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 271

7 diseases · 9 shared-gene connections
7 Diseases
17 Unique genes
0.185 Avg. similarity score
Frontal lobe epilepsy Most-connected disease (5 links)
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Disease Searched: familial sleep-related hypermotor epilepsy 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 ⇵
Frontal lobe epilepsy 5 5 5
Focal onset epileptic seizure 3 3 6
Nocturnal frontal lobe epilepsy 3 3 9
familial sleep-related hypermotor epilepsy 3 3 3
Childhood-onset epilepsy syndrome 2 2 3
Intracranial hypertension 1 1 1
intellectual disability, autosomal dominant 42 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
CHRNB2 4 / 7 familial sleep-related hypermotor epilepsy, Focal onset epileptic seizure, Frontal lobe epilepsy, Nocturnal frontal lobe epilepsy
CHRNA4 3 / 7 familial sleep-related hypermotor epilepsy, Frontal lobe epilepsy, Nocturnal frontal lobe epilepsy
KCNT1 3 / 7 Childhood-onset epilepsy syndrome, Frontal lobe epilepsy, Nocturnal frontal lobe epilepsy
CHRNA2 2 / 7 familial sleep-related hypermotor epilepsy, Nocturnal frontal lobe epilepsy
CRH 2 / 7 Frontal lobe epilepsy, Nocturnal frontal lobe epilepsy
GNB1 2 / 7 Focal onset epileptic seizure, intellectual disability, autosomal dominant 42
SLC4A10 2 / 7 Frontal lobe epilepsy, Intracranial hypertension
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 ⇵
Highly calcium permeable nicotinic acetylcholine receptors
CHRNA2, CHRNA4, CHRNB2
 Reactome 3 / 9 235× 1.97e-7 1.13e-5 ✓ sig.
Highly calcium permeable postsynaptic nicotinic acetylcholine receptors
CHRNA2, CHRNA4, CHRNB2
 Reactome 3 / 12 177× 5.14e-7 2.62e-5 ✓ sig.
Nicotine addiction
CHRNA4, CHRNB2, GABRG2
 KEGG 3 / 41 51.7× 2.43e-5 6.88e-4 ✓ sig.
Highly sodium permeable postsynaptic acetylcholine nicotinic receptors
CHRNA4, CHRNB2
 Reactome 2 / 7 202× 3.94e-5 1.03e-3 ✓ sig.
Neuroactive ligand-receptor interaction
CHRNA2, CHRNA4, CHRNB2, CRH, GABRG2
 KEGG 5 / 370 9.5× 1.23e-4 2.58e-3 ✓ sig.
Cholinergic synapse
CHRNA4, CHRNB2, GNB1
 KEGG 3 / 115 18.4× 5.27e-4 8.20e-3 ✓ sig.
Phase 0 - rapid depolarisation
SCN8A, SCN1A
 Reactome 2 / 44 32.1× 1.72e-3 2.04e-2 ✓ sig.
Amino acids regulate mTORC1
DEPDC5, ATP6V0C
 Reactome 2 / 55 25.7× 2.68e-3 2.83e-2 ✓ sig.
GABAergic synapse
GABRG2, GNB1
 KEGG 2 / 89 15.9× 6.87e-3 5.41e-2
Morphine addiction
GABRG2, GNB1
 KEGG 2 / 91 15.5× 7.17e-3 5.57e-2
Negative regulation of the PI3K/AKT network
PHLPP1
 Reactome 1 / 8 88.3× 1.13e-2 7.47e-2
Synthesis of UDP-N-acetyl-glucosamine
AMDHD2
 Reactome 1 / 8 88.3× 1.13e-2 7.47e-2
Activation of the phototransduction cascade
GNB1
 Reactome 1 / 9 78.5× 1.27e-2 8.03e-2
ADORA2B mediated anti-inflammatory cytokines production
CRH, GNB1
 Reactome 2 / 128 11.0× 1.38e-2 8.44e-2
Bicarbonate transporters
SLC4A10
 Reactome 1 / 10 70.6× 1.41e-2 8.52e-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 ⇵
monoatomic ion transport
CHRNA2, CHRNA4, CHRNB2, GABRG2, KCNT1, ATP6V0C, SLC4A10, SCN8A, SCN1A
 GO:0006811 9 / 667 14.8× 1.68e-9 3.52e-7 ✓ sig.
