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 34

18 diseases · 40 shared-gene connections
18 Diseases
63 Unique genes
0.095 Avg. similarity score
Congenital myasthenic syndrome Most-connected disease (14 links)
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Disease Searched: Myasthenic syndrome 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 ⇵
Congenital myasthenic syndrome 14 14 29
Myasthenic syndrome 12 12 40
Postsynaptic congenital myasthenic syndrome 8 8 12
Presynaptic congenital myasthenic syndrome 8 8 11
Fetal akinesia deformation sequence 6 6 12
congenital myasthenic syndrome 7 4 4 1
congenital myasthenic syndrome 8 4 4 1
congenital myasthenic syndrome 10 3 3 1
congenital myasthenic syndrome 6 3 3 1
congenital myasthenic syndrome 9 3 3 1
neuronopathy, distal hereditary motor, type 7A 3 3 1
ALG2-congenital disorder of glycosylation 2 2 1
Ataxia, spastic, autosomal dominant 2 2 2
Intellectual developmental disorder seizures behavioral 2 2 1
congenital myasthenic syndrome 12 2 2 1
myasthenic syndrome, congenital, 1b, fast-channel 2 2 1
Alstrom syndrome 1 1 1
Thyroid gland neoplasms 1 1 13

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

Gene ⇵ Member diseases ⇵ Linked diseases
AGRN 5 / 18 Congenital myasthenic syndrome, congenital myasthenic syndrome 8, Myasthenic syndrome, Postsynaptic congenital myasthenic syndrome and 1 more
DOK7 5 / 18 Congenital myasthenic syndrome, congenital myasthenic syndrome 10, Fetal akinesia deformation sequence, Myasthenic syndrome and 1 more
MUSK 5 / 18 Congenital myasthenic syndrome, congenital myasthenic syndrome 9, Fetal akinesia deformation sequence, Myasthenic syndrome and 1 more
SYT2 5 / 18 Congenital myasthenic syndrome, congenital myasthenic syndrome 7, Myasthenic syndrome, Presynaptic congenital myasthenic syndrome and 1 more
CHAT 4 / 18 Congenital myasthenic syndrome, congenital myasthenic syndrome 6, Myasthenic syndrome, Presynaptic congenital myasthenic syndrome
CHRNA1 4 / 18 Congenital myasthenic syndrome, Myasthenic syndrome, myasthenic syndrome, congenital, 1b, fast-channel, Postsynaptic congenital myasthenic syndrome
COL13A1 4 / 18 Congenital myasthenic syndrome, Myasthenic syndrome, Postsynaptic congenital myasthenic syndrome, Presynaptic congenital myasthenic syndrome
RAPSN 4 / 18 Congenital myasthenic syndrome, Fetal akinesia deformation sequence, Myasthenic syndrome, Postsynaptic congenital myasthenic syndrome
SLC18A3 4 / 18 Congenital myasthenic syndrome, Fetal akinesia deformation sequence, Myasthenic syndrome, Presynaptic congenital myasthenic syndrome
SLC5A7 4 / 18 Congenital myasthenic syndrome, Myasthenic syndrome, neuronopathy, distal hereditary motor, type 7A, Presynaptic congenital myasthenic syndrome
ALG14 3 / 18 Congenital myasthenic syndrome, Intellectual developmental disorder seizures behavioral, Myasthenic syndrome
ALG2 3 / 18 ALG2-congenital disorder of glycosylation, Congenital myasthenic syndrome, Myasthenic syndrome
CHRNB1 3 / 18 Congenital myasthenic syndrome, Myasthenic syndrome, Postsynaptic congenital myasthenic syndrome
