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 81

13 diseases · 28 shared-gene connections
13 Diseases
53 Unique genes
0.214 Avg. similarity score
Bruxism Most-connected disease (7 links)
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Disease Searched: Encephalopathy, neonatal severe 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
Central apnea 6 6 1
Cyclin-dependent kinase-like 5 deficiency 6 6 6
Encephalopathy, neonatal severe 6 6 1
Neonatal encephalopathy 6 6 1
Bulbar palsy 5 5 3
Angelman syndrome 4 4 10
Autism, x-linked 4 4 6
CDKL5 disorder 3 3 1
Chromosome xq28 duplication syndrome 3 3 4
Rett syndrome 3 3 16
Gross motor development delay 2 2 18
Autism, susceptibility to, x-linked 6 (includes intellectual disability) 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
MECP2 11 / 13 Angelman syndrome, Autism, x-linked, Bruxism, Bulbar palsy and 7 more
CDKL5 5 / 13 Angelman syndrome, Bruxism, CDKL5 disorder, Cyclin-dependent kinase-like 5 deficiency and 1 more
CACNA1A 3 / 13 Bulbar palsy, Cyclin-dependent kinase-like 5 deficiency, Gross motor development delay
RS1 2 / 13 Cyclin-dependent kinase-like 5 deficiency, Rett syndrome
TMLHE 2 / 13 Autism, susceptibility to, x-linked 6 (includes intellectual disability), Autism, x-linked
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 ⇵
GABAergic synapse
GABRB3, GABRG3, GABBR2, CACNA1A, GPHN
 KEGG 5 / 89 12.7× 4.33e-5 9.76e-4 ✓ sig.
MECP2 regulates neuronal receptors and channels
MECP2, PTPN1
 Reactome 2 / 4 113× 1.14e-4 2.10e-3 ✓ sig.
Synaptic vesicle cycle
STXBP1, CACNA1A, ATP6V1A, SNAP25
 KEGG 4 / 79 11.5× 3.98e-4 5.60e-3 ✓ sig.
Morphine addiction
GABRB3, GABRG3, GABBR2, CACNA1A
 KEGG 4 / 91 10.0× 6.80e-4 8.46e-3 ✓ sig.
Nicotine addiction
GABRB3, GABRG3, CACNA1A
 KEGG 3 / 41 16.6× 7.68e-4 9.27e-3 ✓ sig.
GABA synthesis, release, reuptake and degradation
STXBP1, SNAP25
 Reactome 2 / 13 34.9× 1.44e-3 1.50e-2 ✓ sig.
GABA receptor activation
GABRB3, GABRG3
 Reactome 2 / 16 28.3× 2.20e-3 2.05e-2 ✓ sig.
Acetylcholine Neurotransmitter Release Cycle
STXBP1, SNAP25
 Reactome 2 / 17 26.7× 2.49e-3 2.23e-2 ✓ sig.
Serotonin Neurotransmitter Release Cycle
STXBP1, SNAP25
 Reactome 2 / 18 25.2× 2.79e-3 2.42e-2 ✓ sig.
Norepinephrine Neurotransmitter Release Cycle
STXBP1, SNAP25
 Reactome 2 / 18 25.2× 2.79e-3 2.42e-2 ✓ sig.
Loss of MECP2 binding ability to 5hmC-DNA
MECP2
 Reactome 1 / 1 227× 4.41e-3 3.36e-2 ✓ sig.
Dopamine Neurotransmitter Release Cycle
STXBP1, SNAP25
 Reactome 2 / 23 19.7× 4.56e-3 3.43e-2 ✓ sig.
Glutamate Neurotransmitter Release Cycle
STXBP1, SNAP25
 Reactome 2 / 24 18.9× 4.96e-3 3.64e-2 ✓ sig.
Neurexins and neuroligins
NLGN3, NLGN4X
 Reactome 2 / 32 14.2× 8.71e-3 5.22e-2
GABA B receptor activation
GABBR2
 Reactome 1 / 2 113× 8.81e-3 5.26e-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 ⇵
social behavior
GABRB3, MECP2, NLGN3, NLGN4X, PTCHD1
 GO:0035176 5 / 58 30.4× 6.18e-7 5.80e-5 ✓ sig.
modulation of chemical synaptic transmission
CDKL5, UBE3A, NTNG1, NLGN3, NLGN4X, CACNA1A
 GO:0050804 6 / 121 17.5× 1.16e-6 9.73e-5 ✓ sig.
synaptic transmission, GABAergic
GABRB3, GABRG3, GABBR2, GPHN
 GO:0051932 4 / 35 40.3× 2.83e-6 2.00e-4 ✓ sig.
