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 243

7 diseases · 11 shared-gene connections
7 Diseases
150 Unique genes
0.160 Avg. similarity score
Limb girdle muscular dystrophy Most-connected disease (5 links)
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Disease Searched: autosomal recessive limb-girdle muscular dystrophy 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 ⇵
Limb girdle muscular dystrophy 5 5 38
Muscular dystrophy 5 5 51
Myopathy 3 3 112
Sarcoglycanopathies 3 3 2
autosomal recessive limb-girdle muscular dystrophy 3 3 14
muscular dystrophy, limb-girdle, autosomal dominant 2 2 4
Axonal neuropathy with neuromyotonia 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
CAPN3 5 / 7 autosomal recessive limb-girdle muscular dystrophy, Limb girdle muscular dystrophy, Muscular dystrophy, muscular dystrophy, limb-girdle, autosomal dominant and 1 more
ANO5 4 / 7 autosomal recessive limb-girdle muscular dystrophy, Limb girdle muscular dystrophy, Muscular dystrophy, Myopathy
DYSF 4 / 7 autosomal recessive limb-girdle muscular dystrophy, Limb girdle muscular dystrophy, Muscular dystrophy, Myopathy
HMGCR 4 / 7 autosomal recessive limb-girdle muscular dystrophy, Limb girdle muscular dystrophy, Muscular dystrophy, Myopathy
SGCA 4 / 7 autosomal recessive limb-girdle muscular dystrophy, Limb girdle muscular dystrophy, Muscular dystrophy, Sarcoglycanopathies
SGCG 4 / 7 autosomal recessive limb-girdle muscular dystrophy, Limb girdle muscular dystrophy, Muscular dystrophy, Sarcoglycanopathies
TRAPPC11 4 / 7 autosomal recessive limb-girdle muscular dystrophy, Limb girdle muscular dystrophy, Muscular dystrophy, Myopathy
TRIM32 4 / 7 autosomal recessive limb-girdle muscular dystrophy, Limb girdle muscular dystrophy, Muscular dystrophy, Myopathy
CRPPA 3 / 7 Limb girdle muscular dystrophy, Muscular dystrophy, Myopathy
DAG1 3 / 7 Limb girdle muscular dystrophy, Muscular dystrophy, Myopathy
DNAJB6 3 / 7 Limb girdle muscular dystrophy, Muscular dystrophy, muscular dystrophy, limb-girdle, autosomal dominant
FKRP 3 / 7 Limb girdle muscular dystrophy, Muscular dystrophy, Myopathy
HNRNPDL 3 / 7 Limb girdle muscular dystrophy, Muscular dystrophy, muscular dystrophy, limb-girdle, autosomal dominant
JAG2 3 / 7 autosomal recessive limb-girdle muscular dystrophy, Limb girdle muscular dystrophy, Muscular dystrophy
LAMA2 3 / 7 Limb girdle muscular dystrophy, Muscular dystrophy, Myopathy
PLEC 3 / 7 Limb girdle muscular dystrophy, Muscular dystrophy, Myopathy
POPDC3 3 / 7 autosomal recessive limb-girdle muscular dystrophy, Limb girdle muscular dystrophy, Muscular dystrophy
SGCB 3 / 7 autosomal recessive limb-girdle muscular dystrophy, Limb girdle muscular dystrophy, Muscular dystrophy
SGCD 3 / 7 autosomal recessive limb-girdle muscular dystrophy, Limb girdle muscular dystrophy, Muscular dystrophy
TCAP 3 / 7 autosomal recessive limb-girdle muscular dystrophy, Limb girdle muscular dystrophy, Muscular dystrophy
TNPO3 3 / 7 Limb girdle muscular dystrophy, Muscular dystrophy, muscular dystrophy, limb-girdle, autosomal dominant
TOR1AIP1 3 / 7 Limb girdle muscular dystrophy, Muscular dystrophy, Myopathy
TTN 3 / 7 Limb girdle muscular dystrophy, Muscular dystrophy, Myopathy
ASTN2 2 / 7 Limb girdle muscular dystrophy, Myopathy
CAV3 2 / 7 Limb girdle muscular dystrophy, Muscular dystrophy
COL6A1 2 / 7 Muscular dystrophy, Myopathy
COL6A2 2 / 7 Muscular dystrophy, Myopathy
COL6A3 2 / 7 Muscular dystrophy, Myopathy
DMD 2 / 7 Muscular dystrophy, Myopathy
FKTN 2 / 7 Limb girdle muscular dystrophy, Muscular dystrophy
GAA 2 / 7 Muscular dystrophy, Myopathy
GMPPB 2 / 7 Limb girdle muscular dystrophy, Muscular dystrophy
HINT1 2 / 7 Axonal neuropathy with neuromyotonia, Myopathy
LMNA 2 / 7 Limb girdle muscular dystrophy, Muscular dystrophy
MYH2 2 / 7 Muscular dystrophy, Myopathy
POGLUT1 2 / 7 autosomal recessive limb-girdle muscular dystrophy, Limb girdle muscular dystrophy
POMGNT1 2 / 7 Limb girdle muscular dystrophy, Muscular dystrophy
POMT1 2 / 7 Limb girdle muscular dystrophy, Muscular dystrophy
POMT2 2 / 7 Limb girdle muscular dystrophy, Muscular dystrophy
SMCHD1 2 / 7 Muscular dystrophy, Myopathy
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 ⇵
Cytoskeleton in muscle cells
CAPN3, DAG1, SGCA, SGCB, SGCD, SGCG, TCAP, TTN, PLEC, LAMA2, LMNA, COL6A1
 KEGG 31 / 232 10.7× 1.64e-23 2.02e-20 ✓ sig.
