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 258

7 diseases · 13 shared-gene connections
7 Diseases
24 Unique genes
0.199 Avg. similarity score
Arthrogryposis 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 ⇵
Arthrogryposis 5 5 11
Digitotalar dysmorphism 5 5 6
Sheldon-hall syndrome 5 5 5
Distal arthrogryposis 4 4 16
Congenital finger flexion contractures 3 3 1
TPM2-related myopathy 3 3 1
childhood-onset nemaline myopathy 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
TPM2 5 / 7 Arthrogryposis, Digitotalar dysmorphism, Distal arthrogryposis, Sheldon-hall syndrome and 1 more
MYH3 4 / 7 Arthrogryposis, Digitotalar dysmorphism, Distal arthrogryposis, Sheldon-hall syndrome
TNNI2 4 / 7 Congenital finger flexion contractures, Digitotalar dysmorphism, Distal arthrogryposis, Sheldon-hall syndrome
NALCN 3 / 7 Digitotalar dysmorphism, Distal arthrogryposis, Sheldon-hall syndrome
TNNT3 3 / 7 Digitotalar dysmorphism, Distal arthrogryposis, Sheldon-hall syndrome
ECEL1 2 / 7 Arthrogryposis, Distal arthrogryposis
MYBPC1 2 / 7 Digitotalar dysmorphism, Distal arthrogryposis
TNNI1 2 / 7 Arthrogryposis, childhood-onset nemaline 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 ⇵
Striated Muscle Contraction
ACTC1, MYH3, TNNI1, TPM2, MYBPC1, MYH8, TNNI2, TNNT3
 Reactome 8 / 36 111× 2.01e-15 7.33e-13 ✓ sig.
Motor proteins
ACTC1, MYH3, MYO9A, TNNI1, TPM2, MYH8, TNNI2, TNNT3
 KEGG 8 / 194 20.6× 2.36e-9 2.39e-7 ✓ sig.
Cytoskeleton in muscle cells
ACTC1, MYH3, TNNI1, TPM2, MYBPC1, MYH8, TNNI2, TNNT3
 KEGG 8 / 232 17.3× 9.68e-9 8.46e-7 ✓ sig.
MET activates STAT3
MET
 Reactome 1 / 3 167× 5.98e-3 4.92e-2 ✓ sig.
MECP2 regulates neuronal receptors and channels
MET
 Reactome 1 / 4 125× 7.97e-3 5.96e-2
MET activates PTPN11
MET
 Reactome 1 / 5 100× 9.95e-3 6.82e-2
MET interacts with TNS proteins
MET
 Reactome 1 / 5 100× 9.95e-3 6.82e-2
Stimuli-sensing channels
NALCN, RYR1
 Reactome 2 / 79 12.7× 1.07e-2 7.18e-2
MET Receptor Activation
MET
 Reactome 1 / 6 83.4× 1.19e-2 7.61e-2
MET activates PI3K/AKT signaling
MET
 Reactome 1 / 6 83.4× 1.19e-2 7.61e-2
Cardiac muscle contraction
ACTC1, TPM2
 KEGG 2 / 87 11.5× 1.29e-2 7.95e-2
Highly sodium permeable postsynaptic acetylcholine nicotinic receptors
CHRNG
 Reactome 1 / 7 71.5× 1.39e-2 8.31e-2
InlB-mediated entry of Listeria monocytogenes into host cell
MET
 Reactome 1 / 7 71.5× 1.39e-2 8.31e-2
Sema4D mediated inhibition of cell attachment and migration
MET
 Reactome 1 / 8 62.6× 1.59e-2 9.02e-2
Hypertrophic cardiomyopathy
ACTC1, TPM2
 KEGG 2 / 99 10.1× 1.65e-2 9.22e-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 ⇵
skeletal muscle contraction
CHRNG, MYH3, TNNI1, MYH8, TNNI2, TNNT3
 GO:0003009 6 / 32 146× 2.02e-12 8.65e-10 ✓ sig.
muscle contraction
CHRNG, MYH3, TPM2, MYH8, RYR1
 GO:0006936 5 / 85 45.8× 6.86e-8 8.85e-6 ✓ sig.
regulation of ATP-dependent activity
TPM2, TNNT3
 GO:0043462 2 / 2 779× 1.58e-6 1.19e-4 ✓ sig.
cardiac muscle contraction
ACTC1, TNNI1, TNNI2
 GO:0060048 3 / 43 54.3× 2.22e-5 9.75e-4 ✓ sig.
sarcomere organization
MYH3, MYBPC1, TNNT3
 GO:0045214 3 / 43 54.3× 2.22e-5 9.75e-4 ✓ sig.
regulation of striated muscle contraction
TNNI1, TNNT3
 GO:0006942 2 / 8 195× 4.41e-5 1.64e-3 ✓ sig.
neuronal action potential propagation
SCN1A, CNTNAP1
 GO:0019227 2 / 11 142× 8.63e-5 2.71e-3 ✓ sig.
monoatomic ion transmembrane transport
CHRNG, SCN1A, NALCN, PIEZO2, RYR1
 GO:0034220 5 / 404 9.6× 1.39e-4 3.87e-3 ✓ sig.
neuromuscular process controlling posture
SCN1A, CNTNAP1
 GO:0050884 2 / 15 104× 1.64e-4 4.39e-3 ✓ sig.
muscle filament sliding
MYH3, MYH8
 GO:0030049 2 / 15 104× 1.64e-4 4.39e-3 ✓ sig.
actin filament-based movement
ACTC1, MYH3
 GO:0030048 2 / 21 74.2× 3.27e-4 7.12e-3 ✓ sig.
striated muscle contraction
TNNT3, RYR1
 GO:0006941 2 / 24 64.9× 4.29e-4 8.60e-3 ✓ sig.
ATP metabolic process
MYH3, MYH8
 GO:0046034 2 / 36 43.3× 9.70e-4 1.47e-2 ✓ sig.
neuromuscular junction development, skeletal muscle fiber
CNTNAP1
 GO:0098529 1 / 1 779× 1.28e-3 1.75e-2 ✓ sig.
positive regulation of vesicle transport along microtubule
STK11
 GO:1901610 1 / 1 779× 1.28e-3 1.75e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Digitotalar dysmorphism Distal arthrogryposis 0.353 6 4.33e-19 8.26e-18 ✓ sig.
Digitotalar dysmorphism Sheldon-hall syndrome 0.714 5 8.32e-19 1.57e-17 ✓ sig.
Distal arthrogryposis Sheldon-hall syndrome 0.294 5 6.06e-16 9.70e-15 ✓ sig.
Arthrogryposis Distal arthrogryposis 0.120 3 1.51e-7 1.09e-6 ✓ sig.
Arthrogryposis Sheldon-hall syndrome 0.133 2 4.63e-6 2.56e-5 ✓ sig.
Arthrogryposis Digitotalar dysmorphism 0.125 2 6.95e-6 3.72e-5 ✓ sig.
Congenital finger flexion contractures Sheldon-hall syndrome 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Sheldon-hall syndrome TPM2-related myopathy 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Congenital finger flexion contractures Digitotalar dysmorphism 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Digitotalar dysmorphism TPM2-related myopathy 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Arthrogryposis childhood-onset nemaline myopathy 0.083 1 7.14e-4 1.31e-3 ✓ sig.
Arthrogryposis TPM2-related myopathy 0.083 1 7.14e-4 1.31e-3 ✓ sig.
Congenital finger flexion contractures Distal arthrogryposis 0.059 1 1.04e-3 1.72e-3 ✓ sig.