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 26

19 diseases · 49 shared-gene connections
19 Diseases
29 Unique genes
0.278 Avg. similarity score
Paroxysmal dystonic choreoathetosis Most-connected disease (11 links)
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Disease Searched: complex neurodevelopmental disorder with motor features 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 ⇵
Paroxysmal dystonic choreoathetosis 11 11 4
Childhood-onset glut1 deficiency syndrome 2 9 9 2
Chromosome 17q23.1-q23.2 deletion syndrome 7 7 1
Epilepsy with myoclonic absence 7 7 1
Episodic kinesigenic dyskinesia 7 7 3
GLUT1 deficiency syndrome 7 7 1
Paroxysmal nonkinesigenic dyskinesia 7 7 4
Familial infantile convulsions with paroxysmal choreoathetosis 6 6 1
Paroxysmal dyskinesia 5 5 5
Paroxysmal dystonia 5 5 1
infantile convulsions and choreoathetosis 5 5 1
Cryohydrocytosis 4 4 2
Epilepsy with myoclonic atonic seizures 4 4 7
Hereditary continuous muscle fiber activity 4 4 1
Cerebellar atrophy with seizures and variable developmental delay 3 3 5
Choreoathetosis 3 3 6
generalized epilepsy-paroxysmal dyskinesia syndrome 2 2 1
Intellectual developmental disorder seizures epilepsy 1 1 1
complex neurodevelopmental disorder with motor features 1 1 6

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

Gene ⇵ Member diseases ⇵ Linked diseases
SLC2A1 9 / 19 Childhood-onset glut1 deficiency syndrome 2, Choreoathetosis, Chromosome 17q23.1-q23.2 deletion syndrome, Cryohydrocytosis and 5 more
PRRT2 8 / 19 Childhood-onset glut1 deficiency syndrome 2, Episodic kinesigenic dyskinesia, Familial infantile convulsions with paroxysmal choreoathetosis, infantile convulsions and choreoathetosis and 4 more
KCNA1 5 / 19 Episodic kinesigenic dyskinesia, Hereditary continuous muscle fiber activity, Paroxysmal dyskinesia, Paroxysmal dystonic choreoathetosis and 1 more
KCNMA1 3 / 19 Cerebellar atrophy with seizures and variable developmental delay, generalized epilepsy-paroxysmal dyskinesia syndrome, Paroxysmal nonkinesigenic dyskinesia
AP2M1 2 / 19 Epilepsy with myoclonic atonic seizures, Intellectual developmental disorder seizures epilepsy
EMC1 2 / 19 Cerebellar atrophy with seizures and variable developmental delay, complex neurodevelopmental disorder with motor features
KCNJ10 2 / 19 Paroxysmal dyskinesia, Paroxysmal dystonic choreoathetosis
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
CACNA2D2, SCN8A, SCN1A
 Reactome 3 / 44 28.2× 1.57e-4 3.14e-3 ✓ sig.
Dopaminergic synapse
GNAO1, SCN1A, COMT, CACNA1B
 KEGG 4 / 132 12.5× 2.68e-4 4.80e-3 ✓ sig.
Presynaptic depolarization and calcium channel opening
CACNA2D2, CACNA1B
 Reactome 2 / 12 69.0× 3.66e-4 6.18e-3 ✓ sig.
Regulation of insulin secretion
CACNA2D2, SLC2A1
 Reactome 2 / 16 51.8× 6.62e-4 9.80e-3 ✓ sig.
Synaptic vesicle cycle
SLC6A1, AP2M1, CACNA1B
 KEGG 3 / 79 15.7× 8.85e-4 1.22e-2 ✓ sig.
GABAergic synapse
GNAO1, SLC6A1, CACNA1B
 KEGG 3 / 89 14.0× 1.25e-3 1.59e-2 ✓ sig.
Defective SLC2A1 causes GLUT1 deficiency syndrome 1 (GLUT1DS1)
SLC2A1
 Reactome 1 / 1 414× 2.41e-3 2.62e-2 ✓ sig.
Defective SLC4A1 causes hereditary spherocytosis type 4 (HSP4), distal renal tubular acidosis (dRTA) and dRTA with hemolytic anemia (dRTA-HA)
SLC4A1
 Reactome 1 / 1 414× 2.41e-3 2.62e-2 ✓ sig.
Nef mediated downregulation of CD28 cell surface expression
AP2M1
 Reactome 1 / 2 207× 4.82e-3 4.27e-2 ✓ sig.
Enzymatic degradation of Dopamine by monoamine oxidase
COMT
 Reactome 1 / 2 207× 4.82e-3 4.27e-2 ✓ sig.