monoatomic ion transmembrane transport
CHRNA2, CHRNA4, CHRNB2, GABRG2, KCNT1, SCN8A, SCN1A
 GO:0034220 7 / 404 19.0× 3.38e-8 4.78e-6 ✓ sig.
synaptic transmission, cholinergic
CHRNA2, CHRNA4, CHRNB2
 GO:0007271 3 / 25 132× 1.42e-6 1.11e-4 ✓ sig.
acetylcholine receptor signaling pathway
CHRNA2, CHRNA4, CHRNB2
 GO:0095500 3 / 28 118× 2.02e-6 1.47e-4 ✓ sig.
membrane depolarization
CHRNA2, CHRNA4, CHRNB2
 GO:0051899 3 / 32 103× 3.05e-6 2.03e-4 ✓ sig.
response to nicotine
CHRNA2, CHRNA4, CHRNB2
 GO:0035094 3 / 40 82.4× 6.05e-6 3.52e-4 ✓ sig.
action potential
CHRNA4, SCN8A, SCN1A
 GO:0001508 3 / 53 62.2× 1.42e-5 6.93e-4 ✓ sig.
regulation of postsynaptic membrane potential
CHRNA2, CHRNB2, GABRG2
 GO:0060078 3 / 59 55.9× 1.97e-5 8.94e-4 ✓ sig.
response to acetylcholine
CHRNA2, CHRNB2
 GO:1905144 2 / 8 275× 2.17e-5 9.65e-4 ✓ sig.
behavioral response to nicotine
CHRNA4, CHRNB2
 GO:0035095 2 / 9 244× 2.79e-5 1.16e-3 ✓ sig.
excitatory postsynaptic potential
CHRNA2, CHRNA4, CHRNB2
 GO:0060079 3 / 69 47.8× 3.16e-5 1.27e-3 ✓ sig.
chemical synaptic transmission
CHRNA4, CHRNB2, CRH, GABRG2
 GO:0007268 4 / 236 18.6× 5.19e-5 1.86e-3 ✓ sig.
regulation of dopamine secretion
CHRNA4, CHRNB2
 GO:0014059 2 / 15 147× 8.12e-5 2.60e-3 ✓ sig.
locomotory exploration behavior
CRH, SLC4A10
 GO:0035641 2 / 16 137× 9.28e-5 2.87e-3 ✓ sig.
cardiac muscle cell action potential involved in contraction
SCN8A, SCN1A
 GO:0086002 2 / 24 91.6× 2.12e-4 5.27e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Frontal lobe epilepsy Nocturnal frontal lobe epilepsy 0.364 4 2.69e-13 3.42e-12 ✓ sig.
familial sleep-related hypermotor epilepsy Nocturnal frontal lobe epilepsy 0.300 3 1.38e-10 1.35e-9 ✓ sig.
familial sleep-related hypermotor epilepsy Frontal lobe epilepsy 0.286 2 2.53e-7 1.65e-6 ✓ sig.
Frontal lobe epilepsy Intracranial hypertension 0.167 1 3.25e-4 7.70e-4 ✓ sig.
Focal onset epileptic seizure intellectual disability, autosomal dominant 42 0.143 1 3.90e-4 8.66e-4 ✓ sig.
Childhood-onset epilepsy syndrome Frontal lobe epilepsy 0.125 1 9.74e-4 1.66e-3 ✓ sig.
familial sleep-related hypermotor epilepsy Focal onset epileptic seizure 0.111 1 1.17e-3 1.89e-3 ✓ sig.
Childhood-onset epilepsy syndrome Nocturnal frontal lobe epilepsy 0.083 1 1.75e-3 2.61e-3 ✓ sig.
Focal onset epileptic seizure Frontal lobe epilepsy 0.091 1 1.95e-3 2.83e-3 ✓ sig.