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 47

15 diseases · 29 shared-gene connections
15 Diseases
128 Unique genes
0.116 Avg. similarity score
Childhood absence epilepsy Most-connected disease (7 links)
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Disease Searched: Myoclonic 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 ⇵
Childhood absence epilepsy 7 7 10
Dravet syndrome 7 7 8
Absence epilepsy 6 6 7
Lennox-gastaut syndrome 6 6 12
Febrile convulsion 5 5 22
Generalized epilepsy with febrile seizures plus 4 4 16
Rolandic epilepsy 4 4 47
Ataxia 3 3 21
Idiopathic generalized epilepsy 3 3 12
Myoclonic epilepsy 3 3 24
Synovial disorder 3 3 6
Conn syndrome 2 2 1
Female restricted epilepsy with intellectual disability 2 2 1
Juvenile absence epilepsy 2 2 1
Cranio-cervical dystonia 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
GABRG2 6 / 15 Childhood absence epilepsy, Dravet syndrome, Febrile convulsion, Generalized epilepsy with febrile seizures plus and 2 more
SCN1A 6 / 15 Dravet syndrome, Febrile convulsion, Generalized epilepsy with febrile seizures plus, Lennox-gastaut syndrome and 2 more
GABRA1 5 / 15 Ataxia, Childhood absence epilepsy, Dravet syndrome, Idiopathic generalized epilepsy and 1 more
SCN1B 5 / 15 Childhood absence epilepsy, Dravet syndrome, Febrile convulsion, Generalized epilepsy with febrile seizures plus and 1 more
SCN2A 5 / 15 Dravet syndrome, Febrile convulsion, Generalized epilepsy with febrile seizures plus, Lennox-gastaut syndrome and 1 more
GABRB3 4 / 15 Absence epilepsy, Childhood absence epilepsy, Lennox-gastaut syndrome, Synovial disorder
SCN9A 4 / 15 Dravet syndrome, Febrile convulsion, Generalized epilepsy with febrile seizures plus, Rolandic epilepsy
SLC2A1 4 / 15 Ataxia, Childhood absence epilepsy, Idiopathic generalized epilepsy, Rolandic epilepsy
CACNA1A 3 / 15 Absence epilepsy, Ataxia, Lennox-gastaut syndrome
CACNA1H 3 / 15 Absence epilepsy, Childhood absence epilepsy, Conn syndrome
CACNB4 3 / 15 Ataxia, Idiopathic generalized epilepsy, Myoclonic epilepsy
CPA6 3 / 15 Febrile convulsion, Generalized epilepsy with febrile seizures plus, Rolandic epilepsy
EFHC1 3 / 15 Absence epilepsy, Juvenile absence epilepsy, Myoclonic epilepsy
GABRD 3 / 15 Generalized epilepsy with febrile seizures plus, Idiopathic generalized epilepsy, Myoclonic epilepsy
HCN1 3 / 15 Ataxia, Febrile convulsion, Generalized epilepsy with febrile seizures plus
JRK 3 / 15 Absence epilepsy, Childhood absence epilepsy, Myoclonic epilepsy
PCDH19 3 / 15 Dravet syndrome, Female restricted epilepsy with intellectual disability, Rolandic epilepsy
ADGRV1 2 / 15 Febrile convulsion, Generalized epilepsy with febrile seizures plus
ANO3 2 / 15 Cranio-cervical dystonia, Febrile convulsion
CACNA2D2 2 / 15 Absence epilepsy, Ataxia
CHD2 2 / 15 Lennox-gastaut syndrome, Rolandic epilepsy
CLCN2 2 / 15 Idiopathic generalized epilepsy, Myoclonic epilepsy
HCN2 2 / 15 Febrile convulsion, Idiopathic generalized epilepsy
KCNQ3 2 / 15 Myoclonic epilepsy, Rolandic epilepsy
PRICKLE2 2 / 15 Myoclonic epilepsy, Rolandic epilepsy
RELN 2 / 15 Generalized epilepsy with febrile seizures plus, Rolandic epilepsy
SCN8A 2 / 15 Ataxia, Febrile convulsion
STX1B 2 / 15 Febrile convulsion, Generalized epilepsy with febrile seizures plus
STXBP1 2 / 15 Dravet syndrome, Myoclonic 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 ⇵
Nicotine addiction
CACNA1A, GABRA1, GABRA4, GABRA6, GABRB3, GABRG2, GABRD, GRIN1, GRIN2A, SLC32A1, GABRA2, GABRA5
 KEGG 13 / 41 29.8× 1.68e-16 7.14e-14 ✓ sig.
