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 253

8 diseases · 18 shared-gene connections
8 Diseases
11 Unique genes
0.289 Avg. similarity score
Familial hemiplegic migraine Most-connected disease (6 links)
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Disease Searched: Febrile seizures, familial, 3a 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 ⇵
Familial hemiplegic migraine 6 6 2
Hemiplegic migraine 6 6 5
Epileptic encephalopathy, early infantile, 6 (dravet syndrome) 5 5 1
Febrile seizures, familial, 3a 5 5 1
Seizure disorders 5 5 1
Benign paroxysmal torticollis of infancy 3 3 1
Epilepsy with myoclonic atonic seizures 3 3 7
Migraine, familial hemiplegic, 1, with progressive cerebellar ataxia 3 3 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
SCN1A 6 / 8 Epilepsy with myoclonic atonic seizures, Epileptic encephalopathy, early infantile, 6 (dravet syndrome), Familial hemiplegic migraine, Febrile seizures, familial, 3a and 2 more
CACNA1A 4 / 8 Benign paroxysmal torticollis of infancy, Familial hemiplegic migraine, Hemiplegic migraine, Migraine, familial hemiplegic, 1, with progressive cerebellar ataxia
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 ⇵
Synaptic vesicle cycle
CACNA1A, SLC6A1, AP2M1
 KEGG 3 / 79 41.5× 4.35e-5 9.80e-4 ✓ sig.
Regulation of insulin secretion
CACNA1A, SLC2A1
 Reactome 2 / 16 136× 9.09e-5 1.76e-3 ✓ sig.
Defective SLC2A1 causes GLUT1 deficiency syndrome 1 (GLUT1DS1)
SLC2A1
 Reactome 1 / 1 1,092× 9.16e-4 1.06e-2 ✓ sig.
Endocrine and other factor-regulated calcium reabsorption
AP2M1, ATP1A2
 KEGG 2 / 53 41.2× 1.02e-3 1.15e-2 ✓ sig.
Nef mediated downregulation of CD28 cell surface expression
AP2M1
 Reactome 1 / 2 546× 1.83e-3 1.78e-2 ✓ sig.
Insulin secretion
SLC2A1, ATP1A2
 KEGG 2 / 86 25.4× 2.67e-3 2.35e-2 ✓ sig.
Lactose synthesis
SLC2A1
 Reactome 1 / 3 364× 2.75e-3 2.39e-2 ✓ sig.
GABAergic synapse
CACNA1A, SLC6A1
 KEGG 2 / 89 24.5× 2.86e-3 2.46e-2 ✓ sig.
Bile secretion
SLC2A1, ATP1A2
 KEGG 2 / 90 24.3× 2.92e-3 2.50e-2 ✓ sig.
Reuptake of GABA
SLC6A1
 Reactome 1 / 4 273× 3.66e-3 2.93e-2 ✓ sig.
Thyroid hormone signaling pathway
SLC2A1, ATP1A2
 KEGG 2 / 122 17.9× 5.30e-3 3.79e-2 ✓ sig.
Dopaminergic synapse
CACNA1A, SCN1A
 KEGG 2 / 132 16.5× 6.18e-3 4.19e-2 ✓ sig.
Nef Mediated CD8 Down-regulation
AP2M1
 Reactome 1 / 7 156× 6.40e-3 4.28e-2 ✓ sig.
Vitamin C (ascorbate) metabolism
SLC2A1
 Reactome 1 / 8 136× 7.31e-3 4.67e-2 ✓ sig.
Nef Mediated CD4 Down-regulation
AP2M1
 Reactome 1 / 9 121× 8.22e-3 5.04e-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 ⇵
transport across blood-brain barrier
SLC6A1, SLC2A1, ATP1A2
 GO:0150104 3 / 85 60.0× 1.46e-5 7.29e-4 ✓ sig.
neuronal action potential propagation
SCN1A, ATP1A2
 GO:0019227 2 / 11 309× 1.73e-5 8.27e-4 ✓ sig.
