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 227

7 diseases · 10 shared-gene connections
7 Diseases
45 Unique genes
0.101 Avg. similarity score
Absence epilepsy 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 ⇵
Absence epilepsy 5 5 7
Childhood absence epilepsy 5 5 10
Ataxia 3 3 21
Conn syndrome 2 2 1
Idiopathic generalized epilepsy 2 2 12
Synovial disorder 2 2 6
Juvenile absence epilepsy 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
CACNA1H 3 / 7 Absence epilepsy, Childhood absence epilepsy, Conn syndrome
GABRA1 3 / 7 Ataxia, Childhood absence epilepsy, Idiopathic generalized epilepsy
GABRB3 3 / 7 Absence epilepsy, Childhood absence epilepsy, Synovial disorder
SLC2A1 3 / 7 Ataxia, Childhood absence epilepsy, Idiopathic generalized epilepsy
CACNA1A 2 / 7 Absence epilepsy, Ataxia
CACNA2D2 2 / 7 Absence epilepsy, Ataxia
CACNB4 2 / 7 Ataxia, Idiopathic generalized epilepsy
EFHC1 2 / 7 Absence epilepsy, Juvenile absence epilepsy
JRK 2 / 7 Absence epilepsy, Childhood absence 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, GABRA5, GABRB2
 KEGG 9 / 41 58.6× 1.99e-14 5.81e-12 ✓ sig.
GABA receptor activation
GABRA1, GABRA4, GABRA6, GABRB3, GABRG2, GABRA5, GABRB2
 Reactome 7 / 16 117× 7.09e-14 1.87e-11 ✓ sig.
GABAergic synapse
CACNA1A, GABRA1, GABRA4, GABRA6, GABRB3, GABRG2, GABRD, SLC12A5, GABRA5, GABRB2
 KEGG 10 / 89 30.0× 7.67e-13 1.71e-10 ✓ sig.
Morphine addiction
CACNA1A, GABRA1, GABRA4, GABRA6, GABRB3, GABRG2, GABRD, GABRA5, GABRB2
 KEGG 9 / 91 26.4× 3.89e-11 6.16e-9 ✓ sig.
Retrograde endocannabinoid signaling
CACNA1A, GABRA1, GABRA4, GABRA6, GABRB3, GABRG2, GABRD, GABRA5, GABRB2
 KEGG 9 / 149 16.1× 3.31e-9 3.27e-7 ✓ sig.
Presynaptic depolarization and calcium channel opening
CACNA1A, CACNA2D2, CACNB4, CACNA2D3
 Reactome 4 / 12 89.0× 8.33e-8 5.58e-6 ✓ sig.
HCN channels
HCN1, HCN2, HCN4
 Reactome 3 / 4 200× 1.96e-7 1.18e-5 ✓ sig.
Phase 0 - rapid depolarisation
CACNA2D2, CACNB4, SCN8A, SCN1B, CACNA2D3
 Reactome 5 / 44 30.3× 5.72e-7 3.00e-5 ✓ sig.
Taste transduction
CACNA1A, GABRA1, GABRA4, GABRA6, HCN4, GABRA5
 KEGG 6 / 86 18.6× 7.36e-7 3.73e-5 ✓ sig.
Neuroactive ligand-receptor interaction
GABRA1, GABRA4, GABRA6, GABRB3, GABRG2, NPY, GABRD, GABRA5, GABRB2
 KEGG 9 / 370 6.5× 7.53e-6 2.64e-4 ✓ sig.
Regulation of insulin secretion
CACNA1A, CACNA2D2, SLC2A1
 Reactome 3 / 16 50.0× 2.66e-5 7.53e-4 ✓ sig.
Phase 2 - plateau phase
CACNA2D2, CACNB4, CACNA2D3
 Reactome 3 / 25 32.0× 1.07e-4 2.37e-3 ✓ sig.
Arrhythmogenic right ventricular cardiomyopathy
CACNA2D2, CACNB4, DMD, CACNA2D3
 KEGG 4 / 86 12.4× 2.92e-4 5.25e-3 ✓ sig.
Hypertrophic cardiomyopathy
CACNA2D2, CACNB4, DMD, CACNA2D3
 KEGG 4 / 99 10.8× 4.99e-4 7.96e-3 ✓ sig.