GABA receptor activation
GABRA1, GABRA4, GABRA6, GABRB3, GABRG2, GABRA2, GABRA5, GABRB2
 Reactome 8 / 16 46.9× 1.60e-12 3.32e-10 ✓ sig.
GABAergic synapse
CACNA1A, GABRA1, GABRA4, GABRA6, GABRB3, GABRG2, GABRD, SLC12A5, SLC6A1, SLC32A1, GABRA2, GABRA5
 KEGG 13 / 89 13.7× 8.74e-12 1.61e-9 ✓ sig.
Phase 0 - rapid depolarisation
CACNA2D2, CACNB4, SCN8A, SCN1B, SCN1A, SCN2A, SCN9A, FGF13, CACNA2D3
 Reactome 9 / 44 19.2× 6.91e-10 8.42e-8 ✓ sig.
Morphine addiction
CACNA1A, GABRA1, GABRA4, GABRA6, GABRB3, GABRG2, GABRD, SLC32A1, GABRA2, GABRA5, GABRB2
 KEGG 11 / 91 11.3× 3.00e-9 3.14e-7 ✓ sig.
Retrograde endocannabinoid signaling
CACNA1A, GABRA1, GABRA4, GABRA6, GABRB3, GABRG2, GABRD, PLCB1, SLC32A1, GABRA2, MAPK10, GABRA5
 KEGG 13 / 149 8.2× 6.06e-9 5.97e-7 ✓ sig.
Taste transduction
CACNA1A, GABRA1, GABRA4, GABRA6, SCN2A, SCN9A, HCN4, PLCB1, GABRA2, GABRA5
 KEGG 10 / 86 10.9× 2.37e-8 1.96e-6 ✓ sig.
Neuroactive ligand-receptor interaction
GABRA1, GABRA4, GABRA6, GABRB3, GABRG2, NPY, POMC, GABRD, GRIN1, GRIN2A, CHRNA1, GABRA2
 KEGG 16 / 370 4.1× 1.92e-6 9.14e-5 ✓ sig.
HCN channels
HCN1, HCN2, HCN4
 Reactome 3 / 4 70.4× 4.69e-6 1.93e-4 ✓ sig.
Presynaptic depolarization and calcium channel opening
CACNA1A, CACNA2D2, CACNB4, CACNA2D3
 Reactome 4 / 12 31.3× 5.70e-6 2.25e-4 ✓ sig.
Synaptic vesicle cycle
CACNA1A, STXBP1, SLC6A1, STX1B, UNC13A, SLC32A1, DNM1
 KEGG 7 / 79 8.3× 2.03e-5 6.39e-4 ✓ sig.
Highly calcium permeable nicotinic acetylcholine receptors
CHRNA1, CHRNA2, CHRNB4
 Reactome 3 / 9 31.3× 9.48e-5 2.22e-3 ✓ sig.
Highly calcium permeable postsynaptic nicotinic acetylcholine receptors
CHRNA1, CHRNA2, CHRNB4
 Reactome 3 / 12 23.5× 2.42e-4 4.66e-3 ✓ sig.
Regulation of insulin secretion
CACNA1A, CACNA2D2, SLC2A1
 Reactome 3 / 16 17.6× 5.98e-4 9.49e-3 ✓ sig.
