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 322

6 diseases · 13 shared-gene connections
6 Diseases
6 Unique genes
0.309 Avg. similarity score
Hereditary hyperekplexia Most-connected disease (5 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 ⇵
Hereditary hyperekplexia 5 5 5
Hyperekplexia 5 5 5
Hyperexplexia hereditary 5 5 4
Retinitis pigmentosa, juvenile cataract, short stature, intellectual disability syndrome 4 4 2
sulfite oxidase deficiency due to molybdenum cofactor deficiency type C 4 4 1
hyperekplexia 3 3 3 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
GPHN 5 / 6 Hereditary hyperekplexia, Hyperekplexia, Hyperexplexia hereditary, Retinitis pigmentosa, juvenile cataract, short stature, intellectual disability syndrome and 1 more
SLC6A5 4 / 6 Hereditary hyperekplexia, Hyperekplexia, hyperekplexia 3, Hyperexplexia hereditary
GLRA1 3 / 6 Hereditary hyperekplexia, Hyperekplexia, Hyperexplexia hereditary
GLRB 3 / 6 Hereditary hyperekplexia, Hyperekplexia, Hyperexplexia hereditary
ATAD1 2 / 6 Hereditary hyperekplexia, Hyperekplexia
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 ⇵
Neurotransmitter receptors and postsynaptic signal transmission
GLRA1, GLRB
 Reactome 2 / 9 445× 7.48e-6 2.63e-4 ✓ sig.
Defective SLC6A5 causes hyperekplexia 3 (HKPX3)
SLC6A5
 Reactome 1 / 1 2,002× 5.00e-4 7.96e-3 ✓ sig.
Biosynthesis of cofactors
GPHN, RDH11
 KEGG 2 / 154 26.0× 2.37e-3 2.58e-2 ✓ sig.
Molybdenum cofactor biosynthesis
GPHN
 Reactome 1 / 6 334× 2.99e-3 3.07e-2 ✓ sig.
Na+/Cl- dependent neurotransmitter transporters
SLC6A5
 Reactome 1 / 19 105× 9.46e-3 6.63e-2
The canonical retinoid cycle in rods (twilight vision)
RDH11
 Reactome 1 / 20 100× 9.95e-3 6.82e-2
Class I peroxisomal membrane protein import
ATAD1
 Reactome 1 / 20 100× 9.95e-3 6.82e-2
RA biosynthesis pathway
RDH11
 Reactome 1 / 22 91.0× 1.09e-2 7.25e-2
Neuroactive ligand-receptor interaction
GLRA1, GLRB
 KEGG 2 / 370 10.8× 1.31e-2 8.01e-2
Folate biosynthesis
GPHN
 KEGG 1 / 28 71.5× 1.39e-2 8.31e-2
Retinoid metabolism and transport
RDH11
 Reactome 1 / 41 48.8× 2.03e-2 1.04e-1
Retinol metabolism
RDH11
 KEGG 1 / 68 29.4× 3.35e-2 1.37e-1
Synaptic vesicle cycle
SLC6A5
 KEGG 1 / 79 25.3× 3.88e-2 1.49e-1
GABAergic synapse
GPHN
 KEGG 1 / 89 22.5× 4.37e-2 1.59e-1
Metabolic pathways
GPHN, RDH11
 KEGG 2 / 1,563 2.6× 1.78e-1 3.41e-1

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 transmission, glycinergic
GLRA1, GLRB, SLC6A5
 GO:0060012 3 / 3 3,115× 1.84e-11 6.34e-9 ✓ sig.
gamma-aminobutyric acid receptor clustering
GLRB, GPHN
 GO:0097112 2 / 6 1,038× 1.29e-6 1.01e-4 ✓ sig.
righting reflex
GLRA1, GLRB
 GO:0060013 2 / 9 692× 3.09e-6 2.04e-4 ✓ sig.
startle response
GLRA1, GLRB
 GO:0001964 2 / 18 346× 1.31e-5 6.45e-4 ✓ sig.
acrosome reaction
GLRA1, GLRB
 GO:0007340 2 / 18 346× 1.31e-5 6.45e-4 ✓ sig.
visual perception
GLRA1, GLRB, RDH11
 GO:0007601 3 / 215 43.5× 2.93e-5 1.20e-3 ✓ sig.
chemical synaptic transmission
GLRA1, GLRB, SLC6A5
 GO:0007268 3 / 236 39.6× 3.87e-5 1.48e-3 ✓ sig.
adult walking behavior
GLRA1, GLRB
 GO:0007628 2 / 34 183× 4.80e-5 1.74e-3 ✓ sig.
neuromuscular process
GLRA1, GLRB
 GO:0050905 2 / 42 148× 7.36e-5 2.41e-3 ✓ sig.
excitatory postsynaptic potential
GLRA1, GLRB
 GO:0060079 2 / 69 90.3× 2.00e-4 5.04e-3 ✓ sig.
chloride transport
GLRA1, GLRB
 GO:0006821 2 / 81 76.9× 2.75e-4 6.32e-3 ✓ sig.
regulation of membrane potential
GLRA1, GLRB
 GO:0042391 2 / 85 73.3× 3.03e-4 6.77e-3 ✓ sig.
glycine receptor clustering
GPHN
 GO:0072579 1 / 1 3,115× 3.21e-4 7.03e-3 ✓ sig.
extraction of mislocalized protein from mitochondrial outer membrane
ATAD1
 GO:0140570 1 / 1 3,115× 3.21e-4 7.03e-3 ✓ sig.
neuropeptide signaling pathway
GLRA1, GLRB
 GO:0007218 2 / 111 56.1× 5.16e-4 9.77e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Hereditary hyperekplexia Hyperekplexia 0.833 5 1.39e-19 2.72e-18 ✓ sig.
Hereditary hyperekplexia Hyperexplexia hereditary 0.667 4 2.14e-15 3.30e-14 ✓ sig.
Hyperekplexia Hyperexplexia hereditary 0.667 4 2.14e-15 3.30e-14 ✓ sig.
Retinitis pigmentosa, juvenile cataract, short stature, intellectual disability syndrome sulfite oxidase deficiency due to molybdenum cofactor deficiency type C 0.333 1 1.30e-4 3.90e-4 ✓ sig.
hyperekplexia 3 Hyperexplexia hereditary 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Hyperexplexia hereditary sulfite oxidase deficiency due to molybdenum cofactor deficiency type C 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Hereditary hyperekplexia sulfite oxidase deficiency due to molybdenum cofactor deficiency type C 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Hereditary hyperekplexia hyperekplexia 3 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Hyperekplexia sulfite oxidase deficiency due to molybdenum cofactor deficiency type C 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Hyperekplexia hyperekplexia 3 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Hyperexplexia hereditary Retinitis pigmentosa, juvenile cataract, short stature, intellectual disability syndrome 0.167 1 5.19e-4 1.04e-3 ✓ sig.
Hereditary hyperekplexia Retinitis pigmentosa, juvenile cataract, short stature, intellectual disability syndrome 0.143 1 6.49e-4 1.22e-3 ✓ sig.
Hyperekplexia Retinitis pigmentosa, juvenile cataract, short stature, intellectual disability syndrome 0.143 1 6.49e-4 1.22e-3 ✓ sig.