Endocrine and other factor-regulated calcium reabsorption
AP2M1, RAB11A
 KEGG 2 / 53 15.6× 7.19e-3 5.57e-2
Enzymatic degradation of dopamine by COMT
COMT
 Reactome 1 / 3 138× 7.23e-3 5.60e-2
Lactose synthesis
SLC2A1
 Reactome 1 / 3 138× 7.23e-3 5.60e-2
Potassium transport channels
KCNJ10
 Reactome 1 / 3 138× 7.23e-3 5.60e-2
Reuptake of GABA
SLC6A1
 Reactome 1 / 4 104× 9.62e-3 6.77e-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 ⇵
transmembrane transport
CYB561D2, KCNMA1, SLC2A1, SCN8A, KCNA1, SLC4A1, SCN1A, CACNA1B
 GO:0055085 8 / 557 9.3× 1.46e-6 1.13e-4 ✓ sig.
neuromuscular process controlling posture
PRRT2, SCN1A, PNKD
 GO:0050884 3 / 15 129× 1.51e-6 1.16e-4 ✓ sig.
monoatomic ion transmembrane transport
CACNA2D2, KCNMA1, SCN8A, KCNA1, SCN1A, KCNJ10, CACNA1B
 GO:0034220 7 / 404 11.2× 2.17e-6 1.55e-4 ✓ sig.
regulation of long-term neuronal synaptic plasticity
SYNGAP1, KCNJ10, RAB11A
 GO:0048169 3 / 18 107× 2.70e-6 1.84e-4 ✓ sig.
monoatomic ion transport
CACNA2D2, KCNMA1, SCN8A, KCNA1, SLC4A1, SCN1A, KCNJ10, CACNA1B
 GO:0006811 8 / 667 7.7× 5.57e-6 3.30e-4 ✓ sig.
regulation of membrane potential
KCNMA1, KCNA1, SCN1A, KCNJ10
 GO:0042391 4 / 85 30.3× 8.68e-6 4.72e-4 ✓ sig.
action potential
SCN8A, KCNA1, SCN1A
 GO:0001508 3 / 53 36.5× 7.47e-5 2.44e-3 ✓ sig.
detection of mechanical stimulus involved in sensory perception of pain
KCNA1, SCN1A
 GO:0050966 2 / 14 92.1× 2.09e-4 5.22e-3 ✓ sig.
vesicle-mediated transport in synapse
AP2M1, RAB11A
 GO:0099003 2 / 15 85.9× 2.41e-4 5.76e-3 ✓ sig.
startle response
KCNA1, COMT
 GO:0001964 2 / 18 71.6× 3.50e-4 7.51e-3 ✓ sig.
cardiac muscle cell action potential involved in contraction
SCN8A, SCN1A
 GO:0086002 2 / 24 53.7× 6.28e-4 1.13e-2 ✓ sig.
vesicle docking involved in exocytosis
GNAO1, RAB11A
 GO:0006904 2 / 29 44.4× 9.20e-4 1.45e-2 ✓ sig.
sodium ion transmembrane transport
SCN8A, SLC6A1, SCN1A
 GO:0035725 3 / 134 14.4× 1.15e-3 1.65e-2 ✓ sig.
adult walking behavior
SCN1A, KCNJ10
 GO:0007628 2 / 34 37.9× 1.26e-3 1.76e-2 ✓ sig.
neuronal action potential
KCNA1, SCN1A
 GO:0019228 2 / 34 37.9× 1.26e-3 1.76e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Paroxysmal dyskinesia Paroxysmal dystonic choreoathetosis 0.667 4 2.14e-15 3.12e-14 ✓ sig.
Childhood-onset glut1 deficiency syndrome 2 Paroxysmal dystonic choreoathetosis 0.400 2 5.06e-8 3.71e-7 ✓ sig.
Childhood-onset glut1 deficiency syndrome 2 Paroxysmal dyskinesia 0.333 2 8.44e-8 5.94e-7 ✓ sig.
Episodic kinesigenic dyskinesia Paroxysmal nonkinesigenic dyskinesia 0.333 2 1.52e-7 1.03e-6 ✓ sig.
Episodic kinesigenic dyskinesia Paroxysmal dystonic choreoathetosis 0.333 2 1.52e-7 1.03e-6 ✓ sig.
Episodic kinesigenic dyskinesia Paroxysmal dyskinesia 0.286 2 2.53e-7 1.65e-6 ✓ sig.
Paroxysmal dystonic choreoathetosis Paroxysmal nonkinesigenic dyskinesia 0.286 2 3.04e-7 1.95e-6 ✓ sig.
Paroxysmal dyskinesia Paroxysmal nonkinesigenic dyskinesia 0.250 2 5.06e-7 3.14e-6 ✓ sig.