Adipocytokine signaling pathway
SLC2A1, NPY, POMC, TNFRSF1A, MAPK10
 KEGG 5 / 70 6.7× 8.84e-4 1.27e-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 ⇵
monoatomic ion transmembrane transport
CACNA1A, CACNA2D2, CACNB4, GABRA1, GABRA4, HCN1, SCN8A, CACNA1H, GABRA6, GABRB3, GABRG2, ANO3
 GO:0034220 33 / 404 11.9× 2.03e-26 7.46e-23 ✓ sig.
monoatomic ion transport
ATP7A, CACNA1A, CACNA2D2, CACNB4, GABRA1, GABRA4, HCN1, SCN8A, CACNA1H, GABRA6, GABRB3, GABRG2
 GO:0006811 37 / 667 8.1× 1.03e-23 2.86e-20 ✓ sig.
chloride transmembrane transport
GABRA1, GABRA4, GABRA6, GABRB3, GABRG2, ANO3, CASR, CLCN2, GABRD, SLC12A5, SLC6A1, OCA2
 GO:1902476 16 / 114 20.5× 6.58e-17 6.42e-14 ✓ sig.
regulation of postsynaptic membrane potential
GABRA1, GABRA4, HCN1, GABRA6, GABRG2, GABRD, GRIN2A, CHRNA1, GABRA2, CHRNA2, CHRNB4, GABRA5
 GO:0060078 13 / 59 32.2× 1.21e-16 1.13e-13 ✓ sig.
gamma-aminobutyric acid signaling pathway
CACNB4, GABRA1, GABRA4, GABRA6, GABRB3, GABRG2, GABRD, GABRA2, GABRA5, GABRB2
 GO:0007214 10 / 30 48.7× 4.25e-15 3.01e-12 ✓ sig.
inhibitory synapse assembly
GABRA1, GABRA4, GABRA6, GABRB3, GABRG2, FGF13, GABRA2, GABRA5, GABRB2
 GO:1904862 9 / 25 52.6× 4.65e-14 2.73e-11 ✓ sig.
regulation of membrane potential
CACNB4, HCN1, CACNA1H, SCN1A, KCNMA1, HCN2, HCN4, GRIN1, GRIN2A, CHRNA1, CHRNB4, WWP2
 GO:0042391 12 / 85 20.6× 5.44e-13 2.62e-10 ✓ sig.
synaptic transmission, GABAergic
GABRA1, GABRA4, GABRA6, GABRB3, GABRG2, GABRD, GABRA2, GABRA5, GABRB2
 GO:0051932 9 / 35 37.5× 1.52e-12 6.79e-10 ✓ sig.
chemical synaptic transmission
CACNA1A, CACNB4, SNCA, GABRB3, GABRG2, NPY, PMP22, GABRD, SLC12A5, GRIN1, GRIN2A, KCNQ3
 GO:0007268 16 / 236 9.9× 6.70e-12 2.58e-9 ✓ sig.
chloride transport
GABRA1, GABRA4, GABRA6, GABRB3, GABRG2, CLCN2, GABRD, SLC12A5, GABRA2, GABRA5, GABRB2
 GO:0006821 11 / 81 19.8× 8.13e-12 3.06e-9 ✓ sig.
sodium ion transmembrane transport
HCN1, SCN8A, SCN1B, SCN1A, SCN2A, SCN9A, KCNK9, HCN2, HCN4, GRIN1, GRIN2A, SLC6A1
 GO:0035725 12 / 134 13.1× 1.31e-10 3.74e-8 ✓ sig.
neuronal action potential
HCN1, SCN1A, SCN2A, SCN9A, KCNQ3, CHRNA1, CHRNB4
 GO:0019228 7 / 34 30.1× 2.77e-9 5.51e-7 ✓ sig.
transmembrane transport
ABCB7, CACNA1A, HCN1, SCN8A, SLC2A1, CACNA1H, SCN1A, SCN2A, SCN9A, CLCN2, SLC12A5, KCNMA1
 GO:0055085 18 / 557 4.7× 4.76e-8 6.56e-6 ✓ sig.
sodium ion transport
HCN1, SCN8A, SCN1B, SCN1A, SCN2A, SCN9A, KCNK9, HCN2, HCN4, FGF13
 GO:0006814 10 / 144 10.1× 5.64e-8 7.54e-6 ✓ sig.
positive regulation of excitatory postsynaptic potential
GRIN1, GRIN2A, RELN, TBC1D24, STX1B, CUX2
 GO:2000463 6 / 32 27.4× 7.19e-8 9.27e-6 ✓ 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 0.300 9 4.23e-23 9.26e-22 ✓ sig.