CHRND 3 / 18 Congenital myasthenic syndrome, Myasthenic syndrome, Postsynaptic congenital myasthenic syndrome
CHRNE 3 / 18 Congenital myasthenic syndrome, Myasthenic syndrome, Postsynaptic congenital myasthenic syndrome
GFPT1 3 / 18 Congenital myasthenic syndrome, congenital myasthenic syndrome 12, Myasthenic syndrome
LRP4 3 / 18 Congenital myasthenic syndrome, Myasthenic syndrome, Postsynaptic congenital myasthenic syndrome
MYO9A 3 / 18 Congenital myasthenic syndrome, Myasthenic syndrome, Presynaptic congenital myasthenic syndrome
SCN4A 3 / 18 Congenital myasthenic syndrome, Myasthenic syndrome, Postsynaptic congenital myasthenic syndrome
SLC25A1 3 / 18 Congenital myasthenic syndrome, Myasthenic syndrome, Presynaptic congenital myasthenic syndrome
SNAP25 3 / 18 Congenital myasthenic syndrome, Myasthenic syndrome, Presynaptic congenital myasthenic syndrome
VAMP1 3 / 18 Ataxia, spastic, autosomal dominant, Myasthenic syndrome, Presynaptic congenital myasthenic syndrome
ALMS1 2 / 18 Alstrom syndrome, Fetal akinesia deformation sequence
CHD8 2 / 18 Congenital myasthenic syndrome, Myasthenic syndrome
COLQ 2 / 18 Congenital myasthenic syndrome, Myasthenic syndrome
DPAGT1 2 / 18 Congenital myasthenic syndrome, Myasthenic syndrome
GMPPB 2 / 18 Congenital myasthenic syndrome, Myasthenic syndrome
PLEC 2 / 18 Congenital myasthenic syndrome, Myasthenic syndrome
PREPL 2 / 18 Congenital myasthenic syndrome, Myasthenic syndrome
RPH3A 2 / 18 Congenital myasthenic syndrome, Myasthenic syndrome
TAPBPL 2 / 18 Ataxia, spastic, autosomal dominant, Myasthenic syndrome
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 ⇵
Acetylcholine Neurotransmitter Release Cycle
CHAT, SLC18A3, SLC5A7, SNAP25
 Reactome 4 / 17 44.9× 1.55e-6 7.65e-5 ✓ sig.
Highly sodium permeable postsynaptic acetylcholine nicotinic receptors
CHRND, CHRNE, CHRNG
 Reactome 3 / 7 81.7× 4.74e-6 1.94e-4 ✓ sig.
Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein
ALG14, ALG2, DPAGT1
 Reactome 3 / 11 52.0× 2.20e-5 6.82e-4 ✓ sig.
N-Glycan biosynthesis
ALG14, ALG2, DPAGT1
 KEGG 3 / 55 10.4× 2.97e-3 3.14e-2 ✓ sig.
Defective DPAGT1 causes DPAGT1-CDG (CDG-1j) and CMSTA2
DPAGT1
 Reactome 1 / 1 191× 5.25e-3 4.67e-2 ✓ sig.
Defective GFPT1 causes CMSTA1
GFPT1
 Reactome 1 / 1 191× 5.25e-3 4.67e-2 ✓ sig.
Imatinib-resistant PDGFR mutants
PDGFRA
 Reactome 1 / 1 191× 5.25e-3 4.67e-2 ✓ sig.
Sunitinib-resistant PDGFR mutants
PDGFRA
 Reactome 1 / 1 191× 5.25e-3 4.67e-2 ✓ sig.
Regorafenib-resistant PDGFR mutants
PDGFRA
 Reactome 1 / 1 191× 5.25e-3 4.67e-2 ✓ sig.
Sorafenib-resistant PDGFR mutants
PDGFRA
 Reactome 1 / 1 191× 5.25e-3 4.67e-2 ✓ sig.
PDGFR mutants bind TKIs
PDGFRA
 Reactome 1 / 1 191× 5.25e-3 4.67e-2 ✓ sig.
Defective SLC5A7 causes distal hereditary motor neuronopathy 7A (HMN7A)
SLC5A7
 Reactome 1 / 1 191× 5.25e-3 4.67e-2 ✓ sig.
Defective SLC22A5 causes systemic primary carnitine deficiency (CDSP)
SLC22A5
 Reactome 1 / 1 191× 5.25e-3 4.67e-2 ✓ sig.
Defective ALG2 causes ALG2-CDG (CDG-1i)
ALG2
 Reactome 1 / 1 191× 5.25e-3 4.67e-2 ✓ sig.
