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 58

15 diseases · 38 shared-gene connections
15 Diseases
22 Unique genes
0.345 Avg. similarity score
Alpha-actinopathy Most-connected disease (8 links)
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Disease Searched: Congenital myopathy 2a, typical, autosomal dominant 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 ⇵
Alpha-actinopathy 8 8 1
Congenital nemaline myopathy 8 8 5
Myopathy, actin, congenital, with excess of thin myofilaments 8 8 1
Nemaline myopathy 3, autosomal dominant or recessive 8 8 1
Zebra body myopathy 8 8 1
Congenital myopathy 2a, typical, autosomal dominant 7 7 1
Rigid spine muscular dystrophy 6 6 3
Congenital myopathy 2b, severe infantile, autosomal recessive 5 5 1
Congenital myopathy 2c, severe infantile, autosomal dominant 5 5 1
Nemaline myopathy 5 5 20
Nemaline myopathy 10 2 2 1
Nemaline myopathy 8 2 2 1
Nemaline myopathy 9 2 2 1
Congenital myopathy 3 with rigid spine 1 1 1
Nemaline myopathy 7 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
ACTA1 10 / 15 Alpha-actinopathy, Congenital myopathy 2a, typical, autosomal dominant, Congenital myopathy 2b, severe infantile, autosomal recessive, Congenital myopathy 2c, severe infantile, autosomal dominant and 6 more
KLHL40 3 / 15 Congenital nemaline myopathy, Nemaline myopathy, Nemaline myopathy 8
KLHL41 3 / 15 Congenital nemaline myopathy, Nemaline myopathy, Nemaline myopathy 9
LMOD3 3 / 15 Congenital nemaline myopathy, Nemaline myopathy, Nemaline myopathy 10
CFL2 2 / 15 Nemaline myopathy, Nemaline myopathy 7
NEB 2 / 15 Congenital nemaline myopathy, Nemaline myopathy
SELENON 2 / 15 Congenital myopathy 3 with rigid spine, Rigid spine 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 ⇵
Cytoskeleton in muscle cells
ACTA1, MYPN, NEB, TPM2, TPM3, ANKRD1, FLNC, TNNT1, TNNT3, LMOD3, TNNI1
 KEGG 11 / 232 25.9× 6.46e-14 1.57e-11 ✓ sig.
Striated Muscle Contraction
ACTA1, NEB, TPM2, TPM3, TNNT1, TNNT3, TNNI1
 Reactome 7 / 36 106× 1.93e-13 4.23e-11 ✓ sig.
Motor proteins
ACTA1, TPM2, TPM3, MYO18B, TNNT1, TNNT3, TNNI1
 KEGG 7 / 194 19.7× 3.58e-8 2.28e-6 ✓ sig.
Cholesterol biosynthesis
HMGCS1, MVK
 Reactome 2 / 21 52.0× 6.59e-4 8.26e-3 ✓ sig.
Terpenoid backbone biosynthesis
HMGCS1, MVK
 KEGG 2 / 23 47.5× 7.92e-4 9.48e-3 ✓ sig.
Smooth Muscle Contraction
TPM2, TPM3
 Reactome 2 / 34 32.1× 1.73e-3 1.72e-2 ✓ sig.
Activation of gene expression by SREBF (SREBP)
HMGCS1, MVK
 Reactome 2 / 42 26.0× 2.64e-3 2.33e-2 ✓ sig.
Cardiac muscle contraction
TPM2, TPM3
 KEGG 2 / 87 12.5× 1.09e-2 6.01e-2
Hypertrophic cardiomyopathy
TPM2, TPM3
 KEGG 2 / 99 11.0× 1.40e-2 6.96e-2
Dilated cardiomyopathy
TPM2, TPM3
 KEGG 2 / 105 10.4× 1.56e-2 7.44e-2
PPARA activates gene expression
HMGCS1, ANKRD1
 Reactome 2 / 115 9.5× 1.85e-2 8.21e-2
Cell-extracellular matrix interactions
FLNC
 Reactome 1 / 12 45.5× 2.18e-2 9.00e-2
Adrenergic signaling in cardiomyocytes
TPM2, TPM3
 KEGG 2 / 154 7.1× 3.19e-2 1.12e-1
Unblocking of NMDA receptors, glutamate binding and activation
NEFL
 Reactome 1 / 22 24.8× 3.96e-2 1.27e-1
Butanoate metabolism
HMGCS1
 KEGG 1 / 27 20.2× 4.83e-2 1.42e-1

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
sarcomere organization
MYPN, ANKRD1, CFL2, FLNC, TNNT1, TNNT3
 GO:0045214 6 / 43 119× 7.49e-12 2.92e-9 ✓ sig.
striated muscle contraction
KLHL41, TNNT3, LMOD3, RYR3
 GO:0006941 4 / 24 142× 1.51e-8 2.52e-6 ✓ sig.
skeletal muscle fiber development
ACTA1, SELENON, LMOD3, KLHL40
 GO:0048741 4 / 31 110× 4.44e-8 6.42e-6 ✓ sig.
actin filament organization
KBTBD13, TPM2, TPM3, CFL2, LMOD3
 GO:0007015 5 / 152 27.9× 7.85e-7 7.03e-5 ✓ sig.
