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 136

11 diseases · 35 shared-gene connections
11 Diseases
6 Unique genes
0.383 Avg. similarity score
Deafness, onychodystrophy, osteodystrophy, impaired intellectual development, and seizures syndrome Most-connected disease (9 links)
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Disease Searched: Epilepsy, rolandic, with paroxysmal exercise-induce dystonia and writer's cramp 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 ⇵
Deafness, onychodystrophy, osteodystrophy, impaired intellectual development, and seizures syndrome 9 9 1
Epilepsy, rolandic, with paroxysmal exercise-induce dystonia and writer's cramp 9 9 1
Focal epilepsy-intellectual disability-cerebro-cerebellar malformation 9 9 1
Deafness with congenital onychodystrophy 8 8 2
Deafness, autosomal dominant 65 6 6 1
Deafness, autosomal recessive 86 6 6 1
Digitrenocerebral syndrome 6 6 3
Doors syndrome 6 6 2
Infantile myoclonic epilepsy 5 5 2
Deafness-onychodystrophy syndrome 3 3 1
Periodic paralysis 3 3 3

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

Gene ⇵ Member diseases ⇵ Linked diseases
TBC1D24 10 / 11 Deafness with congenital onychodystrophy, Deafness, autosomal dominant 65, Deafness, autosomal recessive 86, Deafness, onychodystrophy, osteodystrophy, impaired intellectual development, and seizures syndrome and 6 more
ATP6V1B2 4 / 11 Deafness with congenital onychodystrophy, Deafness-onychodystrophy syndrome, Digitrenocerebral syndrome, Doors 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 ⇵
Synaptic vesicle cycle
ATP6V1B2, ATP6V1C1, CPLX1
 KEGG 3 / 79 76.0× 5.40e-6 1.75e-4 ✓ sig.
Oxidative phosphorylation
ATP6V1B2, ATP6V1C1, ATP6
 KEGG 3 / 137 43.8× 2.83e-5 6.91e-4 ✓ sig.
Ion channel transport
ATP6V1B2, ATP6V1C1
 Reactome 2 / 24 167× 5.71e-5 1.21e-3 ✓ sig.
Insulin receptor recycling
ATP6V1B2, ATP6V1C1
 Reactome 2 / 26 154× 6.72e-5 1.38e-3 ✓ sig.
Collecting duct acid secretion
ATP6V1B2, ATP6V1C1
 KEGG 2 / 28 143× 7.82e-5 1.56e-3 ✓ sig.
Transferrin endocytosis and recycling
ATP6V1B2, ATP6V1C1
 Reactome 2 / 31 129× 9.61e-5 1.84e-3 ✓ sig.
ROS and RNS production in phagocytes
ATP6V1B2, ATP6V1C1
 Reactome 2 / 34 118× 1.16e-4 2.13e-3 ✓ sig.
Vibrio cholerae infection
ATP6V1B2, ATP6V1C1
 KEGG 2 / 51 78.5× 2.62e-4 4.06e-3 ✓ sig.
Amino acids regulate mTORC1
ATP6V1B2, ATP6V1C1
 Reactome 2 / 55 72.8× 3.05e-4 4.57e-3 ✓ sig.
Epithelial cell signaling in Helicobacter pylori infection
ATP6V1B2, ATP6V1C1
 KEGG 2 / 71 56.4× 5.09e-4 6.76e-3 ✓ sig.
Rheumatoid arthritis
ATP6V1B2, ATP6V1C1
 KEGG 2 / 95 42.1× 9.10e-4 1.06e-2 ✓ sig.
Classical Kir channels
KCNJ2
 Reactome 1 / 4 500× 2.00e-3 1.90e-2 ✓ sig.
Phagosome
ATP6V1B2, ATP6V1C1
 KEGG 2 / 155 25.8× 2.40e-3 2.18e-2 ✓ sig.
mTOR signaling pathway
ATP6V1B2, ATP6V1C1
 KEGG 2 / 158 25.3× 2.49e-3 2.23e-2 ✓ sig.
GABA synthesis, release, reuptake and degradation
CPLX1
 Reactome 1 / 13 154× 6.48e-3 4.32e-2 ✓ 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 ⇵
synaptic vesicle lumen acidification
ATP6V1B2, ATP6V1C1
 GO:0097401 2 / 18 346× 1.31e-5 6.71e-4 ✓ sig.
proton transmembrane transport
ATP6V1B2, ATP6V1C1, ATP6
 GO:1902600 3 / 181 51.6× 1.75e-5 8.35e-4 ✓ sig.
monoatomic ion transport
ATP6V1B2, ATP6V1C1, ATP6, KCNJ2
 GO:0006811 4 / 667 18.7× 2.28e-5 1.02e-3 ✓ sig.
regulation of macroautophagy
ATP6V1B2, ATP6V1C1
 GO:0016241 2 / 57 109× 1.36e-4 3.85e-3 ✓ sig.
regulation of skeletal muscle contraction via regulation of action potential
KCNJ2
 GO:0014861 1 / 1 3,115× 3.21e-4 7.04e-3 ✓ sig.
regulation of exocytic insertion of neurotransmitter receptor to postsynaptic membrane
CPLX1
 GO:0099145 1 / 1 3,115× 3.21e-4 7.04e-3 ✓ sig.
cardiac muscle cell action potential
KCNJ2
 GO:0086001 1 / 3 1,038× 9.63e-4 1.42e-2 ✓ sig.
relaxation of skeletal muscle
KCNJ2
 GO:0090076 1 / 3 1,038× 9.63e-4 1.42e-2 ✓ sig.
negative regulation of cellular response to oxidative stress
TBC1D24
 GO:1900408 1 / 5 623× 1.60e-3 1.88e-2 ✓ sig.
regulation of synaptic vesicle fusion to presynaptic active zone membrane
CPLX1
 GO:0031630 1 / 7 445× 2.25e-3 2.24e-2 ✓ sig.
membrane repolarization during action potential
KCNJ2
 GO:0086011 1 / 10 311× 3.21e-3 2.69e-2 ✓ sig.
membrane repolarization during cardiac muscle cell action potential
KCNJ2
 GO:0086013 1 / 10 311× 3.21e-3 2.69e-2 ✓ sig.
membrane depolarization during cardiac muscle cell action potential
KCNJ2
 GO:0086012 1 / 12 260× 3.85e-3 2.94e-2 ✓ sig.
relaxation of cardiac muscle
KCNJ2
 GO:0055119 1 / 13 240× 4.17e-3 3.06e-2 ✓ sig.
regulation of resting membrane potential
KCNJ2
 GO:0060075 1 / 13 240× 4.17e-3 3.06e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Deafness with congenital onychodystrophy Doors syndrome 0.667 2 8.34e-9 6.60e-8 ✓ sig.
