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 285

8 diseases · 13 shared-gene connections
8 Diseases
19 Unique genes
0.215 Avg. similarity score
Benign neonatal-infantile seizures Most-connected disease (5 links)
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Disease Searched: Epileptic encephalopathy, early infantile, 11 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 ⇵
Benign neonatal-infantile seizures 5 5 2
Benign infantile epilepsy 4 4 6
Benign neonatal epilepsy 4 4 4
Epilepsy of infancy with migrating focal seizures 4 4 9
Epileptic encephalopathy, early infantile, 11 4 4 1
Hemiplegia 3 3 5
Epileptic encephalopathy, early infantile, 34 1 1 1
Woodhouse sakati syndrome 1 1 2

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

Gene ⇵ Member diseases ⇵ Linked diseases
SCN2A 6 / 8 Benign infantile epilepsy, Benign neonatal epilepsy, Benign neonatal-infantile seizures, Epilepsy of infancy with migrating focal seizures and 2 more
KCNQ2 4 / 8 Benign infantile epilepsy, Benign neonatal epilepsy, Benign neonatal-infantile seizures, Epilepsy of infancy with migrating focal seizures
KCNQ3 2 / 8 Benign infantile epilepsy, Benign neonatal epilepsy
METTL8 2 / 8 Hemiplegia, Woodhouse sakati syndrome
SLC12A5 2 / 8 Epilepsy of infancy with migrating focal seizures, Epileptic encephalopathy, early infantile, 34
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 ⇵
Phase 0 - rapid depolarisation
SCN2A, SCN8A, SCN1A
 Reactome 3 / 44 43.1× 4.27e-5 9.65e-4 ✓ sig.
Thyroid hormone synthesis
ATP1A2, PLCB1, CGA
 KEGG 3 / 75 25.3× 2.11e-4 3.42e-3 ✓ sig.
Cholinergic synapse
KCNQ2, KCNQ3, PLCB1
 KEGG 3 / 115 16.5× 7.41e-4 9.03e-3 ✓ sig.
Voltage gated Potassium channels
KCNQ2, KCNQ3
 Reactome 2 / 43 29.4× 2.06e-3 1.94e-2 ✓ sig.
Carbohydrate digestion and absorption
ATP1A2, PLCB1
 KEGG 2 / 48 26.3× 2.56e-3 2.28e-2 ✓ sig.
Endocrine and other factor-regulated calcium reabsorption
ATP1A2, PLCB1
 KEGG 2 / 53 23.9× 3.11e-3 2.62e-2 ✓ sig.
GnRH secretion
PLCB1, CGA
 KEGG 2 / 65 19.4× 4.65e-3 3.48e-2 ✓ sig.
Gastric acid secretion
ATP1A2, PLCB1
 KEGG 2 / 76 16.6× 6.30e-3 4.25e-2 ✓ sig.
Taste transduction
SCN2A, PLCB1
 KEGG 2 / 86 14.7× 8.01e-3 4.96e-2 ✓ sig.
Insulin secretion
ATP1A2, PLCB1
 KEGG 2 / 86 14.7× 8.01e-3 4.96e-2 ✓ sig.
GnRH signaling pathway
PLCB1, CGA
 KEGG 2 / 93 13.6× 9.31e-3 5.43e-2
Salivary secretion
ATP1A2, PLCB1
 KEGG 2 / 93 13.6× 9.31e-3 5.43e-2
Mineralocorticoid biosynthesis
CGA
 Reactome 1 / 6 105× 9.46e-3 5.49e-2
Aldosterone synthesis and secretion
ATP1A2, PLCB1
 KEGG 2 / 98 12.9× 1.03e-2 5.80e-2
Cation-coupled Chloride cotransporters
SLC12A5
 Reactome 1 / 7 90.3× 1.10e-2 6.03e-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, KCNQ2, KCNQ3, SCN2A, SCN8A, ATP1A2, KCNT1, SCN1A, SLC12A5, SLC25A22
 GO:0006811 10 / 667 14.7× 2.17e-10 6.12e-8 ✓ sig.
monoatomic ion transmembrane transport
