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 95

13 diseases · 22 shared-gene connections
13 Diseases
108 Unique genes
0.108 Avg. similarity score
Dravet syndrome Most-connected disease (7 links)
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Disease Searched: Early-onset generalized dystonia 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 ⇵
Dravet syndrome 7 7 8
Febrile convulsion 7 7 22
Generalized epilepsy with febrile seizures plus 5 5 17
Rolandic epilepsy 5 5 47
Lennox-gastaut syndrome 4 4 12
Epileptic encephalopathy, early infantile 3 3 12
Female restricted epilepsy with intellectual disability 3 3 1
Genetic developmental and epileptic encephalopathy 3 3 36
Febrile seizures, familial, 2 2 2 1
Febrile seizures, familial, 8 2 2 1
Cranio-cervical dystonia 1 1 1
Early-onset generalized dystonia 1 1 1
Epileptic encephalopathy, early infantile, 21 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
GABRG2 6 / 13 Dravet syndrome, Febrile convulsion, Febrile seizures, familial, 8, Generalized epilepsy with febrile seizures plus and 2 more
SCN1A 6 / 13 Dravet syndrome, Febrile convulsion, Generalized epilepsy with febrile seizures plus, Genetic developmental and epileptic encephalopathy and 2 more
SCN1B 5 / 13 Dravet syndrome, Febrile convulsion, Generalized epilepsy with febrile seizures plus, Genetic developmental and epileptic encephalopathy and 1 more
SCN2A 5 / 13 Dravet syndrome, Febrile convulsion, Generalized epilepsy with febrile seizures plus, Lennox-gastaut syndrome and 1 more
PCDH19 4 / 13 Dravet syndrome, Epileptic encephalopathy, early infantile, Female restricted epilepsy with intellectual disability, Rolandic epilepsy
SCN9A 4 / 13 Dravet syndrome, Febrile convulsion, Generalized epilepsy with febrile seizures plus, Rolandic epilepsy
CPA6 3 / 13 Febrile convulsion, Generalized epilepsy with febrile seizures plus, Rolandic epilepsy
HCN1 3 / 13 Epileptic encephalopathy, early infantile, Febrile convulsion, Generalized epilepsy with febrile seizures plus
HCN2 3 / 13 Febrile convulsion, Febrile seizures, familial, 2, Generalized epilepsy with febrile seizures plus
STXBP1 3 / 13 Dravet syndrome, Epileptic encephalopathy, early infantile, Genetic developmental and epileptic encephalopathy
WWOX 3 / 13 Epileptic encephalopathy, early infantile, Genetic developmental and epileptic encephalopathy, Rolandic epilepsy
ADGRV1 2 / 13 Febrile convulsion, Generalized epilepsy with febrile seizures plus
ANO3 2 / 13 Cranio-cervical dystonia, Febrile convulsion
ARFGEF3 2 / 13 Early-onset generalized dystonia, Febrile convulsion
CHD2 2 / 13 Lennox-gastaut syndrome, Rolandic epilepsy
CSTB 2 / 13 Genetic developmental and epileptic encephalopathy, Rolandic epilepsy
CUX2 2 / 13 Genetic developmental and epileptic encephalopathy, Lennox-gastaut syndrome
DNM1 2 / 13 Genetic developmental and epileptic encephalopathy, Lennox-gastaut syndrome
DOCK7 2 / 13 Epileptic encephalopathy, early infantile, Genetic developmental and epileptic encephalopathy
GABRB3 2 / 13 Genetic developmental and epileptic encephalopathy, Lennox-gastaut syndrome
KCNQ3 2 / 13 Genetic developmental and epileptic encephalopathy, Rolandic epilepsy
NECAP1 2 / 13 Epileptic encephalopathy, early infantile, 21, Genetic developmental and epileptic encephalopathy
PLCB1 2 / 13 Genetic developmental and epileptic encephalopathy, Rolandic epilepsy
RELN 2 / 13 Generalized epilepsy with febrile seizures plus, Rolandic epilepsy
SCN8A 2 / 13 Epileptic encephalopathy, early infantile, Febrile convulsion
SLC25A22 2 / 13 Epileptic encephalopathy, early infantile, Genetic developmental and epileptic encephalopathy
SPTAN1 2 / 13 Genetic developmental and epileptic encephalopathy, Rolandic epilepsy
STX1B 2 / 13 Febrile convulsion, Generalized epilepsy with febrile seizures plus
SZT2 2 / 13 Genetic developmental and epileptic encephalopathy, Rolandic epilepsy
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 ⇵
GABAergic synapse
GABRA1, GABRG2, SLC6A1, SLC32A1, GABRD, CACNA1A, GABRB3, ABAT, GABRB1, GLUL, GNAO1, SLC12A5
 KEGG 12 / 89 15.0× 2.00e-11 2.84e-9 ✓ sig.