Deafness with congenital onychodystrophy Digitrenocerebral syndrome 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Digitrenocerebral syndrome Doors syndrome 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Deafness, onychodystrophy, osteodystrophy, impaired intellectual development, and seizures syndrome Focal epilepsy-intellectual disability-cerebro-cerebellar malformation 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Epilepsy, rolandic, with paroxysmal exercise-induce dystonia and writer's cramp Focal epilepsy-intellectual disability-cerebro-cerebellar malformation 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Deafness, onychodystrophy, osteodystrophy, impaired intellectual development, and seizures syndrome Epilepsy, rolandic, with paroxysmal exercise-induce dystonia and writer's cramp 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Deafness, autosomal recessive 86 Epilepsy, rolandic, with paroxysmal exercise-induce dystonia and writer's cramp 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Deafness, autosomal recessive 86 Focal epilepsy-intellectual disability-cerebro-cerebellar malformation 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Deafness, autosomal recessive 86 Deafness, onychodystrophy, osteodystrophy, impaired intellectual development, and seizures syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Deafness, autosomal dominant 65 Deafness, autosomal recessive 86 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Deafness, autosomal dominant 65 Focal epilepsy-intellectual disability-cerebro-cerebellar malformation 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Deafness, autosomal dominant 65 Deafness, onychodystrophy, osteodystrophy, impaired intellectual development, and seizures syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Deafness, autosomal dominant 65 Epilepsy, rolandic, with paroxysmal exercise-induce dystonia and writer's cramp 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Deafness, autosomal recessive 86 Infantile myoclonic epilepsy 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Epilepsy, rolandic, with paroxysmal exercise-induce dystonia and writer's cramp Infantile myoclonic epilepsy 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Focal epilepsy-intellectual disability-cerebro-cerebellar malformation Infantile myoclonic epilepsy 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Deafness, onychodystrophy, osteodystrophy, impaired intellectual development, and seizures syndrome Infantile myoclonic epilepsy 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Deafness with congenital onychodystrophy Deafness, onychodystrophy, osteodystrophy, impaired intellectual development, and seizures syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Doors syndrome Epilepsy, rolandic, with paroxysmal exercise-induce dystonia and writer's cramp 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Doors syndrome Focal epilepsy-intellectual disability-cerebro-cerebellar malformation 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Deafness, onychodystrophy, osteodystrophy, impaired intellectual development, and seizures syndrome Doors syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Deafness, autosomal dominant 65 Infantile myoclonic epilepsy 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Deafness with congenital onychodystrophy Focal epilepsy-intellectual disability-cerebro-cerebellar malformation 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Deafness with congenital onychodystrophy Epilepsy, rolandic, with paroxysmal exercise-induce dystonia and writer's cramp 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Deafness with congenital onychodystrophy Deafness-onychodystrophy syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Deafness with congenital onychodystrophy Deafness, autosomal recessive 86 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Deafness-onychodystrophy syndrome Doors syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Deafness with congenital onychodystrophy Deafness, autosomal dominant 65 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Deafness, onychodystrophy, osteodystrophy, impaired intellectual development, and seizures syndrome Periodic paralysis 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Focal epilepsy-intellectual disability-cerebro-cerebellar malformation Periodic paralysis 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Epilepsy, rolandic, with paroxysmal exercise-induce dystonia and writer's cramp Periodic paralysis 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Digitrenocerebral syndrome Epilepsy, rolandic, with paroxysmal exercise-induce dystonia and writer's cramp 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Digitrenocerebral syndrome Focal epilepsy-intellectual disability-cerebro-cerebellar malformation 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Deafness, onychodystrophy, osteodystrophy, impaired intellectual development, and seizures syndrome Digitrenocerebral syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Deafness-onychodystrophy syndrome Digitrenocerebral syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.