Laminin interactions
LAMA5, LAMB2
 Reactome 2 / 28 13.6× 9.38e-3 6.82e-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 ⇵
synaptic transmission, cholinergic
CHRNA1, SLC5A7, CHRNB1, CHRND, CHRNE, RAPSN, CHRNG
 GO:0007271 7 / 25 83.1× 1.61e-12 7.15e-10 ✓ sig.
neuromuscular junction development
CHRNA1, AGRN, DOK7, LAMB2, MUSK, RAPSN
 GO:0007528 6 / 35 50.8× 1.73e-9 3.67e-7 ✓ sig.
skeletal muscle acetylcholine-gated channel clustering
COLQ, LRP4, MUSK, RAPSN
 GO:0071340 4 / 9 132× 1.46e-8 2.37e-6 ✓ sig.
acetylcholine receptor signaling pathway
CHRNA1, CHRNB1, CHRND, CHRNE, CHRNG
 GO:0095500 5 / 28 53.0× 3.43e-8 4.93e-6 ✓ sig.
membrane depolarization
CHRNA1, CHRNB1, CHRND, CHRNE, CHRNG
 GO:0051899 5 / 32 46.3× 6.95e-8 9.01e-6 ✓ sig.
skeletal muscle contraction
CHRNA1, CHRNB1, CHRND, CHRNE, CHRNG
 GO:0003009 5 / 32 46.3× 6.95e-8 9.01e-6 ✓ sig.
muscle contraction
CHRNB1, CHRND, CHRNE, SCN4A, RYR1, CHRNG
 GO:0006936 6 / 85 20.9× 4.09e-7 4.04e-5 ✓ sig.
regulation of postsynaptic membrane potential
CHRNA1, CHRNB1, CHRND, CHRNE, CHRNG
 GO:0060078 5 / 59 25.1× 1.61e-6 1.25e-4 ✓ sig.
neuromuscular synaptic transmission
CHRNA1, CHAT, SLC5A7, CHRNB1
 GO:0007274 4 / 31 38.3× 3.45e-6 2.30e-4 ✓ sig.
excitatory postsynaptic potential
CHRNA1, CHRNB1, CHRND, CHRNE, CHRNG
 GO:0060079 5 / 69 21.5× 3.53e-6 2.34e-4 ✓ sig.
regulation of synaptic assembly at neuromuscular junction
AGRN, COLQ, MUSK
 GO:0008582 3 / 10 89.0× 4.31e-6 2.74e-4 ✓ sig.
chemical synaptic transmission
SLC18A3, SNAP25, CHRND, CHRNE, RAPSN, MINK1, CHRNG
 GO:0007268 7 / 236 8.8× 1.42e-5 7.13e-4 ✓ sig.
acetylcholine biosynthetic process
CHAT, SLC5A7
 GO:0008292 2 / 3 198× 3.35e-5 1.37e-3 ✓ sig.
dolichol-linked oligosaccharide biosynthetic process
ALG14, ALG2, DPAGT1
 GO:0006488 3 / 19 46.8× 3.40e-5 1.39e-3 ✓ sig.
protein N-linked glycosylation
ALG14, ALG2, DPAGT1, GFPT1
 GO:0006487 4 / 62 19.1× 5.65e-5 2.04e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Congenital myasthenic syndrome Myasthenic syndrome 0.667 28 2.85e-77 2.19e-75 ✓ sig.
Congenital myasthenic syndrome Postsynaptic congenital myasthenic syndrome 0.355 11 1.44e-30 4.46e-29 ✓ sig.
Myasthenic syndrome Postsynaptic congenital myasthenic syndrome 0.262 11 9.62e-29 2.80e-27 ✓ sig.
Myasthenic syndrome Presynaptic congenital myasthenic syndrome 0.238 10 4.52e-26 1.16e-24 ✓ sig.
Congenital myasthenic syndrome Presynaptic congenital myasthenic syndrome 0.281 9 4.11e-24 9.53e-23 ✓ sig.
Congenital myasthenic syndrome Fetal akinesia deformation sequence 0.105 4 4.97e-9 4.19e-8 ✓ sig.
Fetal akinesia deformation sequence Myasthenic syndrome 0.082 4 1.90e-8 1.49e-7 ✓ sig.
Fetal akinesia deformation sequence Postsynaptic congenital myasthenic syndrome 0.136 3 7.92e-8 5.64e-7 ✓ sig.
Ataxia, spastic, autosomal dominant Myasthenic syndrome 0.049 2 6.58e-6 3.34e-5 ✓ sig.
