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 154

9 diseases · 8 shared-gene connections
9 Diseases
37 Unique genes
0.026 Avg. similarity score
Glycogen storage disease 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 ⇵
Glycogen storage disease 8 8 37
Danon disease 1 1 1
Dimauro disease 1 1 1
PGM1-congenital disorder of glycosylation 1 1 1
glycogen storage disease III 1 1 1
glycogen storage disease V 1 1 1
glycogen storage disease VI 1 1 1
glycogen storage disease due to muscle and heart glycogen synthase deficiency 1 1 1
polyglucosan body myopathy type 2 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
AGL 2 / 9 Glycogen storage disease, glycogen storage disease III
GYG1 2 / 9 Glycogen storage disease, polyglucosan body myopathy type 2
GYS1 2 / 9 Glycogen storage disease, glycogen storage disease due to muscle and heart glycogen synthase deficiency
LAMP2 2 / 9 Danon disease, Glycogen storage disease
PGAM2 2 / 9 Dimauro disease, Glycogen storage disease
PGM1 2 / 9 Glycogen storage disease, PGM1-congenital disorder of glycosylation
PYGL 2 / 9 Glycogen storage disease, glycogen storage disease VI
PYGM 2 / 9 Glycogen storage disease, glycogen storage disease V
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 ⇵
Glucagon signaling pathway
PGAM2, G6PC1, GYS1, GYS2, PFKM, PHKA1, PHKA2, PHKG2, PRKAG2, PYGL, PYGM, SLC2A2
 KEGG 16 / 107 48.5× 5.42e-24 8.80e-21 ✓ sig.
Glycogen breakdown (glycogenolysis)
AGL, GAA, GYG1, PHKA1, PHKA2, PHKG2, PYGL, PYGM, PHKB, PHKG1
 Reactome 10 / 16 203× 1.61e-22 2.09e-19 ✓ sig.
Starch and sucrose metabolism
AGL, G6PC1, GAA, GBE1, GYG1, GYS1, GYS2, PYGL, PYGM, PGM1
 KEGG 10 / 36 90.2× 4.90e-18 2.83e-15 ✓ sig.
Insulin signaling pathway
G6PC1, GYS1, GYS2, PHKA1, PHKA2, PHKG2, PRKAG2, PYGL, PYGM, PHKB, PHKG1, PIK3CA
 KEGG 12 / 138 28.2× 4.73e-15 1.60e-12 ✓ sig.
Glycolysis / Gluconeogenesis
PGAM2, G6PC1, PFKM, ALDOA, LDHB, LDHA, ENO3, PGK1, PGM1
 KEGG 9 / 67 43.6× 3.30e-13 7.70e-11 ✓ sig.
Glycogen synthesis
GBE1, GYG1, GYS1, GYS2, PGM1
 Reactome 5 / 16 101× 8.93e-10 1.02e-7 ✓ sig.
Insulin resistance
G6PC1, GYS1, GYS2, PRKAG2, PYGL, PYGM, SLC2A2, PIK3CA
 KEGG 8 / 109 23.8× 1.10e-9 1.23e-7 ✓ sig.
Glycolysis
PGAM2, PFKM, ALDOA, ENO3, PGK1
 Reactome 5 / 28 58.0× 1.96e-8 1.57e-6 ✓ sig.
Metabolic pathways
PGAM2, AGL, G6PC1, GAA, GBE1, GYG1, GYS1, GYS2, PFKM, PYGL, PYGM, ALDOA
 KEGG 19 / 1,563 3.9× 2.30e-8 1.83e-6 ✓ sig.
HIF-1 signaling pathway
PFKM, ALDOA, LDHB, LDHA, ENO3, PGK1, PIK3CA
 KEGG 7 / 110 20.7× 3.66e-8 2.71e-6 ✓ sig.
Gluconeogenesis
PGAM2, SLC37A4, ALDOA, ENO3, PGK1
 Reactome 5 / 34 47.7× 5.47e-8 3.86e-6 ✓ sig.
Central carbon metabolism in cancer
PGAM2, PFKM, SLC2A2, LDHB, LDHA, PIK3CA
 KEGG 6 / 71 27.4× 6.92e-8 4.76e-6 ✓ sig.
Biosynthesis of amino acids
PGAM2, PFKM, ALDOA, ENO3, PGK1, ASS1
 KEGG 6 / 75 26.0× 9.65e-8 6.33e-6 ✓ sig.