Nicotine addiction
GABRA1, GABRG2, GRIN1, GRIN2A, SLC32A1, GABRD, CACNA1A, GABRB3, GABRB1
 KEGG 9 / 41 24.4× 7.56e-11 9.17e-9 ✓ sig.
Phase 0 - rapid depolarisation
SCN1A, SCN1B, SCN2A, SCN9A, SCN8A, FGF13, FGF12, SCN3A
 Reactome 8 / 44 20.2× 4.46e-9 3.59e-7 ✓ sig.
Synaptic vesicle cycle
STXBP1, SLC6A1, STX1B, UNC13A, SLC32A1, CACNA1A, DNM1, SNAP25
 KEGG 8 / 79 11.3× 5.06e-7 2.31e-5 ✓ sig.
Retrograde endocannabinoid signaling
GABRA1, GABRG2, PLCB1, SLC32A1, GABRD, CACNA1A, GABRB3, MAPK10, GABRB1, GNAO1
 KEGG 10 / 149 7.5× 8.75e-7 3.71e-5 ✓ sig.
Morphine addiction
GABRA1, GABRG2, SLC32A1, GABRD, CACNA1A, GABRB3, GABRB1, GNAO1
 KEGG 8 / 91 9.8× 1.51e-6 5.95e-5 ✓ sig.
GABA receptor activation
GABRA1, GABRG2, GABRB3, GABRB1
 Reactome 4 / 16 27.8× 1.04e-5 3.00e-4 ✓ sig.
Taste transduction
GABRA1, SCN2A, SCN9A, PLCB1, CACNA1A, SCN3A
 KEGG 6 / 86 7.8× 1.21e-4 2.20e-3 ✓ sig.
GABA synthesis, release, reuptake and degradation
STXBP1, SLC32A1, SNAP25
 Reactome 3 / 13 25.7× 1.89e-4 3.15e-3 ✓ sig.
Toxicity of botulinum toxin type C (BoNT/C)
STX1B, SNAP25
 Reactome 2 / 3 74.1× 2.39e-4 3.77e-3 ✓ sig.
Regulation of insulin secretion
SLC2A1, CACNA1A, CACNA1E
 Reactome 3 / 16 20.9× 3.64e-4 5.22e-3 ✓ sig.
Acetylcholine Neurotransmitter Release Cycle
STXBP1, CHAT, SNAP25
 Reactome 3 / 17 19.6× 4.39e-4 6.03e-3 ✓ sig.
HCN channels
HCN1, HCN2
 Reactome 2 / 4 55.6× 4.75e-4 6.42e-3 ✓ sig.
Voltage gated Potassium channels
KCNQ3, KCNA2, KCNC2, KCNB1
 Reactome 4 / 43 10.3× 5.83e-4 7.52e-3 ✓ sig.
Cholinergic synapse
KCNQ3, PLCB1, CHAT, CACNA1A, CHRNB4, GNAO1
 KEGG 6 / 115 5.8× 5.85e-4 7.54e-3 ✓ 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 ⇵
monoatomic ion transmembrane transport
ANO3, GABRA1, GABRG2, SCN1A, SCN2A, SCN9A, GRIN1, GRIN2A, KCNQ3, KCNT1, HCN1, SCN8A
 GO:0034220 25 / 404 10.7× 4.71e-19 6.59e-16 ✓ sig.
monoatomic ion transport
GABRA1, GABRG2, SCN1A, SCN1B, SCN2A, SCN9A, GRIN1, GRIN2A, KCNQ3, KCNT1, HCN1, SCN8A
 GO:0006811 28 / 667 7.3× 7.02e-17 7.09e-14 ✓ sig.
transmembrane transport
SCN1A, SCN2A, SCN9A, KCNQ3, SLC2A1, HCN1, MFSD2A, OCA2, SCN8A, SLC30A3, HCN2, CACNA1A
 GO:0055085 20 / 557 6.2× 5.59e-11 1.81e-8 ✓ sig.
cardiac muscle cell action potential involved in contraction
SCN1A, SCN1B, SCN2A, SCN9A, SCN8A, FGF12, SCN3A
 GO:0086002 7 / 24 50.5× 5.65e-11 1.83e-8 ✓ sig.
sodium ion transmembrane transport
SCN1A, SCN1B, SCN2A, SCN9A, GRIN1, GRIN2A, SLC6A1, HCN1, SCN8A, HCN2, SCN3A
 GO:0035725 11 / 134 14.2× 3.25e-10 8.77e-8 ✓ sig.
action potential
SCN1A, SCN2A, SCN9A, SCN8A, KCNA2, KCNC2, SCN3A, KCNB1
 GO:0001508 8 / 53 26.1× 6.84e-10 1.67e-7 ✓ sig.
neuronal action potential
SCN1A, SCN2A, SCN9A, KCNQ3, HCN1, CHRNB4, KCNA2
 GO:0019228 7 / 34 35.6× 8.37e-10 1.99e-7 ✓ sig.