Postsynaptic congenital myasthenic syndrome Presynaptic congenital myasthenic syndrome 0.091 2 3.05e-5 1.41e-4 ✓ sig.
congenital myasthenic syndrome 7 Presynaptic congenital myasthenic syndrome 0.083 1 7.14e-4 1.34e-3 ✓ sig.
neuronopathy, distal hereditary motor, type 7A Presynaptic congenital myasthenic syndrome 0.083 1 7.14e-4 1.34e-3 ✓ sig.
congenital myasthenic syndrome 8 Presynaptic congenital myasthenic syndrome 0.083 1 7.14e-4 1.34e-3 ✓ sig.
congenital myasthenic syndrome 6 Presynaptic congenital myasthenic syndrome 0.083 1 7.14e-4 1.34e-3 ✓ sig.
myasthenic syndrome, congenital, 1b, fast-channel Postsynaptic congenital myasthenic syndrome 0.077 1 7.79e-4 1.41e-3 ✓ sig.
Alstrom syndrome Fetal akinesia deformation sequence 0.077 1 7.79e-4 1.41e-3 ✓ sig.
congenital myasthenic syndrome 10 Fetal akinesia deformation sequence 0.077 1 7.79e-4 1.41e-3 ✓ sig.
congenital myasthenic syndrome 8 Postsynaptic congenital myasthenic syndrome 0.077 1 7.79e-4 1.41e-3 ✓ sig.
congenital myasthenic syndrome 10 Postsynaptic congenital myasthenic syndrome 0.077 1 7.79e-4 1.41e-3 ✓ sig.
congenital myasthenic syndrome 9 Fetal akinesia deformation sequence 0.077 1 7.79e-4 1.41e-3 ✓ sig.
congenital myasthenic syndrome 9 Postsynaptic congenital myasthenic syndrome 0.077 1 7.79e-4 1.41e-3 ✓ sig.
congenital myasthenic syndrome 7 Thyroid gland neoplasms 0.071 1 8.44e-4 1.50e-3 ✓ sig.
Ataxia, spastic, autosomal dominant Presynaptic congenital myasthenic syndrome 0.077 1 1.43e-3 2.23e-3 ✓ sig.
Congenital myasthenic syndrome congenital myasthenic syndrome 10 0.033 1 1.88e-3 2.76e-3 ✓ sig.
Congenital myasthenic syndrome myasthenic syndrome, congenital, 1b, fast-channel 0.033 1 1.88e-3 2.76e-3 ✓ sig.
Congenital myasthenic syndrome Intellectual developmental disorder seizures behavioral 0.033 1 1.88e-3 2.76e-3 ✓ sig.
Congenital myasthenic syndrome congenital myasthenic syndrome 9 0.033 1 1.88e-3 2.76e-3 ✓ sig.
Congenital myasthenic syndrome congenital myasthenic syndrome 8 0.033 1 1.88e-3 2.76e-3 ✓ sig.
Congenital myasthenic syndrome congenital myasthenic syndrome 12 0.033 1 1.88e-3 2.76e-3 ✓ sig.
ALG2-congenital disorder of glycosylation Congenital myasthenic syndrome 0.033 1 1.88e-3 2.76e-3 ✓ sig.
Congenital myasthenic syndrome congenital myasthenic syndrome 7 0.033 1 1.88e-3 2.76e-3 ✓ sig.
Congenital myasthenic syndrome neuronopathy, distal hereditary motor, type 7A 0.033 1 1.88e-3 2.76e-3 ✓ sig.
Congenital myasthenic syndrome congenital myasthenic syndrome 6 0.033 1 1.88e-3 2.76e-3 ✓ sig.
Myasthenic syndrome neuronopathy, distal hereditary motor, type 7A 0.024 1 2.60e-3 3.51e-3 ✓ sig.
congenital myasthenic syndrome 7 Myasthenic syndrome 0.024 1 2.60e-3 3.51e-3 ✓ sig.
Intellectual developmental disorder seizures behavioral Myasthenic syndrome 0.024 1 2.60e-3 3.51e-3 ✓ sig.
congenital myasthenic syndrome 8 Myasthenic syndrome 0.024 1 2.60e-3 3.51e-3 ✓ sig.
congenital myasthenic syndrome 6 Myasthenic syndrome 0.024 1 2.60e-3 3.51e-3 ✓ sig.
congenital myasthenic syndrome 12 Myasthenic syndrome 0.024 1 2.60e-3 3.51e-3 ✓ sig.
ALG2-congenital disorder of glycosylation Myasthenic syndrome 0.024 1 2.60e-3 3.51e-3 ✓ sig.