Dilated cardiomyopathy
CACNA2D2, CACNB4, DMD, CACNA2D3
 KEGG 4 / 105 10.2× 6.24e-4 9.49e-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 transport
ATP7A, CACNA1A, CACNA2D2, CACNB4, GABRA1, GABRA4, HCN1, SCN8A, CACNA1H, GABRA6, GABRB3, GABRG2
 GO:0006811 24 / 667 14.9× 2.27e-23 5.98e-20 ✓ sig.
monoatomic ion transmembrane transport
CACNA1A, CACNA2D2, CACNB4, GABRA1, GABRA4, HCN1, SCN8A, CACNA1H, GABRA6, GABRB3, GABRG2, KCNK9
 GO:0034220 20 / 404 20.6× 6.02e-22 1.28e-18 ✓ sig.
gamma-aminobutyric acid signaling pathway
CACNB4, GABRA1, GABRA4, GABRA6, GABRB3, GABRG2, GABRD, GABRA5, GABRB2
 GO:0007214 9 / 30 125× 1.60e-17 1.80e-14 ✓ sig.
chloride transmembrane transport
GABRA1, GABRA4, GABRA6, GABRB3, GABRG2, CASR, CLCN2, GABRD, SLC12A5, GABRA5, GABRB2
 GO:1902476 11 / 114 40.1× 2.27e-15 1.67e-12 ✓ sig.
chloride transport
GABRA1, GABRA4, GABRA6, GABRB3, GABRG2, CLCN2, GABRD, SLC12A5, GABRA5, GABRB2
 GO:0006821 10 / 81 51.3× 3.72e-15 2.64e-12 ✓ sig.
synaptic transmission, GABAergic
GABRA1, GABRA4, GABRA6, GABRB3, GABRG2, GABRD, GABRA5, GABRB2
 GO:0051932 8 / 35 94.9× 1.31e-14 8.37e-12 ✓ sig.
inhibitory synapse assembly
GABRA1, GABRA4, GABRA6, GABRB3, GABRG2, GABRA5, GABRB2
 GO:1904862 7 / 25 116× 1.34e-13 7.22e-11 ✓ sig.
regulation of postsynaptic membrane potential
GABRA1, GABRA4, HCN1, GABRA6, GABRG2, GABRD, GABRA5, GABRB2
 GO:0060078 8 / 59 56.3× 1.19e-12 5.38e-10 ✓ sig.
chemical synaptic transmission
CACNA1A, CACNB4, SNCA, GABRB3, GABRG2, NPY, GABRD, SLC12A5, GABRA5, GABRB2
 GO:0007268 10 / 236 17.6× 1.85e-10 4.98e-8 ✓ sig.
regulation of membrane potential
CACNB4, HCN1, CACNA1H, KCNMA1, HCN2, HCN4, WWP2
 GO:0042391 7 / 85 34.2× 1.24e-9 2.71e-7 ✓ sig.
transmembrane transport
ABCB7, CACNA1A, HCN1, SCN8A, SLC2A1, CACNA1H, CLCN2, SLC12A5, KCNMA1, HCN2, HCN4
 GO:0055085 11 / 557 8.2× 6.05e-8 7.96e-6 ✓ sig.
potassium ion import across plasma membrane
HCN1, KCNK9, SLC12A5, HCN2, HCN4
 GO:1990573 5 / 46 45.1× 8.20e-8 1.02e-5 ✓ sig.
cellular response to histamine
GABRB3, GABRG2, GABRB2
 GO:0071420 3 / 6 208× 2.60e-7 2.70e-5 ✓ sig.
inner ear receptor cell development
GABRB3, GABRA5, GABRB2
 GO:0060119 3 / 8 156× 7.25e-7 6.40e-5 ✓ sig.
sodium ion transmembrane transport
HCN1, SCN8A, SCN1B, KCNK9, HCN2, HCN4
 GO:0035725 6 / 134 18.6× 7.87e-7 6.82e-5 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Absence epilepsy Childhood absence epilepsy 0.200 3 6.89e-9 6.09e-8 ✓ sig.
Ataxia Idiopathic generalized epilepsy 0.097 3 4.77e-7 3.14e-6 ✓ sig.
Childhood absence epilepsy Idiopathic generalized epilepsy 0.095 2 2.50e-5 1.23e-4 ✓ sig.
Absence epilepsy Ataxia 0.074 2 3.70e-5 1.79e-4 ✓ sig.
Ataxia Childhood absence epilepsy 0.067 2 7.92e-5 2.84e-4 ✓ sig.
Absence epilepsy Conn syndrome 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Absence epilepsy Juvenile absence epilepsy 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Childhood absence epilepsy Conn syndrome 0.091 1 6.49e-4 1.22e-3 ✓ sig.
Absence epilepsy Synovial disorder 0.077 1 2.72e-3 3.65e-3 ✓ sig.
Childhood absence epilepsy Synovial disorder 0.063 1 3.89e-3 4.94e-3 ✓ sig.