 7.98e-4 1.15e-2 ✓ sig.
Defective GNE causes sialuria, Nonaka myopathy and inclusion body myopathy 2
GNE
 Reactome 1 / 1 801× 1.25e-3 1.60e-2 ✓ sig.
Cytoskeleton in muscle cells
MYH7, TTN, FLNC
 KEGG 3 / 232 10.4× 2.73e-3 2.88e-2 ✓ sig.
Viral myocarditis
MYH7, CAV3
 KEGG 2 / 70 22.9× 3.35e-3 3.33e-2 ✓ sig.
Mitophagy - animal
VCP, SQSTM1
 KEGG 2 / 105 15.3× 7.38e-3 5.67e-2
Amyotrophic lateral sclerosis
VCP, MATR3, SQSTM1
 KEGG 3 / 368 6.5× 9.87e-3 6.81e-2
Pexophagy
SQSTM1
 Reactome 1 / 10 80.1× 1.24e-2 7.78e-2
Fluid shear stress and atherosclerosis
SQSTM1, CAV3
 KEGG 2 / 141 11.4× 1.30e-2 7.97e-2
HSF1 activation
VCP
 Reactome 1 / 12 66.7× 1.49e-2 8.66e-2
Cell-extracellular matrix interactions
FLNC
 Reactome 1 / 12 66.7× 1.49e-2 8.66e-2
Josephin domain DUBs
VCP
 Reactome 1 / 12 66.7× 1.49e-2 8.66e-2
p75NTR recruits signalling complexes
SQSTM1
 Reactome 1 / 13 61.6× 1.61e-2 9.11e-2
NF-kB is activated and signals survival
SQSTM1
 Reactome 1 / 13 61.6× 1.61e-2 9.11e-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 ⇵
detection of muscle stretch
TTN, CAV3
 GO:0035995 2 / 7 356× 1.26e-5 6.25e-4 ✓ sig.
visual perception
BEST1, IMPG1, IMPG2, PRPH2
 GO:0007601 4 / 215 23.2× 2.11e-5 9.36e-4 ✓ sig.
cardiac muscle hypertrophy
TTN, CAV3
 GO:0003300 2 / 13 192× 4.67e-5 1.71e-3 ✓ sig.
muscle filament sliding
MYH7, TTN
 GO:0030049 2 / 15 166× 6.28e-5 2.13e-3 ✓ sig.
detection of light stimulus involved in visual perception
BEST1, PRPH2
 GO:0050908 2 / 24 104× 1.64e-4 4.39e-3 ✓ sig.
striated muscle contraction
MYH7, TTN
 GO:0006941 2 / 24 104× 1.64e-4 4.39e-3 ✓ sig.
cardiac muscle cell development
TTN, CAV3
 GO:0055013 2 / 25 99.7× 1.79e-4 4.67e-3 ✓ sig.
regulation of calcium ion transport
BEST1, CAV3
 GO:0051924 2 / 25 99.7× 1.79e-4 4.67e-3 ✓ sig.
positive regulation of ubiquitin-dependent protein catabolic process
VCP, CAV3
 GO:2000060 2 / 30 83.1× 2.58e-4 6.05e-3 ✓ sig.
skeletal muscle contraction
MYH7, TTN
 GO:0003009 2 / 32 77.9× 2.94e-4 6.62e-3 ✓ sig.
ATP metabolic process
VCP, MYH7
 GO:0046034 2 / 36 69.2× 3.73e-4 7.80e-3 ✓ sig.
regulation of heart rate
MYH7, CAV3
 GO:0002027 2 / 39 63.9× 4.38e-4 8.72e-3 ✓ sig.
intracellular protein localization
IMPG2, SQSTM1, CAV3
 GO:0008104 3 / 194 19.3× 4.57e-4 8.99e-3 ✓ sig.
cardiac muscle contraction
MYH7, TTN
 GO:0060048 2 / 43 57.9× 5.33e-4 9.98e-3 ✓ sig.
sarcomere organization
TTN, FLNC
 GO:0045214 2 / 43 57.9× 5.33e-4 9.98e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Distal myopathy Vitelliform macular dystrophy 0.250 4 2.14e-12 2.61e-11 ✓ sig.
Benign concentric annular macular dystrophy IMPG1-related dominant retinopathy 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Benign concentric annular macular dystrophy IMPG1-related recessive retinopathy 0.500 1 6.49e-5 2.34e-4 ✓ sig.
IMPG1-related dominant retinopathy IMPG1-related recessive retinopathy 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Benign concentric annular macular dystrophy Vitelliform macular dystrophy 0.167 1 3.25e-4 7.58e-4 ✓ sig.
IMPG1-related dominant retinopathy Vitelliform macular dystrophy 0.167 1 3.25e-4 7.58e-4 ✓ sig.
IMPG1-related recessive retinopathy Vitelliform macular dystrophy 0.167 1 3.25e-4 7.58e-4 ✓ sig.
IMPG2-related recessive retinopathy Vitelliform macular dystrophy 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Benign concentric annular macular dystrophy Distal myopathy 0.067 1 9.09e-4 1.56e-3 ✓ sig.
Distal myopathy IMPG1-related dominant retinopathy 0.067 1 9.09e-4 1.56e-3 ✓ sig.
Distal myopathy IMPG1-related recessive retinopathy 0.067 1 9.09e-4 1.56e-3 ✓ sig.
Distal myopathy IMPG2-related recessive retinopathy 0.067 1 9.09e-4 1.56e-3 ✓ sig.