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 121

11 diseases · 31 shared-gene connections
11 Diseases
8 Unique genes
0.378 Avg. similarity score
Ataxia-hypogonadism-choroidal dystrophy syndrome Most-connected disease (8 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 ⇵
Ataxia-hypogonadism-choroidal dystrophy syndrome 8 8 1
Boucher-neuhauser syndrome 8 8 1
Chorioretinal dystrophy, spinocerebellar ataxia, hypogonadotropic hypogonadism syndrome 8 8 1
Trichomegaly-retina pigmentary degeneration-dwarfism syndrome 8 8 1
Mucolipidosis 7 7 7
retinal dystrophy-ataxia-pituitary hormone abnormality-hypogonadism syndrome 6 6 1
Cerebellar ataxia and hypogonadotropic hypogonadism 5 5 2
Cerebellar ataxia-hypogonadism 5 5 2
PNPLA6-related spastic paraplegia with or without ataxia 5 5 1
Beta-sarcoglycanopathy 1 1 1
GNPTG-mucolipidosis 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
PNPLA6 9 / 11 Ataxia-hypogonadism-choroidal dystrophy syndrome, Boucher-neuhauser syndrome, Cerebellar ataxia and hypogonadotropic hypogonadism, Cerebellar ataxia-hypogonadism and 5 more
GNPTG 2 / 11 GNPTG-mucolipidosis, Mucolipidosis
RNF216 2 / 11 Cerebellar ataxia and hypogonadotropic hypogonadism, Cerebellar ataxia-hypogonadism
SGCB 2 / 11 Beta-sarcoglycanopathy, Mucolipidosis
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 ⇵
Lysosome
GNPTAB, GNPTG, MCOLN1, NEU1
 KEGG 4 / 133 45.2× 9.72e-7 4.75e-5 ✓ sig.
Glycerophospholipid catabolism
PNPLA6
 Reactome 1 / 3 500× 2.00e-3 2.28e-2 ✓ sig.
Defective NEU1 causes sialidosis
NEU1
 Reactome 1 / 3 500× 2.00e-3 2.28e-2 ✓ sig.
Other glycan degradation
NEU1
 KEGG 1 / 18 83.4× 1.19e-2 7.61e-2
Negative regulators of DDX58/IFIH1 signaling
RNF216
 Reactome 1 / 27 55.6× 1.78e-2 9.67e-2
TRP channels
MCOLN1
 Reactome 1 / 28 53.6× 1.85e-2 9.85e-2
Transferrin endocytosis and recycling
MCOLN1
 Reactome 1 / 31 48.4× 2.05e-2 1.04e-1
Sialic acid metabolism
NEU1
 Reactome 1 / 33 45.5× 2.18e-2 1.08e-1
Glycosphingolipid metabolism
NEU1
 Reactome 1 / 46 32.6× 3.02e-2 1.29e-1
Sphingolipid metabolism
NEU1
 KEGG 1 / 54 27.8× 3.54e-2 1.42e-1
Viral myocarditis
SGCB
 KEGG 1 / 70 21.4× 4.57e-2 1.63e-1
Arrhythmogenic right ventricular cardiomyopathy
SGCB
 KEGG 1 / 86 17.5× 5.59e-2 1.82e-1
Hypertrophic cardiomyopathy
SGCB
 KEGG 1 / 99 15.2× 6.41e-2 1.95e-1
Glycerophospholipid metabolism
PNPLA6
 KEGG 1 / 102 14.7× 6.60e-2 1.98e-1
Dilated cardiomyopathy
SGCB
 KEGG 1 / 105 14.3× 6.79e-2 2.01e-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 ⇵
N-glycan processing to lysosome
GNPTAB, GNPTG
 GO:0016256 2 / 2 2,336× 1.60e-7 1.80e-5 ✓ sig.
carbohydrate phosphorylation
GNPTAB, GNPTG
 GO:0046835 2 / 24 195× 4.41e-5 1.64e-3 ✓ sig.
lysosome organization
GNPTAB, MCOLN1
 GO:0007040 2 / 65 71.9× 3.29e-4 7.15e-3 ✓ sig.
lipid catabolic process
PNPLA6, NEU1
 GO:0016042 2 / 119 39.3× 1.10e-3 1.60e-2 ✓ sig.
calcium ion export
MCOLN1
 GO:1901660 1 / 3 779× 1.28e-3 1.75e-2 ✓ sig.
positive regulation of lysosome organization
MCOLN1
 GO:1905673 1 / 4 584× 1.71e-3 2.07e-2 ✓ sig.
regulation of interferon-beta production
RNF216
 GO:0032648 1 / 4 584× 1.71e-3 2.07e-2 ✓ sig.
secretion of lysosomal enzymes
GNPTAB
 GO:0033299 1 / 5 467× 2.14e-3 2.34e-2 ✓ sig.
glucose import in response to insulin stimulus
SGCB
 GO:0044381 1 / 6 389× 2.57e-3 2.58e-2 ✓ sig.