L-ascorbic acid metabolic process
SLC2A1, ATP1A2
 GO:0019852 2 / 11 309× 1.73e-5 8.27e-4 ✓ sig.
neuromuscular process controlling posture
SCN1A, PRRT2
 GO:0050884 2 / 15 227× 3.29e-5 1.35e-3 ✓ sig.
sodium ion transmembrane transport
SLC6A1, SCN1A, ATP1A2
 GO:0035725 3 / 134 38.0× 5.70e-5 2.03e-3 ✓ sig.
visual learning
SYNGAP1, ATP1A2
 GO:0008542 2 / 54 62.9× 4.43e-4 8.75e-3 ✓ sig.
olfactory cortex development
ATP1A2
 GO:0021989 1 / 1 1,699× 5.89e-4 1.06e-2 ✓ sig.
negative regulation of short-term synaptic potentiation
PRRT2
 GO:1905513 1 / 1 1,699× 5.89e-4 1.06e-2 ✓ sig.
cellular response to mechanical stimulus
SLC2A1, ATP1A2
 GO:0071260 2 / 76 44.7× 8.77e-4 1.35e-2 ✓ sig.
regulation of glutamate uptake involved in transmission of nerve impulse
ATP1A2
 GO:0051946 1 / 2 849× 1.18e-3 1.59e-2 ✓ sig.
regulation of calcium-dependent activation of synaptic vesicle fusion
PRRT2
 GO:0150037 1 / 2 849× 1.18e-3 1.59e-2 ✓ sig.
inorganic anion import across plasma membrane
SLC6A1
 GO:0098658 1 / 2 849× 1.18e-3 1.59e-2 ✓ sig.
response to Thyroglobulin triiodothyronine
SLC2A1
 GO:1904016 1 / 2 849× 1.18e-3 1.59e-2 ✓ sig.
negative regulation of SNARE complex assembly
PRRT2
 GO:0035544 1 / 2 849× 1.18e-3 1.59e-2 ✓ sig.
negative regulation of striated muscle contraction
ATP1A2
 GO:0045988 1 / 3 566× 1.76e-3 1.99e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Familial hemiplegic migraine Hemiplegic migraine 0.333 2 8.34e-8 5.85e-7 ✓ sig.
Benign paroxysmal torticollis of infancy Migraine, familial hemiplegic, 1, with progressive cerebellar ataxia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Epileptic encephalopathy, early infantile, 6 (dravet syndrome) Febrile seizures, familial, 3a 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Epileptic encephalopathy, early infantile, 6 (dravet syndrome) Seizure disorders 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Febrile seizures, familial, 3a Seizure disorders 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Benign paroxysmal torticollis of infancy Familial hemiplegic migraine 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Familial hemiplegic migraine Seizure disorders 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Epileptic encephalopathy, early infantile, 6 (dravet syndrome) Familial hemiplegic migraine 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Familial hemiplegic migraine Migraine, familial hemiplegic, 1, with progressive cerebellar ataxia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Familial hemiplegic migraine Febrile seizures, familial, 3a 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Hemiplegic migraine Seizure disorders 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Hemiplegic migraine Migraine, familial hemiplegic, 1, with progressive cerebellar ataxia 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Febrile seizures, familial, 3a Hemiplegic migraine 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Epileptic encephalopathy, early infantile, 6 (dravet syndrome) Hemiplegic migraine 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Benign paroxysmal torticollis of infancy Hemiplegic migraine 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Epilepsy with myoclonic atonic seizures Seizure disorders 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Epilepsy with myoclonic atonic seizures Epileptic encephalopathy, early infantile, 6 (dravet syndrome) 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Epilepsy with myoclonic atonic seizures Febrile seizures, familial, 3a 0.125 1 4.52e-4 8.26e-4 ✓ sig.