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 170

9 diseases · 20 shared-gene connections
9 Diseases
23 Unique genes
0.255 Avg. similarity score
Myotonia Most-connected disease (6 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 ⇵
Myotonia 6 6 1
Paramyotonia congenita 6 6 2
Potassium-aggravated myotonia 6 6 1
SCN4A-related myopathy, autosomal recessive 6 6 1
Hyperkalemic periodic paralysis 5 5 3
Male reproductive organ cancer 5 5 17
Sotos syndrome 3 3 5
familial acute necrotizing encephalopathy 2 2 1
hearing impairment and infertile male syndrome 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
SCN4A 7 / 9 Hyperkalemic periodic paralysis, Male reproductive organ cancer, Myotonia, Paramyotonia congenita and 3 more
RANBP2 3 / 9 familial acute necrotizing encephalopathy, Hyperkalemic periodic paralysis, Paramyotonia congenita
CDC14A 2 / 9 hearing impairment and infertile male syndrome, Male reproductive organ cancer
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 ⇵
Endometrial cancer
APC2, PIK3CA
 KEGG 2 / 59 17.7× 5.62e-3 4.73e-2 ✓ sig.
Lysine degradation
NSD1, SETD2
 KEGG 2 / 63 16.6× 6.38e-3 5.14e-2
PKMTs methylate histone lysines
NSD1, SETD2
 Reactome 2 / 71 14.7× 8.05e-3 5.99e-2
Caffeine metabolism
XDH
 KEGG 1 / 6 87.0× 1.14e-2 7.44e-2
MET activates PI3K/AKT signaling
PIK3CA
 Reactome 1 / 6 87.0× 1.14e-2 7.44e-2
IRS-mediated signalling
PIK3CA
 Reactome 1 / 6 87.0× 1.14e-2 7.44e-2
Colorectal cancer
APC2, PIK3CA
 KEGG 2 / 87 12.0× 1.19e-2 7.61e-2
PI3K/AKT activation
PIK3CA
 Reactome 1 / 9 58.0× 1.71e-2 9.45e-2
PI3K events in ERBB4 signaling
PIK3CA
 Reactome 1 / 10 52.2× 1.90e-2 9.98e-2
Signaling by FGFR3 fusions in cancer
PIK3CA
 Reactome 1 / 10 52.2× 1.90e-2 9.98e-2
Signaling by FGFR4 in disease
PIK3CA
 Reactome 1 / 11 47.5× 2.09e-2 1.05e-1
Costimulation by the CD28 family
PIK3CA
 Reactome 1 / 11 47.5× 2.09e-2 1.05e-1
Purine catabolism
XDH
 Reactome 1 / 12 43.5× 2.28e-2 1.11e-1
Butyrophilin (BTN) family interactions
XDH
 Reactome 1 / 12 43.5× 2.28e-2 1.11e-1
Erythropoietin activates Phosphoinositide-3-kinase (PI3K)
PIK3CA
 Reactome 1 / 12 43.5× 2.28e-2 1.11e-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 ⇵
regulation of skeletal muscle contraction by action potential
SCN4A
 GO:0100001 1 / 1 812× 1.23e-3 1.72e-2 ✓ sig.
hypoxanthine catabolic process
XDH
 GO:0009114 1 / 1 812× 1.23e-3 1.72e-2 ✓ sig.
xanthine catabolic process
XDH
 GO:0009115 1 / 1 812× 1.23e-3 1.72e-2 ✓ sig.
regulation of peptidyl-serine phosphorylation
NSD1
 GO:0033135 1 / 1 812× 1.23e-3 1.72e-2 ✓ sig.
regulation of RNA polymerase II regulatory region sequence-specific DNA binding
NSD1
 GO:1903025 1 / 1 812× 1.23e-3 1.72e-2 ✓ sig.
response to butyrate
PIK3CA
 GO:1903544 1 / 1 812× 1.23e-3 1.72e-2 ✓ sig.
glycoRNA biosynthetic process
DTWD2
 GO:0141217 1 / 1 812× 1.23e-3 1.72e-2 ✓ sig.
inosine catabolic process
XDH
 GO:0006148 1 / 2 406× 2.46e-3 2.53e-2 ✓ sig.
deoxyinosine catabolic process
XDH
 GO:0006149 1 / 2 406× 2.46e-3 2.53e-2 ✓ sig.
guanine catabolic process
XDH
 GO:0006147 1 / 2 406× 2.46e-3 2.53e-2 ✓ sig.
deoxyguanosine catabolic process
XDH
 GO:0006161 1 / 2 406× 2.46e-3 2.53e-2 ✓ sig.
response to muscle inactivity
PIK3CA
 GO:0014870 1 / 2 406× 2.46e-3 2.53e-2 ✓ sig.
cellular response to hydrostatic pressure
PIK3CA
 GO:0071464 1 / 3 271× 3.69e-3 3.17e-2 ✓ sig.
deoxyadenosine catabolic process
XDH
 GO:0006157 1 / 3 271× 3.69e-3 3.17e-2 ✓ sig.
regulation of protein localization to chromatin
SETD2
 GO:1905634 1 / 3 271× 3.69e-3 3.17e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Hyperkalemic periodic paralysis Paramyotonia congenita 0.500 2 2.53e-8 2.03e-7 ✓ sig.
Potassium-aggravated myotonia SCN4A-related myopathy, autosomal recessive 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Myotonia Potassium-aggravated myotonia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Myotonia SCN4A-related myopathy, autosomal recessive 0.500 1 6.49e-5 2.34e-4 ✓ sig.
familial acute necrotizing encephalopathy Paramyotonia congenita 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Paramyotonia congenita SCN4A-related myopathy, autosomal recessive 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Paramyotonia congenita Potassium-aggravated myotonia 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Myotonia Paramyotonia congenita 0.333 1 1.30e-4 3.90e-4 ✓ sig.
familial acute necrotizing encephalopathy Hyperkalemic periodic paralysis 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Hyperkalemic periodic paralysis Myotonia 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Hyperkalemic periodic paralysis Potassium-aggravated myotonia 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Hyperkalemic periodic paralysis SCN4A-related myopathy, autosomal recessive 0.250 1 1.95e-4 5.28e-4 ✓ sig.
SCN4A-related myopathy, autosomal recessive Sotos syndrome 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Potassium-aggravated myotonia Sotos syndrome 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Myotonia Sotos syndrome 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Male reproductive organ cancer SCN4A-related myopathy, autosomal recessive 0.056 1 1.10e-3 1.81e-3 ✓ sig.
Male reproductive organ cancer Potassium-aggravated myotonia 0.056 1 1.10e-3 1.81e-3 ✓ sig.
Male reproductive organ cancer Myotonia 0.056 1 1.10e-3 1.81e-3 ✓ sig.
hearing impairment and infertile male syndrome Male reproductive organ cancer 0.056 1 1.10e-3 1.81e-3 ✓ sig.
Male reproductive organ cancer Paramyotonia congenita 0.053 1 2.21e-3 3.10e-3 ✓ sig.