regulation of ATP-dependent activity
TPM2, TNNT3
 GO:0043462 2 / 2 849× 1.32e-6 1.08e-4 ✓ sig.
muscle contraction
ACTA1, TPM2, TPM3, LMOD3
 GO:0006936 4 / 85 40.0× 2.74e-6 1.95e-4 ✓ sig.
skeletal muscle contraction
TNNT1, TNNT3, TNNI1
 GO:0003009 3 / 32 79.6× 6.87e-6 4.06e-4 ✓ sig.
skeletal muscle thin filament assembly
ACTA1, LMOD3
 GO:0030240 2 / 6 283× 1.98e-5 9.16e-4 ✓ sig.
regulation of striated muscle contraction
TNNT3, TNNI1
 GO:0006942 2 / 8 212× 3.69e-5 1.47e-3 ✓ sig.
transition between fast and slow fiber
TNNT1, TNNI1
 GO:0014883 2 / 9 189× 4.74e-5 1.78e-3 ✓ sig.
cellular response to caffeine
SELENON, RYR3
 GO:0071313 2 / 11 154× 7.23e-5 2.43e-3 ✓ sig.
isoprenoid biosynthetic process
HMGCS1, MVK
 GO:0008299 2 / 13 131× 1.02e-4 3.15e-3 ✓ sig.
myofibril assembly
KLHL41, LMOD3
 GO:0030239 2 / 15 113× 1.38e-4 3.88e-3 ✓ sig.
regulation of muscle contraction
TNNT1, TNNT3
 GO:0006937 2 / 16 106× 1.57e-4 4.29e-3 ✓ sig.
sterol biosynthetic process
HMGCS1, MVK
 GO:0016126 2 / 31 54.8× 6.03e-4 1.08e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Congenital nemaline myopathy Nemaline myopathy 0.238 5 2.09e-15 2.56e-14 ✓ sig.
Congenital myopathy 2c, severe infantile, autosomal dominant Zebra body myopathy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Nemaline myopathy 3, autosomal dominant or recessive Zebra body myopathy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Myopathy, actin, congenital, with excess of thin myofilaments Nemaline myopathy 3, autosomal dominant or recessive 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Myopathy, actin, congenital, with excess of thin myofilaments Zebra body myopathy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Alpha-actinopathy Zebra body myopathy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital myopathy 2a, typical, autosomal dominant Congenital myopathy 2c, severe infantile, autosomal dominant 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital myopathy 2c, severe infantile, autosomal dominant Myopathy, actin, congenital, with excess of thin myofilaments 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital myopathy 2c, severe infantile, autosomal dominant Nemaline myopathy 3, autosomal dominant or recessive 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Alpha-actinopathy Congenital myopathy 2c, severe infantile, autosomal dominant 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital myopathy 2b, severe infantile, autosomal recessive Myopathy, actin, congenital, with excess of thin myofilaments 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital myopathy 2b, severe infantile, autosomal recessive Nemaline myopathy 3, autosomal dominant or recessive 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital myopathy 2b, severe infantile, autosomal recessive Zebra body myopathy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital myopathy 2a, typical, autosomal dominant Congenital myopathy 2b, severe infantile, autosomal recessive 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital myopathy 2a, typical, autosomal dominant Myopathy, actin, congenital, with excess of thin myofilaments 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital myopathy 2a, typical, autosomal dominant Nemaline myopathy 3, autosomal dominant or recessive 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital myopathy 2a, typical, autosomal dominant Zebra body myopathy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Alpha-actinopathy Congenital myopathy 2b, severe infantile, autosomal recessive 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Alpha-actinopathy Congenital myopathy 2a, typical, autosomal dominant 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Alpha-actinopathy Myopathy, actin, congenital, with excess of thin myofilaments 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Alpha-actinopathy Nemaline myopathy 3, autosomal dominant or recessive 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital myopathy 2a, typical, autosomal dominant Rigid spine muscular dystrophy 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Myopathy, actin, congenital, with excess of thin myofilaments Rigid spine muscular dystrophy 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Nemaline myopathy 3, autosomal dominant or recessive Rigid spine muscular dystrophy 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Rigid spine muscular dystrophy Zebra body myopathy 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Alpha-actinopathy Rigid spine muscular dystrophy 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Congenital myopathy 3 with rigid spine Rigid spine muscular dystrophy 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Congenital nemaline myopathy Nemaline myopathy 10 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Congenital nemaline myopathy Nemaline myopathy 8 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Congenital nemaline myopathy Nemaline myopathy 9 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Congenital nemaline myopathy Myopathy, actin, congenital, with excess of thin myofilaments 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Congenital nemaline myopathy Nemaline myopathy 3, autosomal dominant or recessive 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Congenital nemaline myopathy Zebra body myopathy 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Alpha-actinopathy Congenital nemaline myopathy 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Nemaline myopathy Nemaline myopathy 10 0.048 1 1.29e-3 1.89e-3 ✓ sig.
Nemaline myopathy Nemaline myopathy 7 0.048 1 1.29e-3 1.89e-3 ✓ sig.
Nemaline myopathy Nemaline myopathy 8 0.048 1 1.29e-3 1.89e-3 ✓ sig.
Nemaline myopathy Nemaline myopathy 9 0.048 1 1.29e-3 1.89e-3 ✓ sig.