Familial infantile convulsions with paroxysmal choreoathetosis Paroxysmal dystonia 0.500 1 6.49e-5 2.33e-4 ✓ sig.
infantile convulsions and choreoathetosis Paroxysmal dystonia 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Chromosome 17q23.1-q23.2 deletion syndrome GLUT1 deficiency syndrome 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Chromosome 17q23.1-q23.2 deletion syndrome Epilepsy with myoclonic absence 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Epilepsy with myoclonic absence GLUT1 deficiency syndrome 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Familial infantile convulsions with paroxysmal choreoathetosis infantile convulsions and choreoathetosis 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Childhood-onset glut1 deficiency syndrome 2 Familial infantile convulsions with paroxysmal choreoathetosis 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Childhood-onset glut1 deficiency syndrome 2 infantile convulsions and choreoathetosis 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Cryohydrocytosis Epilepsy with myoclonic absence 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Cryohydrocytosis GLUT1 deficiency syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Chromosome 17q23.1-q23.2 deletion syndrome Cryohydrocytosis 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Childhood-onset glut1 deficiency syndrome 2 Paroxysmal dystonia 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Childhood-onset glut1 deficiency syndrome 2 Epilepsy with myoclonic absence 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Childhood-onset glut1 deficiency syndrome 2 GLUT1 deficiency syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Childhood-onset glut1 deficiency syndrome 2 Chromosome 17q23.1-q23.2 deletion syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Episodic kinesigenic dyskinesia infantile convulsions and choreoathetosis 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Episodic kinesigenic dyskinesia Paroxysmal dystonia 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Episodic kinesigenic dyskinesia Hereditary continuous muscle fiber activity 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Episodic kinesigenic dyskinesia Familial infantile convulsions with paroxysmal choreoathetosis 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Childhood-onset glut1 deficiency syndrome 2 Cryohydrocytosis 0.250 1 2.60e-4 6.51e-4 ✓ sig.
Hereditary continuous muscle fiber activity Paroxysmal dystonic choreoathetosis 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Hereditary continuous muscle fiber activity Paroxysmal nonkinesigenic dyskinesia 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Familial infantile convulsions with paroxysmal choreoathetosis Paroxysmal nonkinesigenic dyskinesia 0.200 1 2.60e-4 6.51e-4 ✓ sig.
infantile convulsions and choreoathetosis Paroxysmal dystonic choreoathetosis 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Paroxysmal dystonia Paroxysmal dystonic choreoathetosis 0.200 1 2.60e-4 6.51e-4 ✓ sig.
GLUT1 deficiency syndrome Paroxysmal dystonic choreoathetosis 0.200 1 2.60e-4 6.51e-4 ✓ sig.
generalized epilepsy-paroxysmal dyskinesia syndrome Paroxysmal nonkinesigenic dyskinesia 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Familial infantile convulsions with paroxysmal choreoathetosis Paroxysmal dystonic choreoathetosis 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Epilepsy with myoclonic absence Paroxysmal dystonic choreoathetosis 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Chromosome 17q23.1-q23.2 deletion syndrome Paroxysmal dystonic choreoathetosis 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Hereditary continuous muscle fiber activity Paroxysmal dyskinesia 0.167 1 3.25e-4 7.70e-4 ✓ sig.
Cerebellar atrophy with seizures and variable developmental delay generalized epilepsy-paroxysmal dyskinesia syndrome 0.167 1 3.25e-4 7.70e-4 ✓ sig.
Choreoathetosis Epilepsy with myoclonic absence 0.143 1 3.90e-4 8.66e-4 ✓ sig.
Choreoathetosis GLUT1 deficiency syndrome 0.143 1 3.90e-4 8.66e-4 ✓ sig.
Choreoathetosis Chromosome 17q23.1-q23.2 deletion syndrome 0.143 1 3.90e-4 8.66e-4 ✓ sig.
Epilepsy with myoclonic atonic seizures Intellectual developmental disorder seizures epilepsy 0.125 1 4.55e-4 9.72e-4 ✓ sig.
Epilepsy with myoclonic absence Epilepsy with myoclonic atonic seizures 0.125 1 4.55e-4 9.72e-4 ✓ sig.
Epilepsy with myoclonic atonic seizures GLUT1 deficiency syndrome 0.125 1 4.55e-4 9.72e-4 ✓ sig.
Chromosome 17q23.1-q23.2 deletion syndrome Epilepsy with myoclonic atonic seizures 0.125 1 4.55e-4 9.72e-4 ✓ sig.
Cerebellar atrophy with seizures and variable developmental delay Paroxysmal nonkinesigenic dyskinesia 0.111 1 1.30e-3 2.06e-3 ✓ sig.
Cerebellar atrophy with seizures and variable developmental delay complex neurodevelopmental disorder with motor features 0.091 1 1.95e-3 2.83e-3 ✓ sig.