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 189

8 diseases · 9 shared-gene connections
8 Diseases
98 Unique genes
0.119 Avg. similarity score
Centronuclear myopathy Most-connected disease (4 links)
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Disease Searched: myopathy, centronuclear, 5 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 ⇵
Centronuclear myopathy 4 4 22
Congenital fiber type disproportion myopathy 3 3 11
Congenital myopathy 3 3 45
Neuromuscular disease 3 3 40
Congenital structural myopathy 2 2 12
Bjornstad syndrome 1 1 1
Developmental delay with hypotonia, myopathy, and brain abnormalities 1 1 1
myopathy, centronuclear, 5 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
RYR1 5 / 8 Centronuclear myopathy, Congenital fiber type disproportion myopathy, Congenital myopathy, Congenital structural myopathy and 1 more
ACTA1 4 / 8 Centronuclear myopathy, Congenital fiber type disproportion myopathy, Congenital myopathy, Neuromuscular disease
TPM3 4 / 8 Centronuclear myopathy, Congenital fiber type disproportion myopathy, Congenital myopathy, Congenital structural myopathy
CCDC78 3 / 8 Centronuclear myopathy, Congenital myopathy, Congenital structural myopathy
MTM1 3 / 8 Centronuclear myopathy, Congenital fiber type disproportion myopathy, Congenital structural myopathy
MYH7 3 / 8 Congenital fiber type disproportion myopathy, Congenital myopathy, Neuromuscular disease
TTN 3 / 8 Centronuclear myopathy, Congenital myopathy, Neuromuscular disease
ACTN2 2 / 8 Congenital myopathy, Neuromuscular disease
BCS1L 2 / 8 Bjornstad syndrome, Neuromuscular disease
BIN1 2 / 8 Centronuclear myopathy, Congenital structural myopathy
CACNA1S 2 / 8 Centronuclear myopathy, Congenital myopathy
CHRNA1 2 / 8 Centronuclear myopathy, Congenital myopathy
DNM2 2 / 8 Centronuclear myopathy, Congenital structural myopathy
GOLGA2 2 / 8 Developmental delay with hypotonia, myopathy, and brain abnormalities, Neuromuscular disease
HACD1 2 / 8 Congenital fiber type disproportion myopathy, Congenital myopathy
ITGA7 2 / 8 Congenital fiber type disproportion myopathy, Congenital myopathy
LMNA 2 / 8 Congenital myopathy, Neuromuscular disease
MAP3K20 2 / 8 Centronuclear myopathy, Congenital fiber type disproportion myopathy
MTMR14 2 / 8 Centronuclear myopathy, Congenital structural myopathy
MYF6 2 / 8 Centronuclear myopathy, Congenital structural myopathy
SCN4A 2 / 8 Congenital myopathy, Neuromuscular disease
SELENON 2 / 8 Congenital fiber type disproportion myopathy, Congenital myopathy
SPEG 2 / 8 Centronuclear myopathy, myopathy, centronuclear, 5
TPM2 2 / 8 Congenital fiber type disproportion myopathy, Congenital 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
TTN, ACTA1, FHL1, TPM3, ITGA7, MYH7, MYL2, TPM2, COL6A6, MYL1, TNNT3, LMNA
 KEGG 25 / 232 13.2× 1.51e-21 1.40e-18 ✓ sig.
Striated Muscle Contraction
TTN, ACTA1, TPM3, MYL2, TPM2, MYL1, TNNT3, TNNC2, MYBPC1, ACTN2, NEB, MYH8
 Reactome 12 / 36 40.9× 4.64e-17 2.14e-14 ✓ sig.
Motor proteins
ACTA1, TPM3, MYH7, MYL2, TPM2, MYL1, TNNT3, MYO15B, TNNC2, TUBA4A, MYH2, MYH8
 KEGG 14 / 194 8.8× 5.12e-10 6.44e-8 ✓ sig.
Hypertrophic cardiomyopathy
TTN, CACNA1S, TPM3, ITGA7, MYH7, MYL2, TPM2, LMNA, EMD, SGCD
 KEGG 10 / 99 12.4× 7.02e-9 6.75e-7 ✓ sig.
Dilated cardiomyopathy
TTN, CACNA1S, TPM3, ITGA7, MYH7, MYL2, TPM2, LMNA, EMD, SGCD
 KEGG 10 / 105 11.7× 1.25e-8 1.11e-6 ✓ sig.
Arrhythmogenic right ventricular cardiomyopathy
CACNA1S, ITGA7, LMNA, ACTN2, EMD, SGCD
 KEGG 6 / 86 8.6× 7.03e-5 1.76e-3 ✓ sig.
Cardiac muscle contraction
CACNA1S, TPM3, MYH7, MYL2, TPM2, ATP1A1
 KEGG 6 / 87 8.5× 7.50e-5 1.85e-3 ✓ sig.
ALKBH3 mediated reversal of alkylation damage
ASCC1, ASCC3
 Reactome 2 / 4 61.3× 3.91e-4 6.83e-3 ✓ sig.
Ion homeostasis
RYR1, RYR3, STIM1, ATP1A1
 Reactome 4 / 54 9.1× 9.65e-4 1.37e-2 ✓ sig.
Adrenergic signaling in cardiomyocytes
CACNA1S, TPM3, MYH7, MYL2, TPM2, ATP1A1
 KEGG 6 / 154 4.8× 1.61e-3 2.02e-2 ✓ sig.