regulation of defense response to virus by host
RNF216
 GO:0050691 1 / 8 292× 3.42e-3 3.03e-2 ✓ sig.
ganglioside catabolic process
NEU1
 GO:0006689 1 / 8 292× 3.42e-3 3.03e-2 ✓ sig.
cellular response to pH
MCOLN1
 GO:0071467 1 / 9 260× 3.85e-3 3.22e-2 ✓ sig.
vascular associated smooth muscle cell development
SGCB
 GO:0097084 1 / 10 234× 4.27e-3 3.38e-2 ✓ sig.
phagosome maturation
MCOLN1
 GO:0090382 1 / 11 212× 4.70e-3 3.56e-2 ✓ sig.
iron ion transmembrane transport
MCOLN1
 GO:0034755 1 / 11 212× 4.70e-3 3.56e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Cerebellar ataxia and hypogonadotropic hypogonadism Cerebellar ataxia-hypogonadism 0.667 2 8.44e-9 7.20e-8 ✓ sig.
Ataxia-hypogonadism-choroidal dystrophy syndrome Chorioretinal dystrophy, spinocerebellar ataxia, hypogonadotropic hypogonadism syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
retinal dystrophy-ataxia-pituitary hormone abnormality-hypogonadism syndrome Trichomegaly-retina pigmentary degeneration-dwarfism syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
PNPLA6-related spastic paraplegia with or without ataxia retinal dystrophy-ataxia-pituitary hormone abnormality-hypogonadism syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
PNPLA6-related spastic paraplegia with or without ataxia Trichomegaly-retina pigmentary degeneration-dwarfism syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Chorioretinal dystrophy, spinocerebellar ataxia, hypogonadotropic hypogonadism syndrome PNPLA6-related spastic paraplegia with or without ataxia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Chorioretinal dystrophy, spinocerebellar ataxia, hypogonadotropic hypogonadism syndrome retinal dystrophy-ataxia-pituitary hormone abnormality-hypogonadism syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Chorioretinal dystrophy, spinocerebellar ataxia, hypogonadotropic hypogonadism syndrome Trichomegaly-retina pigmentary degeneration-dwarfism syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Boucher-neuhauser syndrome PNPLA6-related spastic paraplegia with or without ataxia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Boucher-neuhauser syndrome Trichomegaly-retina pigmentary degeneration-dwarfism syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Ataxia-hypogonadism-choroidal dystrophy syndrome Boucher-neuhauser syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Ataxia-hypogonadism-choroidal dystrophy syndrome Trichomegaly-retina pigmentary degeneration-dwarfism syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Ataxia-hypogonadism-choroidal dystrophy syndrome retinal dystrophy-ataxia-pituitary hormone abnormality-hypogonadism syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Ataxia-hypogonadism-choroidal dystrophy syndrome PNPLA6-related spastic paraplegia with or without ataxia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Boucher-neuhauser syndrome Chorioretinal dystrophy, spinocerebellar ataxia, hypogonadotropic hypogonadism syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Boucher-neuhauser syndrome retinal dystrophy-ataxia-pituitary hormone abnormality-hypogonadism syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Ataxia-hypogonadism-choroidal dystrophy syndrome Cerebellar ataxia-hypogonadism 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Boucher-neuhauser syndrome Cerebellar ataxia-hypogonadism 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Cerebellar ataxia-hypogonadism Chorioretinal dystrophy, spinocerebellar ataxia, hypogonadotropic hypogonadism syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Cerebellar ataxia-hypogonadism Trichomegaly-retina pigmentary degeneration-dwarfism syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Cerebellar ataxia and hypogonadotropic hypogonadism Trichomegaly-retina pigmentary degeneration-dwarfism syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Cerebellar ataxia and hypogonadotropic hypogonadism Chorioretinal dystrophy, spinocerebellar ataxia, hypogonadotropic hypogonadism syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Boucher-neuhauser syndrome Cerebellar ataxia and hypogonadotropic hypogonadism 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Ataxia-hypogonadism-choroidal dystrophy syndrome Cerebellar ataxia and hypogonadotropic hypogonadism 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Beta-sarcoglycanopathy Mucolipidosis 0.125 1 4.55e-4 9.55e-4 ✓ sig.
GNPTG-mucolipidosis Mucolipidosis 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Ataxia-hypogonadism-choroidal dystrophy syndrome Mucolipidosis 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Boucher-neuhauser syndrome Mucolipidosis 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Chorioretinal dystrophy, spinocerebellar ataxia, hypogonadotropic hypogonadism syndrome Mucolipidosis 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Mucolipidosis Trichomegaly-retina pigmentary degeneration-dwarfism syndrome 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Mucolipidosis retinal dystrophy-ataxia-pituitary hormone abnormality-hypogonadism syndrome 0.125 1 4.55e-4 9.55e-4 ✓ sig.