chemical synaptic transmission
GABRG2, GRIN1, GRIN2A, KCNQ3, SLC6A1, UNC13A, GABRD, CACNA1A, GABRB3, CACNA1E, FGF12, SLC12A5
 GO:0007268 13 / 236 9.5× 1.07e-9 2.45e-7 ✓ sig.
chloride transmembrane transport
ANO3, GABRA1, GABRG2, SLC6A1, OCA2, ANO4, GABRD, GABRB3, GABRB1, SLC12A5
 GO:1902476 10 / 114 15.2× 1.12e-9 2.57e-7 ✓ sig.
regulation of postsynaptic membrane potential
GABRA1, GABRG2, GRIN2A, HCN1, GABRD, CHRNB4, GABRB1, KCNA2
 GO:0060078 8 / 59 23.5× 1.66e-9 3.62e-7 ✓ sig.
learning
CNTNAP2, GRIN2A, PLCB1, RELN, FGF13, GABRB3, SLC12A5, SYNJ1
 GO:0007612 8 / 64 21.6× 3.24e-9 6.53e-7 ✓ sig.
positive regulation of excitatory postsynaptic potential
GRIN1, GRIN2A, RELN, TBC1D24, STX1B, CUX2
 GO:2000463 6 / 32 32.4× 2.60e-8 4.06e-6 ✓ sig.
sodium ion transport
SCN1A, SCN1B, SCN2A, SCN9A, HCN1, SCN8A, HCN2, FGF13, SCN3A
 GO:0006814 9 / 144 10.8× 1.53e-7 1.82e-5 ✓ sig.
potassium ion transmembrane transport
KCNQ3, KCNT1, HCN1, HCN2, KCNA2, KCNC2, SLC12A5, SNAP25, KCNB1
 GO:0071805 9 / 150 10.4× 2.16e-7 2.41e-5 ✓ sig.
regulation of membrane potential
SCN1A, GRIN1, GRIN2A, HCN1, HCN2, CHRNB4, GABRB1
 GO:0042391 7 / 85 14.2× 6.03e-7 5.70e-5 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Febrile convulsion Generalized epilepsy with febrile seizures plus 0.333 10 5.73e-26 1.00e-24 ✓ sig.
Dravet syndrome Rolandic epilepsy 0.120 6 1.56e-14 1.85e-13 ✓ sig.
Generalized epilepsy with febrile seizures plus Rolandic epilepsy 0.121 7 2.82e-14 3.30e-13 ✓ sig.
Dravet syndrome Generalized epilepsy with febrile seizures plus 0.238 5 4.66e-14 5.37e-13 ✓ sig.
Genetic developmental and epileptic encephalopathy Rolandic epilepsy 0.105 8 1.09e-13 1.23e-12 ✓ sig.
Dravet syndrome Febrile convulsion 0.192 5 1.98e-13 2.22e-12 ✓ sig.
Febrile convulsion Rolandic epilepsy 0.094 6 4.03e-11 3.91e-10 ✓ sig.
Epileptic encephalopathy, early infantile Genetic developmental and epileptic encephalopathy 0.089 4 1.20e-8 9.41e-8 ✓ sig.
Dravet syndrome Lennox-gastaut syndrome 0.167 3 1.99e-8 1.53e-7 ✓ sig.
Generalized epilepsy with febrile seizures plus Lennox-gastaut syndrome 0.111 3 2.40e-7 1.59e-6 ✓ sig.
Febrile convulsion Lennox-gastaut syndrome 0.094 3 5.43e-7 3.43e-6 ✓ sig.
Dravet syndrome Epileptic encephalopathy, early infantile 0.105 2 1.54e-5 8.15e-5 ✓ sig.
Dravet syndrome Febrile seizures, familial, 8 0.111 1 5.17e-4 9.13e-4 ✓ sig.
Dravet syndrome Female restricted epilepsy with intellectual disability 0.111 1 5.17e-4 9.13e-4 ✓ sig.
Febrile seizures, familial, 8 Lennox-gastaut syndrome 0.077 1 7.75e-4 1.25e-3 ✓ sig.
Epileptic encephalopathy, early infantile Female restricted epilepsy with intellectual disability 0.077 1 7.75e-4 1.25e-3 ✓ sig.
Febrile seizures, familial, 2 Generalized epilepsy with febrile seizures plus 0.056 1 1.10e-3 1.65e-3 ✓ sig.
Early-onset generalized dystonia Febrile convulsion 0.043 1 1.42e-3 2.04e-3 ✓ sig.
Febrile convulsion Febrile seizures, familial, 2 0.043 1 1.42e-3 2.04e-3 ✓ sig.
Cranio-cervical dystonia Febrile convulsion 0.043 1 1.42e-3 2.04e-3 ✓ sig.
Epileptic encephalopathy, early infantile, 21 Genetic developmental and epileptic encephalopathy 0.027 1 2.32e-3 3.05e-3 ✓ sig.
Female restricted epilepsy with intellectual disability Rolandic epilepsy 0.021 1 3.03e-3 3.86e-3 ✓ sig.