Nuclear Envelope Breakdown
LMNA, EMD
 Reactome 2 / 9 27.2× 2.29e-3 2.61e-2 ✓ sig.
Fructose and mannose metabolism
GMPPB, SORD, TPI1
 KEGG 3 / 34 10.8× 2.62e-3 2.88e-2 ✓ sig.
Smooth Muscle Contraction
TPM3, TPM2, DYSF
 Reactome 3 / 34 10.8× 2.62e-3 2.88e-2 ✓ sig.
Biosynthesis of nucleotide sugars
GNE, GMPPB, GPI
 KEGG 3 / 37 9.9× 3.35e-3 3.41e-2 ✓ sig.
Amino sugar and nucleotide sugar metabolism
GNE, GMPPB, GPI
 KEGG 3 / 38 9.7× 3.61e-3 3.61e-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 organ development
MYF6, SPEG, FHL1, ITGA7, FXR1, CHKB, JPH1, LARGE1, LMNA, SRPK3, MEGF10, MYOD1
 GO:0007517 16 / 114 26.8× 7.75e-19 9.93e-16 ✓ sig.
muscle contraction
RYR1, TTN, ACTA1, CACNA1S, CHRND, TPM3, MYH7, TPM2, MYL1, SCN4A, FKRP, MYH2
 GO:0006936 14 / 85 31.4× 1.27e-17 1.41e-14 ✓ sig.
skeletal muscle contraction
TTN, CCDC78, CHRNA1, CHRND, MYH7, TNNT3, STAC3, TNNC2, MYH8
 GO:0003009 9 / 32 53.6× 5.23e-14 3.02e-11 ✓ sig.
skeletal muscle fiber development
RYR1, ACTA1, CACNA1S, SELENON, LARGE1, STAC3, MYOD1, XK
 GO:0048741 8 / 31 49.2× 3.05e-12 1.28e-9 ✓ sig.
striated muscle contraction
RYR1, TTN, CACNA1S, MYH7, RYR3, TNNT3, LARGE1
 GO:0006941 7 / 24 55.6× 2.82e-11 9.46e-9 ✓ sig.
sarcomere organization
TTN, CFL2, TNNT3, MYPN, MYBPC1, ACTN2, ANKRD1, LDB3
 GO:0045214 8 / 43 35.5× 5.33e-11 1.66e-8 ✓ sig.
skeletal muscle tissue development
MYF6, CACNA1S, CFL2, SELENON, FKRP, SRPK3, MYOD1, PAX7
 GO:0007519 8 / 68 22.4× 2.44e-9 4.95e-7 ✓ sig.
skeletal muscle tissue regeneration
MYF6, SELENON, FKRP, LARGE1, MYOD1, PAX7
 GO:0043403 6 / 26 44.0× 3.77e-9 7.23e-7 ✓ sig.
muscle filament sliding
TTN, MYH7, MYL1, MYH2, MYH8
 GO:0030049 5 / 15 63.6× 1.03e-8 1.74e-6 ✓ sig.
cellular response to caffeine
RYR1, CACNA1S, SELENON, RYR3
 GO:0071313 4 / 11 69.3× 2.28e-7 2.50e-5 ✓ sig.
muscle structure development
SELENON, FXR1, FKRP, LDB3
 GO:0061061 4 / 19 40.1× 2.59e-6 1.84e-4 ✓ sig.
skeletal muscle tissue growth
CHRNA1, CHRND, MTM1
 GO:0048630 3 / 6 95.3× 2.77e-6 1.93e-4 ✓ sig.
muscle cell development
CACNA1S, MYL2, MEGF10, ACTN2
 GO:0055001 4 / 23 33.2× 5.83e-6 3.51e-4 ✓ sig.
cardiac muscle cell development
TTN, LARGE1, ACTN2, SGCD
 GO:0055013 4 / 25 30.5× 8.27e-6 4.67e-4 ✓ sig.
muscle cell cellular homeostasis
CFL2, CHRNA1, MTM1, LARGE1
 GO:0046716 4 / 26 29.3× 9.73e-6 5.28e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Centronuclear myopathy Congenital structural myopathy 0.296 8 2.02e-21 4.06e-20 ✓ sig.
Congenital fiber type disproportion myopathy Congenital myopathy 0.163 8 4.52e-19 8.15e-18 ✓ sig.
Centronuclear myopathy Congenital myopathy 0.115 7 1.84e-13 2.36e-12 ✓ sig.
Centronuclear myopathy Congenital fiber type disproportion myopathy 0.172 5 1.68e-12 1.96e-11 ✓ sig.
Congenital myopathy Neuromuscular disease 0.089 7 1.94e-11 2.07e-10 ✓ sig.
Congenital fiber type disproportion myopathy Congenital structural myopathy 0.143 3 5.95e-8 4.33e-7 ✓ sig.
Centronuclear myopathy myopathy, centronuclear, 5 0.043 1 1.43e-3 2.23e-3 ✓ sig.
Bjornstad syndrome Neuromuscular disease 0.024 1 2.60e-3 3.51e-3 ✓ sig.
Developmental delay with hypotonia, myopathy, and brain abnormalities Neuromuscular disease 0.024 1 2.60e-3 3.51e-3 ✓ sig.