AMPK signaling pathway
G6PC1, GYS1, GYS2, PFKM, PRKAG2, PIK3CA
 KEGG 6 / 122 16.0× 1.75e-6 7.84e-5 ✓ sig.
Galactose metabolism
G6PC1, GAA, PFKM, PGM1
 KEGG 4 / 32 40.6× 2.58e-6 1.10e-4 ✓ 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 ⇵
glycogen metabolic process
AGL, G6PC1, GAA, GBE1, GYS1, PHKA1, PHKA2, PHKG2, PRKAG2, PYGL, PYGM, PHKB
 GO:0005977 13 / 40 164× 7.66e-27 2.91e-23 ✓ sig.
glycogen catabolic process
AGL, G6PC1, GAA, PFKM, PHKG2, PYGL, PYGM
 GO:0005980 7 / 11 321× 2.14e-17 2.36e-14 ✓ sig.
carbohydrate metabolic process
AGL, GAA, GBE1, PHKA1, PHKA2, PYGL, PYGM, SLC2A2, PHKB, PHKG1, PGM1
 GO:0005975 11 / 175 31.7× 2.45e-14 1.49e-11 ✓ sig.
glycolytic process
PGAM2, PFKM, ALDOA, LDHA, ENO3, PGK1, PGM1
 GO:0006096 7 / 49 72.2× 5.29e-12 2.07e-9 ✓ sig.
glycogen biosynthetic process
AGL, GBE1, GYG1, GYS1, GYS2
 GO:0005978 5 / 18 140× 1.93e-10 5.18e-8 ✓ sig.
gluconeogenesis
PGAM2, G6PC1, SLC37A4, ENO3, PGK1, PGM1
 GO:0006094 6 / 56 54.1× 1.19e-9 2.62e-7 ✓ sig.
generation of precursor metabolites and energy
GBE1, PHKA1, PHKA2, PHKG2, PHKB
 GO:0006091 5 / 49 51.5× 4.11e-8 5.75e-6 ✓ sig.
canonical glycolysis
PGAM2, PFKM, ENO3, PGK1
 GO:0061621 4 / 22 91.8× 9.27e-8 1.13e-5 ✓ sig.
striated muscle contraction
PGAM2, GAA, ALDOA, TNNT2
 GO:0006941 4 / 24 84.2× 1.34e-7 1.55e-5 ✓ sig.
muscle cell cellular homeostasis
LAMP2, GAA, PFKM, ALDOA
 GO:0046716 4 / 26 77.7× 1.88e-7 2.06e-5 ✓ sig.
glucose metabolic process
GAA, SLC37A4, PIK3CA, PGM1
 GO:0006006 4 / 66 30.6× 8.59e-6 4.63e-4 ✓ sig.
positive regulation of glycogen catabolic process
PHKA1, PHKG2
 GO:0045819 2 / 4 253× 2.28e-5 9.94e-4 ✓ sig.
glucose-6-phosphate transport
G6PC1, SLC37A4
 GO:0015760 2 / 7 144× 7.96e-5 2.55e-3 ✓ sig.
cardiac muscle contraction
GAA, PIK3CA, TNNT2
 GO:0060048 3 / 43 35.2× 8.35e-5 2.64e-3 ✓ sig.
fructose 1,6-bisphosphate metabolic process
PFKM, ALDOA
 GO:0030388 2 / 8 126× 1.06e-4 3.16e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Danon disease Glycogen storage disease 0.026 1 2.40e-3 3.30e-3 ✓ sig.
Dimauro disease Glycogen storage disease 0.026 1 2.40e-3 3.30e-3 ✓ sig.
Glycogen storage disease glycogen storage disease due to muscle and heart glycogen synthase deficiency 0.026 1 2.40e-3 3.30e-3 ✓ sig.
Glycogen storage disease glycogen storage disease III 0.026 1 2.40e-3 3.30e-3 ✓ sig.
Glycogen storage disease glycogen storage disease V 0.026 1 2.40e-3 3.30e-3 ✓ sig.
Glycogen storage disease glycogen storage disease VI 0.026 1 2.40e-3 3.30e-3 ✓ sig.
Glycogen storage disease PGM1-congenital disorder of glycosylation 0.026 1 2.40e-3 3.30e-3 ✓ sig.
Glycogen storage disease polyglucosan body myopathy type 2 0.026 1 2.40e-3 3.30e-3 ✓ sig.