chemical synaptic transmission
GABRB3, MECP2, GABBR2, NLGN3, PTCHD1, CACNA1A, SNAP25
 GO:0007268 7 / 236 10.5× 4.41e-6 2.87e-4 ✓ sig.
learning
GABRB3, MECP2, NLGN3, NLGN4X
 GO:0007612 4 / 64 22.0× 3.23e-5 1.33e-3 ✓ sig.
central nervous system neuron development
FOXG1, MAP2, PALS1
 GO:0021954 3 / 23 46.0× 3.67e-5 1.46e-3 ✓ sig.
striated muscle contraction
MYH7, RYR1, TTN
 GO:0006941 3 / 24 44.1× 4.18e-5 1.61e-3 ✓ sig.
presynaptic dense core vesicle exocytosis
STXBP1, SNAP25
 GO:0099525 2 / 4 176× 4.72e-5 1.77e-3 ✓ sig.
synapse organization
NLGN3, NLGN4X, RAB39B, GPHN
 GO:0050808 4 / 72 19.6× 5.14e-5 1.89e-3 ✓ sig.
brain development
GABRB3, MECP2, UBE3A, MFSD2A, EGR2, FOXG1
 GO:0007420 6 / 244 8.7× 6.40e-5 2.23e-3 ✓ sig.
gamma-aminobutyric acid signaling pathway
GABRB3, GABRG3, GABBR2
 GO:0007214 3 / 30 35.3× 8.29e-5 2.69e-3 ✓ sig.
muscle contraction
MYH7, RYR1, SCN4A, TTN
 GO:0006936 4 / 85 16.6× 9.85e-5 3.06e-3 ✓ sig.
regulation of neuron projection arborization
NTNG1, MFSD2A
 GO:0150011 2 / 6 118× 1.18e-4 3.48e-3 ✓ sig.
monoatomic ion transmembrane transport
GABRB3, GABRG3, ATP10A, CACNA1A, CLIC2, RYR1, SCN4A
 GO:0034220 7 / 404 6.1× 1.37e-4 3.87e-3 ✓ sig.
presynaptic membrane assembly
NLGN3, NLGN4X
 GO:0097105 2 / 9 78.4× 2.81e-4 6.46e-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 1.81e-8 1.40e-7 ✓ sig.
Bruxism Cyclin-dependent kinase-like 5 deficiency 0.250 2 3.75e-7 2.42e-6 ✓ sig.
Bulbar palsy Cyclin-dependent kinase-like 5 deficiency 0.250 2 3.75e-7 2.42e-6 ✓ sig.
Angelman syndrome Bruxism 0.167 2 1.13e-6 6.81e-6 ✓ sig.
Bruxism Rett syndrome 0.111 2 3.00e-6 1.72e-5 ✓ sig.
Bulbar palsy Gross motor development delay 0.100 2 3.82e-6 2.16e-5 ✓ sig.
Angelman syndrome Cyclin-dependent kinase-like 5 deficiency 0.133 2 5.62e-6 3.11e-5 ✓ sig.
Cyclin-dependent kinase-like 5 deficiency Gross motor development delay 0.087 2 1.91e-5 1.00e-4 ✓ sig.
Encephalopathy, neonatal severe Neonatal encephalopathy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Central apnea Encephalopathy, neonatal severe 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Central apnea Neonatal encephalopathy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Angelman syndrome Rett syndrome 0.080 2 4.48e-5 1.98e-4 ✓ sig.
Bulbar palsy Central apnea 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Bruxism Encephalopathy, neonatal severe 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Bruxism Neonatal encephalopathy 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Bruxism Central apnea 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Bruxism CDKL5 disorder 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Bulbar palsy Encephalopathy, neonatal severe 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Bulbar palsy Neonatal encephalopathy 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Central apnea Chromosome xq28 duplication syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Chromosome xq28 duplication syndrome Neonatal encephalopathy 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Chromosome xq28 duplication syndrome Encephalopathy, neonatal severe 0.200 1 2.58e-4 5.38e-4 ✓ sig.
CDKL5 disorder Cyclin-dependent kinase-like 5 deficiency 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Autism, x-linked Encephalopathy, neonatal severe 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Autism, x-linked Neonatal encephalopathy 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Autism, x-linked Central apnea 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Autism, susceptibility to, x-linked 6 (includes intellectual disability) Autism, x-linked 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Angelman syndrome CDKL5 disorder 0.091 1 6.46e-4 1.09e-3 ✓ sig.