CHRNA2, KCNQ2, KCNQ3, SCN2A, SCN8A, KCNT1, SCN1A
 GO:0034220 7 / 404 17.0× 8.44e-8 1.10e-5 ✓ sig.
action potential
KCNQ2, SCN2A, SCN8A, SCN1A
 GO:0001508 4 / 53 74.2× 2.17e-7 2.41e-5 ✓ sig.
potassium ion transmembrane transport
KCNQ2, KCNQ3, ATP1A2, KCNT1, SLC12A5
 GO:0071805 5 / 150 32.8× 3.31e-7 3.45e-5 ✓ sig.
potassium ion transport
KCNQ2, KCNQ3, ATP1A2, KCNT1, SLC12A5
 GO:0006813 5 / 152 32.4× 3.54e-7 3.64e-5 ✓ sig.
transmembrane transport
KCNQ2, KCNQ3, SCN2A, SCN8A, SCN1A, SLC12A5, SLC25A22
 GO:0055085 7 / 557 12.4× 7.43e-7 6.73e-5 ✓ sig.
cardiac muscle cell action potential involved in contraction
SCN2A, SCN8A, SCN1A
 GO:0086002 3 / 24 123× 1.78e-6 1.38e-4 ✓ sig.
neuronal action potential
KCNQ3, SCN2A, SCN1A
 GO:0019228 3 / 34 86.8× 5.23e-6 3.28e-4 ✓ sig.
sodium ion transmembrane transport
SCN2A, SCN8A, ATP1A2, SCN1A
 GO:0035725 4 / 134 29.4× 9.01e-6 5.02e-4 ✓ sig.
sodium ion transport
SCN2A, SCN8A, ATP1A2, SCN1A
 GO:0006814 4 / 144 27.3× 1.20e-5 6.26e-4 ✓ sig.
neuronal action potential propagation
ATP1A2, SCN1A
 GO:0019227 2 / 11 179× 5.36e-5 1.94e-3 ✓ sig.
neuromuscular process controlling posture
PRRT2, SCN1A
 GO:0050884 2 / 15 131× 1.02e-4 3.14e-3 ✓ sig.
nerve development
KCNQ3, SCN1A
 GO:0021675 2 / 19 104× 1.66e-4 4.44e-3 ✓ sig.
response to auditory stimulus
KCNQ3, ATP1A2
 GO:0010996 2 / 23 85.5× 2.45e-4 5.86e-3 ✓ sig.
membrane depolarization
CHRNA2, ATP1A2
 GO:0051899 2 / 32 61.5× 4.77e-4 9.23e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Benign infantile epilepsy Benign neonatal epilepsy 0.375 3 1.29e-10 1.20e-9 ✓ sig.
Benign neonatal epilepsy Benign neonatal-infantile seizures 0.400 2 5.00e-8 3.63e-7 ✓ sig.
Benign infantile epilepsy Benign neonatal-infantile seizures 0.286 2 1.25e-7 8.63e-7 ✓ sig.
Benign neonatal-infantile seizures Epilepsy of infancy with migrating focal seizures 0.200 2 3.00e-7 1.96e-6 ✓ sig.
Benign neonatal epilepsy Epilepsy of infancy with migrating focal seizures 0.167 2 1.80e-6 1.06e-5 ✓ sig.
Benign infantile epilepsy Epilepsy of infancy with migrating focal seizures 0.143 2 4.50e-6 2.52e-5 ✓ sig.
Benign neonatal-infantile seizures Epileptic encephalopathy, early infantile, 11 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Benign neonatal epilepsy Epileptic encephalopathy, early infantile, 11 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Epileptic encephalopathy, early infantile, 11 Hemiplegia 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Benign infantile epilepsy Epileptic encephalopathy, early infantile, 11 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Epilepsy of infancy with migrating focal seizures Epileptic encephalopathy, early infantile, 34 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Benign neonatal-infantile seizures Hemiplegia 0.143 1 6.46e-4 1.09e-3 ✓ sig.
Hemiplegia Woodhouse sakati syndrome 0.143 1 6.46e-4 1.09e-3 ✓ sig.