Dilated cardiomyopathy
CAV3, DAG1, SGCA, SGCB, SGCD, SGCG, TTN, LAMA2, LMNA, DES, DMD, ADCY2
 KEGG 17 / 105 13.0× 1.12e-14 3.14e-12 ✓ sig.
Hypertrophic cardiomyopathy
CAV3, DAG1, SGCA, SGCB, SGCD, SGCG, TTN, LAMA2, LMNA, DES, DMD, EMD
 KEGG 16 / 99 12.9× 7.26e-14 1.74e-11 ✓ sig.
Mannose type O-glycan biosynthesis
CRPPA, FKRP, POMT1, FKTN, POMT2, POMGNT1, POMK, LARGE1
 KEGG 8 / 23 27.8× 2.05e-10 2.61e-8 ✓ sig.
Striated Muscle Contraction
TCAP, TTN, DES, DMD, NEB, ACTA1, TNNI2, TNNT1, TPM3
 Reactome 9 / 36 20.0× 4.10e-10 4.80e-8 ✓ sig.
Arrhythmogenic right ventricular cardiomyopathy
CAV3, DAG1, SGCA, SGCB, SGCD, SGCG, LAMA2, LMNA, DES, DMD, EMD, ITGA7
 KEGG 12 / 86 11.2× 6.40e-10 7.13e-8 ✓ sig.
O-linked glycosylation
DAG1, POMT1, POMT2, POMGNT1, POMK, LARGE1
 Reactome 6 / 10 48.0× 6.92e-10 7.64e-8 ✓ sig.
Viral myocarditis
CAV3, DAG1, SGCA, SGCB, SGCD, SGCG, LAMA2, DMD, MYH7
 KEGG 9 / 70 10.3× 1.98e-7 1.14e-5 ✓ sig.
Defective POMT2 causes MDDGA2, MDDGB2 and MDDGC2
DAG1, POMT1, POMT2
 Reactome 3 / 3 80.1× 1.91e-6 8.11e-5 ✓ sig.
Defective POMT1 causes MDDGA1, MDDGB1 and MDDGC1
DAG1, POMT1, POMT2
 Reactome 3 / 3 80.1× 1.91e-6 8.11e-5 ✓ sig.
Assembly of collagen fibrils and other multimeric structures
PLEC, COL6A1, COL6A2, COL6A3, COL6A6, CTSB
 Reactome 6 / 51 9.4× 3.89e-5 1.01e-3 ✓ sig.
ECM proteoglycans
DAG1, COL6A1, COL6A2, COL6A3, COL6A6, ITGA7
 Reactome 6 / 51 9.4× 3.89e-5 1.01e-3 ✓ sig.
NCAM1 interactions
COL6A1, COL6A2, COL6A3, COL6A6
 Reactome 4 / 21 15.3× 1.19e-4 2.50e-3 ✓ sig.
ECM-receptor interaction
DAG1, LAMA2, COL6A1, COL6A2, COL6A3, COL6A6, ITGA7
 KEGG 7 / 89 6.3× 1.21e-4 2.54e-3 ✓ sig.
Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3
DAG1, POMGNT1
 Reactome 2 / 2 80.1× 1.55e-4 3.11e-3 ✓ 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 organ development
CAPN3, CAV3, BVES, SGCA, SGCB, SGCD, SGCG, FKTN, LAMA2, LMNA, CHKB, COL6A1
 GO:0007517 20 / 114 21.9× 1.70e-21 3.37e-18 ✓ sig.
muscle contraction
SGCA, FKRP, TTN, DES, DMD, MYH2, MYOT, ACTA1, CLCN1, EMD, MYH7, P2RX6
 GO:0006936 15 / 85 22.0× 2.02e-16 1.82e-13 ✓ sig.
protein O-linked glycosylation via mannose
CRPPA, FKRP, POMT1, FKTN, POMT2, POMGNT1, LARGE1, DPM3
 GO:0035269 8 / 18 55.4× 5.84e-13 2.74e-10 ✓ sig.
cardiac muscle cell development
CAV3, SGCB, SGCD, TCAP, TTN, PLEC, LARGE1
 GO:0055013 7 / 25 34.9× 7.94e-10 1.82e-7 ✓ sig.
muscle cell cellular homeostasis
CAPN3, TRIM32, DMD, GAA, LARGE1, MTM1, TGFB1
 GO:0046716 7 / 26 33.5× 1.08e-9 2.39e-7 ✓ sig.
basement membrane organization
DAG1, FKRP, FKTN, POMT2, POMGNT1, COL6A1, LARGE1
 GO:0071711 7 / 29 30.1× 2.51e-9 5.01e-7 ✓ sig.
cardiac muscle contraction
SGCD, TCAP, TTN, DMD, GAA, MYH7, TNNI2
 GO:0060048 7 / 43 20.3× 4.72e-8 6.39e-6 ✓ sig.
skeletal muscle tissue development
BVES, POPDC3, FKRP, PLEC, COL6A1, DMD, SELENON, CASQ1
 GO:0007519 8 / 68 14.7× 7.03e-8 8.87e-6 ✓ sig.
protein O-linked glycosylation
POGLUT1, POMT1, FKTN, POMT2, POMGNT1, POMK, LARGE1, PLOD1
 GO:0006493 8 / 71 14.0× 9.91e-8 1.19e-5 ✓ sig.
skeletal muscle fiber development
PLEC, COL6A1, LARGE1, SELENON, ACTA1, RYR1
 GO:0048741 6 / 31 24.1× 1.51e-7 1.71e-5 ✓ sig.
protein glycosylation
GMPPB, CRPPA, POGLUT1, FKRP, POMT1, FKTN, POMT2, POMGNT1, LARGE1, PMM2, DPM3
 GO:0006486 11 / 181 7.6× 2.41e-7 2.53e-5 ✓ sig.
skeletal muscle fiber differentiation
FKRP, FKTN, COL6A1, LARGE1
 GO:0098528 4 / 9 55.4× 4.87e-7 4.56e-5 ✓ sig.
sarcomere organization
CAPN3, TCAP, TTN, PLEC, CASQ1, TNNT1
 GO:0045214 6 / 43 17.4× 1.15e-6 9.35e-5 ✓ sig.
striated muscle contraction
TTN, GAA, LARGE1, MYH7, RYR1
 GO:0006941 5 / 24 26.0× 1.17e-6 9.46e-5 ✓ sig.
skeletal muscle organ development
FKRP, COL6A1, DES, LARGE1
 GO:0060538 4 / 11 45.3× 1.26e-6 1.00e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Limb girdle muscular dystrophy Muscular dystrophy 0.500 30 3.59e-72 2.63e-70 ✓ sig.
autosomal recessive limb-girdle muscular dystrophy Limb girdle muscular dystrophy 0.359 14 2.01e-38 8.11e-37 ✓ sig.
autosomal recessive limb-girdle muscular dystrophy Muscular dystrophy 0.245 13 1.52e-32 5.06e-31 ✓ sig.
Muscular dystrophy Myopathy 0.139 20 1.86e-30 5.73e-29 ✓ sig.
Limb girdle muscular dystrophy Myopathy 0.102 14 4.19e-21 8.38e-20 ✓ sig.
Limb girdle muscular dystrophy muscular dystrophy, limb-girdle, autosomal dominant 0.103 4 3.15e-11 3.30e-10 ✓ sig.
Muscular dystrophy muscular dystrophy, limb-girdle, autosomal dominant 0.077 4 1.07e-10 1.06e-9 ✓ sig.
autosomal recessive limb-girdle muscular dystrophy Sarcoglycanopathies 0.133 2 7.68e-7 4.58e-6 ✓ sig.
Limb girdle muscular dystrophy Sarcoglycanopathies 0.051 2 5.93e-6 3.04e-5 ✓ sig.
Muscular dystrophy Sarcoglycanopathies 0.038 2 1.08e-5 5.30e-5 ✓ sig.
Axonal neuropathy with neuromyotonia Myopathy 0.009 1 7.27e-3 8.57e-3 ✓ sig.