Dravet syndrome Rolandic epilepsy 0.120 6 1.62e-14 2.23e-13 ✓ sig.
Generalized epilepsy with febrile seizures plus Rolandic epilepsy 0.123 7 1.73e-14 2.38e-13 ✓ sig.
Dravet syndrome Generalized epilepsy with febrile seizures plus 0.250 5 3.39e-14 4.54e-13 ✓ sig.
Dravet syndrome Febrile convulsion 0.192 5 2.04e-13 2.60e-12 ✓ sig.
Febrile convulsion Rolandic epilepsy 0.094 6 4.18e-11 4.30e-10 ✓ sig.
Idiopathic generalized epilepsy Myoclonic epilepsy 0.121 4 2.23e-9 1.94e-8 ✓ sig.
Absence epilepsy Childhood absence epilepsy 0.200 3 6.89e-9 5.75e-8 ✓ sig.
Childhood absence epilepsy Dravet syndrome 0.188 3 1.10e-8 8.82e-8 ✓ sig.
Dravet syndrome Lennox-gastaut syndrome 0.167 3 2.02e-8 1.58e-7 ✓ sig.
Dravet syndrome Myoclonic epilepsy 0.100 3 1.85e-7 1.23e-6 ✓ sig.
Generalized epilepsy with febrile seizures plus Lennox-gastaut syndrome 0.115 3 2.01e-7 1.34e-6 ✓ sig.
Ataxia Idiopathic generalized epilepsy 0.097 3 4.77e-7 2.97e-6 ✓ sig.
Febrile convulsion Lennox-gastaut syndrome 0.094 3 5.52e-7 3.40e-6 ✓ sig.
Absence epilepsy Lennox-gastaut syndrome 0.111 2 1.17e-5 5.71e-5 ✓ sig.
Childhood absence epilepsy Lennox-gastaut syndrome 0.095 2 2.50e-5 1.17e-4 ✓ sig.
Childhood absence epilepsy Idiopathic generalized epilepsy 0.095 2 2.50e-5 1.17e-4 ✓ sig.
Absence epilepsy Ataxia 0.074 2 3.70e-5 1.70e-4 ✓ sig.
Ataxia Childhood absence epilepsy 0.067 2 7.92e-5 2.83e-4 ✓ sig.
Absence epilepsy Conn syndrome 0.125 1 4.55e-4 9.73e-4 ✓ sig.
Absence epilepsy Juvenile absence epilepsy 0.125 1 4.55e-4 9.73e-4 ✓ sig.
Dravet syndrome Female restricted epilepsy with intellectual disability 0.111 1 5.20e-4 1.06e-3 ✓ sig.
Childhood absence epilepsy Conn syndrome 0.091 1 6.49e-4 1.24e-3 ✓ sig.
Cranio-cervical dystonia Febrile convulsion 0.043 1 1.43e-3 2.23e-3 ✓ sig.
Juvenile absence epilepsy Myoclonic epilepsy 0.040 1 1.56e-3 2.38e-3 ✓ sig.
Absence epilepsy Synovial disorder 0.077 1 2.72e-3 3.66e-3 ✓ sig.
Female restricted epilepsy with intellectual disability Rolandic epilepsy 0.021 1 3.05e-3 4.03e-3 ✓ sig.
Childhood absence epilepsy Synovial disorder 0.063 1 3.89e-3 4.94e-3 ✓ sig.
Lennox-gastaut syndrome Synovial disorder 0.056 1 4.67e-3 5.79e-3 ✓ sig.