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 55

15 diseases · 28 shared-gene connections
15 Diseases
57 Unique genes
0.166 Avg. similarity score
Bruxism Most-connected disease (7 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 ⇵
Bruxism 7 7 3
Cyclin-dependent kinase-like 5 deficiency 7 7 6
Bulbar palsy 6 6 3
Angelman syndrome 5 5 10
Autism, x-linked 4 4 6
CDKL5 disorder 4 4 1
Central apnea 4 4 1
Neonatal encephalopathy 4 4 1
Rett syndrome 4 4 16
Benign paroxysmal torticollis of infancy 3 3 1
Gross motor development delay 3 3 18
Episodic ataxia 2 2 8
Childhood-onset autosomal recessive slowly progressive spinocerebellar ataxia 1 1 1
Expressive language delay 1 1 1
episodic ataxia type 6 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
MECP2 9 / 15 Angelman syndrome, Autism, x-linked, Bruxism, Bulbar palsy and 5 more
CACNA1A 5 / 15 Benign paroxysmal torticollis of infancy, Bulbar palsy, Cyclin-dependent kinase-like 5 deficiency, Episodic ataxia and 1 more
CDKL5 5 / 15 Angelman syndrome, Bruxism, CDKL5 disorder, Cyclin-dependent kinase-like 5 deficiency and 1 more
KLF7 2 / 15 Expressive language delay, Gross motor development delay
RS1 2 / 15 Cyclin-dependent kinase-like 5 deficiency, Rett syndrome
SLC1A3 2 / 15 Episodic ataxia, episodic ataxia type 6
TPP1 2 / 15 Angelman syndrome, Childhood-onset autosomal recessive slowly progressive spinocerebellar 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
STXBP1, CACNA1A, ATP6V1A, SNAP25, SLC1A3
 KEGG 5 / 79 13.3× 3.47e-5 9.45e-4 ✓ sig.
GABAergic synapse
GABRB3, GABRG3, GABBR2, CACNA1A, GPHN
 KEGG 5 / 89 11.8× 6.17e-5 1.51e-3 ✓ sig.
MECP2 regulates neuronal receptors and channels
MECP2, PTPN1
 Reactome 2 / 4 105× 1.32e-4 2.80e-3 ✓ sig.
Glutamate Neurotransmitter Release Cycle
STXBP1, SNAP25, SLC1A3
 Reactome 3 / 24 26.3× 1.91e-4 3.77e-3 ✓ sig.
Morphine addiction
GABRB3, GABRG3, GABBR2, CACNA1A
 KEGG 4 / 91 9.3× 8.97e-4 1.25e-2 ✓ sig.
Nicotine addiction
GABRB3, GABRG3, CACNA1A
 KEGG 3 / 41 15.4× 9.51e-4 1.31e-2 ✓ sig.
Phase 0 - rapid depolarisation
CACNB4, SCN2A, SCN4A
 Reactome 3 / 44 14.4× 1.17e-3 1.53e-2 ✓ sig.
Presynaptic depolarization and calcium channel opening
CACNA1A, CACNB4
 Reactome 2 / 12 35.1× 1.42e-3 1.76e-2 ✓ sig.
GABA synthesis, release, reuptake and degradation
STXBP1, SNAP25
 Reactome 2 / 13 32.4× 1.67e-3 2.00e-2 ✓ sig.
GABA receptor activation
GABRB3, GABRG3
 Reactome 2 / 16 26.3× 2.54e-3 2.73e-2 ✓ sig.
Acetylcholine Neurotransmitter Release Cycle
STXBP1, SNAP25
 Reactome 2 / 17 24.8× 2.88e-3 2.99e-2 ✓ sig.
Serotonin Neurotransmitter Release Cycle
STXBP1, SNAP25
 Reactome 2 / 18 23.4× 3.22e-3 3.24e-2 ✓ sig.
Norepinephrine Neurotransmitter Release Cycle
STXBP1, SNAP25
 Reactome 2 / 18 23.4× 3.22e-3 3.24e-2 ✓ sig.
Loss of MECP2 binding ability to 5hmC-DNA
MECP2
 Reactome 1 / 1 211× 4.75e-3 4.23e-2 ✓ sig.
Defective SLC1A3 causes episodic ataxia 6 (EA6)
SLC1A3
 Reactome 1 / 1 211× 4.75e-3 4.23e-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 ⇵
chemical synaptic transmission
GABRB3, MECP2, GABBR2, NLGN3, PTCHD1, CACNA1A, SNAP25, CACNB4, SLC1A3
 GO:0007268 9 / 236 12.5× 3.73e-8 5.27e-6 ✓ sig.
social behavior
GABRB3, MECP2, NLGN3, NLGN4X, PTCHD1
 GO:0035176 5 / 58 28.3× 8.94e-7 7.56e-5 ✓ sig.
modulation of chemical synaptic transmission
CDKL5, UBE3A, NTNG1, NLGN3, NLGN4X, CACNA1A
 GO:0050804 6 / 121 16.3× 1.80e-6 1.33e-4 ✓ sig.
