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 487

6 diseases · 14 shared-gene connections
6 Diseases
11 Unique genes
0.296 Avg. similarity score
Cognitive impairment with or without cerebellar ataxia 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 ⇵
Cognitive impairment with or without cerebellar ataxia 5 5 1
Myoclonus, familial, 2 5 5 1
Paroxysmal kinesigenic dyskinesias 5 5 1
Seizures, benign familial infantile, 5 5 5 1
Choreoathetosis 4 4 6
Focal onset epileptic seizure 4 4 6

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

Gene ⇵ Member diseases ⇵ Linked diseases
SCN8A 6 / 6 Choreoathetosis, Cognitive impairment with or without cerebellar ataxia, Focal onset epileptic seizure, Myoclonus, familial, 2 and 2 more
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 ⇵
Cholinergic synapse
GNAO1, CHRNB2, GNB1
 KEGG 3 / 115 28.5× 1.33e-4 2.38e-3 ✓ sig.
Dopaminergic synapse
GNAO1, GNB1, SCN1A
 KEGG 3 / 132 24.8× 2.01e-4 3.29e-3 ✓ sig.
G-protein activation
GNAO1, GNB1
 Reactome 2 / 28 78.0× 2.85e-4 4.33e-3 ✓ sig.
Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding
GNAO1, GNB1
 Reactome 2 / 42 52.0× 6.44e-4 8.12e-3 ✓ sig.
Phase 0 - rapid depolarisation
SCN8A, SCN1A
 Reactome 2 / 44 49.6× 7.07e-4 8.71e-3 ✓ sig.
Defective SLC2A1 causes GLUT1 deficiency syndrome 1 (GLUT1DS1)
SLC2A1
 Reactome 1 / 1 1,092× 9.16e-4 1.06e-2 ✓ sig.
Ca2+ pathway
GNAO1, GNB1
 Reactome 2 / 56 39.0× 1.14e-3 1.25e-2 ✓ sig.
Lactose synthesis
SLC2A1
 Reactome 1 / 3 364× 2.75e-3 2.39e-2 ✓ sig.
GABAergic synapse
GNAO1, GNB1
 KEGG 2 / 89 24.5× 2.86e-3 2.46e-2 ✓ sig.
Morphine addiction
GNAO1, GNB1
 KEGG 2 / 91 24.0× 2.99e-3 2.54e-2 ✓ sig.
Circadian entrainment
GNAO1, GNB1
 KEGG 2 / 97 22.5× 3.39e-3 2.78e-2 ✓ sig.
Serotonergic synapse
GNAO1, GNB1
 KEGG 2 / 115 19.0× 4.72e-3 3.52e-2 ✓ sig.
Glutamatergic synapse
GNAO1, GNB1
 KEGG 2 / 116 18.8× 4.81e-3 3.56e-2 ✓ sig.
Relaxin signaling pathway
GNAO1, GNB1
 KEGG 2 / 130 16.8× 6.00e-3 4.10e-2 ✓ sig.
Highly sodium permeable postsynaptic acetylcholine nicotinic receptors
CHRNB2
 Reactome 1 / 7 156× 6.40e-3 4.28e-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 ⇵
locomotory behavior
GNAO1, NKX2-1, CHRNB2
 GO:0007626 3 / 99 51.5× 2.31e-5 1.03e-3 ✓ sig.
cardiac muscle cell action potential involved in contraction
SCN8A, SCN1A
 GO:0086002 2 / 24 142× 8.63e-5 2.77e-3 ✓ sig.
endoderm development
NKX2-1, NCKAP1
 GO:0007492 2 / 34 99.9× 1.75e-4 4.61e-3 ✓ sig.
action potential
SCN8A, SCN1A
 GO:0001508 2 / 53 64.1× 4.27e-4 8.53e-3 ✓ sig.
lateral geniculate nucleus development
CHRNB2
 GO:0021771 1 / 1 1,699× 5.89e-4 1.06e-2 ✓ sig.
regulation of circadian sleep/wake cycle, REM sleep
CHRNB2
 GO:0042320 1 / 1 1,699× 5.89e-4 1.06e-2 ✓ sig.
developmental induction
NKX2-1
 GO:0031128 1 / 1 1,699× 5.89e-4 1.06e-2 ✓ sig.
histidyl-tRNA aminoacylation
HARS1
 GO:0006427 1 / 2 849× 1.18e-3 1.59e-2 ✓ sig.
response to Thyroglobulin triiodothyronine
SLC2A1
 GO:1904016 1 / 2 849× 1.18e-3 1.59e-2 ✓ sig.
basal protein localization
NCKAP1
 GO:0045175 1 / 2 849× 1.18e-3 1.59e-2 ✓ sig.
zygotic determination of anterior/posterior axis, embryo
NCKAP1
 GO:0007354 1 / 2 849× 1.18e-3 1.59e-2 ✓ sig.
forebrain neuron fate commitment
NKX2-1
 GO:0021877 1 / 2 849× 1.18e-3 1.59e-2 ✓ sig.
monoatomic ion transmembrane transport
SCN8A, CHRNB2, SCN1A
 GO:0034220 3 / 404 12.6× 1.45e-3 1.80e-2 ✓ sig.
regulation of synaptic transmission, dopaminergic
CHRNB2
 GO:0032225 1 / 3 566× 1.76e-3 1.99e-2 ✓ sig.
paraxial mesoderm morphogenesis
NCKAP1
 GO:0048340 1 / 3 566× 1.76e-3 1.99e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Cognitive impairment with or without cerebellar ataxia Seizures, benign familial infantile, 5 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cognitive impairment with or without cerebellar ataxia Paroxysmal kinesigenic dyskinesias 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cognitive impairment with or without cerebellar ataxia Myoclonus, familial, 2 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Myoclonus, familial, 2 Seizures, benign familial infantile, 5 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Myoclonus, familial, 2 Paroxysmal kinesigenic dyskinesias 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Paroxysmal kinesigenic dyskinesias Seizures, benign familial infantile, 5 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Choreoathetosis Cognitive impairment with or without cerebellar ataxia 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Choreoathetosis Seizures, benign familial infantile, 5 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Cognitive impairment with or without cerebellar ataxia Focal onset epileptic seizure 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Focal onset epileptic seizure Seizures, benign familial infantile, 5 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Focal onset epileptic seizure Paroxysmal kinesigenic dyskinesias 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Focal onset epileptic seizure Myoclonus, familial, 2 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Choreoathetosis Myoclonus, familial, 2 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Choreoathetosis Paroxysmal kinesigenic dyskinesias 0.143 1 3.87e-4 7.33e-4 ✓ sig.