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 213

8 diseases · 15 shared-gene connections
8 Diseases
12 Unique genes
0.244 Avg. similarity score
Benign neonatal epilepsy Most-connected disease (6 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 ⇵
Benign neonatal epilepsy 6 6 4
Benign infantile epilepsy 5 5 6
Benign neonatal-infantile seizures 5 5 2
neonatal encephalopathy with non-epileptic myoclonus 4 4 1
neonatal-onset developmental and epileptic encephalopathy 4 4 1
Hemiplegia 3 3 5
self-limited familial neonatal epilepsy 2 2 1
Woodhouse sakati syndrome 1 1 2

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

Gene ⇵ Member diseases ⇵ Linked diseases
KCNQ2 5 / 8 Benign infantile epilepsy, Benign neonatal epilepsy, Benign neonatal-infantile seizures, neonatal encephalopathy with non-epileptic myoclonus and 1 more
SCN2A 4 / 8 Benign infantile epilepsy, Benign neonatal epilepsy, Benign neonatal-infantile seizures, Hemiplegia
KCNQ3 3 / 8 Benign infantile epilepsy, Benign neonatal epilepsy, self-limited familial neonatal epilepsy
METTL8 2 / 8 Hemiplegia, Woodhouse sakati syndrome
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 ⇵
Voltage gated Potassium channels
KCNQ2, KCNQ3
 Reactome 2 / 43 46.6× 8.08e-4 1.16e-2 ✓ sig.
Phase 0 - rapid depolarisation
SCN2A, SCN8A
 Reactome 2 / 44 45.5× 8.46e-4 1.19e-2 ✓ sig.
Thyroid hormone synthesis
ATP1A2, CGA
 KEGG 2 / 75 26.7× 2.44e-3 2.64e-2 ✓ sig.
Cholinergic synapse
KCNQ2, KCNQ3
 KEGG 2 / 115 17.4× 5.63e-3 4.74e-2 ✓ sig.
Mineralocorticoid biosynthesis
CGA
 Reactome 1 / 6 167× 5.98e-3 4.92e-2 ✓ sig.
Thyroxine biosynthesis
CGA
 Reactome 1 / 7 143× 6.97e-3 5.45e-2
Highly calcium permeable nicotinic acetylcholine receptors
CHRNA2
 Reactome 1 / 9 111× 8.96e-3 6.42e-2
Reactions specific to the complex N-glycan synthesis pathway
CGA
 Reactome 1 / 10 100× 9.95e-3 6.82e-2
Androgen biosynthesis
CGA
 Reactome 1 / 11 91.0× 1.09e-2 7.25e-2
Glycoprotein hormones
CGA
 Reactome 1 / 12 83.4× 1.19e-2 7.61e-2
Hormone ligand-binding receptors
CGA
 Reactome 1 / 12 83.4× 1.19e-2 7.61e-2
Highly calcium permeable postsynaptic nicotinic acetylcholine receptors
CHRNA2
 Reactome 1 / 12 83.4× 1.19e-2 7.61e-2
TFAP2 (AP-2) family regulates transcription of growth factors and their receptors
CGA
 Reactome 1 / 15 66.7× 1.49e-2 8.66e-2
cAMP signaling pathway
ATP1A2, CGA
 KEGG 2 / 226 8.9× 2.05e-2 1.04e-1
Proximal tubule bicarbonate reclamation
ATP1A2
 KEGG 1 / 23 43.5× 2.28e-2 1.11e-1

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
 GO:0006811 6 / 667 14.0× 1.55e-6 1.18e-4 ✓ sig.
monoatomic ion transmembrane transport
CHRNA2, KCNQ2, KCNQ3, SCN2A, SCN8A
 GO:0034220 5 / 404 19.3× 3.22e-6 2.11e-4 ✓ sig.
action potential
KCNQ2, SCN2A, SCN8A
 GO:0001508 3 / 53 88.1× 4.65e-6 2.84e-4 ✓ sig.
sodium ion transmembrane transport
SCN2A, SCN8A, ATP1A2
 GO:0035725 3 / 134 34.9× 7.57e-5 2.46e-3 ✓ sig.
sodium ion transport
SCN2A, SCN8A, ATP1A2
 GO:0006814 3 / 144 32.4× 9.37e-5 2.88e-3 ✓ sig.
response to auditory stimulus
KCNQ3, ATP1A2
 GO:0010996 2 / 23 135× 9.49e-5 2.91e-3 ✓ sig.
cardiac muscle cell action potential involved in contraction
SCN2A, SCN8A
 GO:0086002 2 / 24 130× 1.04e-4 3.10e-3 ✓ sig.
potassium ion transmembrane transport
KCNQ2, KCNQ3, ATP1A2
 GO:0071805 3 / 150 31.1× 1.06e-4 3.15e-3 ✓ sig.
potassium ion transport
KCNQ2, KCNQ3, ATP1A2
 GO:0006813 3 / 152 30.7× 1.10e-4 3.24e-3 ✓ sig.
membrane depolarization
CHRNA2, ATP1A2
 GO:0051899 2 / 32 97.3× 1.86e-4 4.79e-3 ✓ sig.
neuronal action potential
KCNQ3, SCN2A
 GO:0019228 2 / 34 91.6× 2.10e-4 5.21e-3 ✓ sig.
response to nicotine
CHRNA2, ATP1A2
 GO:0035094 2 / 40 77.9× 2.91e-4 6.56e-3 ✓ sig.
transmembrane transport
KCNQ2, KCNQ3, SCN2A, SCN8A
 GO:0055085 4 / 557 11.2× 3.19e-4 7.03e-3 ✓ sig.
olfactory cortex development
ATP1A2
 GO:0021989 1 / 1 1,557× 6.42e-4 1.13e-2 ✓ sig.
modulation of inhibitory postsynaptic potential
CHRNA2
 GO:0098828 1 / 1 1,557× 6.42e-4 1.13e-2 ✓ 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 1.31e-10 1.37e-9 ✓ sig.
Benign neonatal epilepsy Benign neonatal-infantile seizures 0.400 2 5.06e-8 3.92e-7 ✓ sig.
Benign infantile epilepsy Benign neonatal-infantile seizures 0.286 2 1.27e-7 9.20e-7 ✓ sig.
neonatal encephalopathy with non-epileptic myoclonus neonatal-onset developmental and epileptic encephalopathy 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Benign neonatal-infantile seizures neonatal-onset developmental and epileptic encephalopathy 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Benign neonatal-infantile seizures neonatal encephalopathy with non-epileptic myoclonus 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Benign neonatal epilepsy neonatal-onset developmental and epileptic encephalopathy 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Benign neonatal epilepsy neonatal encephalopathy with non-epileptic myoclonus 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Benign neonatal epilepsy self-limited familial neonatal epilepsy 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Benign infantile epilepsy neonatal-onset developmental and epileptic encephalopathy 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Benign infantile epilepsy neonatal encephalopathy with non-epileptic myoclonus 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Benign infantile epilepsy self-limited familial neonatal epilepsy 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Benign neonatal-infantile seizures Hemiplegia 0.143 1 6.49e-4 1.22e-3 ✓ sig.
Hemiplegia Woodhouse sakati syndrome 0.143 1 6.49e-4 1.22e-3 ✓ sig.
Benign neonatal epilepsy Hemiplegia 0.111 1 1.30e-3 2.04e-3 ✓ sig.