gamma-aminobutyric acid signaling pathway
GABRB3, GABRG3, GABBR2, CACNB4
 GO:0007214 4 / 30 43.7× 2.01e-6 1.45e-4 ✓ sig.
monoatomic ion transmembrane transport
GABRB3, GABRG3, ATP10A, CACNA1A, CACNB4, KCNA1, SCN2A, RYR1, SCN4A
 GO:0034220 9 / 404 7.3× 3.39e-6 2.20e-4 ✓ sig.
synaptic transmission, GABAergic
GABRB3, GABRG3, GABBR2, GPHN
 GO:0051932 4 / 35 37.5× 3.80e-6 2.41e-4 ✓ sig.
brain development
GABRB3, MECP2, UBE3A, KCNA1, MFSD2A, EGR2, FOXG1
 GO:0007420 7 / 244 9.4× 9.00e-6 4.81e-4 ✓ sig.
cell morphogenesis involved in neuron differentiation
SLC1A3, OPHN1, FOXG1
 GO:0048667 3 / 14 70.3× 9.56e-6 5.04e-4 ✓ sig.
monoatomic ion transport
GABRB3, GABRG3, CACNA1A, ATP6V1A, CACNB4, KCNA1, SCN2A, SLC1A3, RYR1, SCN4A
 GO:0006811 10 / 667 4.9× 2.97e-5 1.21e-3 ✓ sig.
learning
GABRB3, MECP2, NLGN3, NLGN4X
 GO:0007612 4 / 64 20.5× 4.31e-5 1.61e-3 ✓ sig.
central nervous system neuron development
FOXG1, MAP2, PALS1
 GO:0021954 3 / 23 42.8× 4.56e-5 1.68e-3 ✓ sig.
striated muscle contraction
MYH7, RYR1, TTN
 GO:0006941 3 / 24 41.0× 5.20e-5 1.86e-3 ✓ sig.
presynaptic dense core vesicle exocytosis
STXBP1, SNAP25
 GO:0099525 2 / 4 164× 5.46e-5 1.92e-3 ✓ sig.
muscle contraction
MYH7, RYR1, SCN4A, TTN
 GO:0006936 4 / 85 15.4× 1.31e-4 3.71e-3 ✓ sig.
regulation of neuron projection arborization
NTNG1, MFSD2A
 GO:0150011 2 / 6 109× 1.36e-4 3.80e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Cyclin-dependent kinase-like 5 deficiency Rett syndrome 0.150 3 1.84e-8 1.52e-7 ✓ sig.
Bulbar palsy Cyclin-dependent kinase-like 5 deficiency 0.250 2 3.80e-7 2.53e-6 ✓ sig.
Bruxism Cyclin-dependent kinase-like 5 deficiency 0.250 2 3.80e-7 2.53e-6 ✓ sig.
Angelman syndrome Bruxism 0.167 2 1.14e-6 6.99e-6 ✓ sig.
Bruxism Rett syndrome 0.111 2 3.04e-6 1.72e-5 ✓ sig.
Bulbar palsy Gross motor development delay 0.100 2 3.87e-6 2.16e-5 ✓ sig.
Angelman syndrome Cyclin-dependent kinase-like 5 deficiency 0.133 2 5.69e-6 3.09e-5 ✓ sig.
Cyclin-dependent kinase-like 5 deficiency Gross motor development delay 0.087 2 1.93e-5 9.70e-5 ✓ sig.
Angelman syndrome Rett syndrome 0.080 2 4.53e-5 2.18e-4 ✓ sig.
Central apnea Neonatal encephalopathy 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Bruxism CDKL5 disorder 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Bruxism Central apnea 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Bruxism Neonatal encephalopathy 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Bulbar palsy Central apnea 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Bulbar palsy Neonatal encephalopathy 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Benign paroxysmal torticollis of infancy Bulbar palsy 0.250 1 1.95e-4 5.28e-4 ✓ sig.
CDKL5 disorder Cyclin-dependent kinase-like 5 deficiency 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Autism, x-linked Central apnea 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Autism, x-linked Neonatal encephalopathy 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Benign paroxysmal torticollis of infancy Cyclin-dependent kinase-like 5 deficiency 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Episodic ataxia episodic ataxia type 6 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Benign paroxysmal torticollis of infancy Episodic ataxia 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Angelman syndrome CDKL5 disorder 0.091 1 6.49e-4 1.22e-3 ✓ sig.
Angelman syndrome Childhood-onset autosomal recessive slowly progressive spinocerebellar ataxia 0.091 1 6.49e-4 1.22e-3 ✓ sig.
CDKL5 disorder Rett syndrome 0.059 1 1.04e-3 1.72e-3 ✓ sig.
Autism, x-linked Bruxism 0.111 1 1.17e-3 1.88e-3 ✓ sig.
Autism, x-linked Bulbar palsy 0.111 1 1.17e-3 1.88e-3 ✓ sig.
Expressive language delay Gross motor development delay 0.053 1 1.17e-3 1.88e-3 ✓ sig.