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 371

5 diseases · 7 shared-gene connections
5 Diseases
10 Unique genes
0.175 Avg. similarity score
Carbohydrate metabolism disease Most-connected disease (4 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 ⇵
Carbohydrate metabolism disease 4 4 10
Carbohydrate metabolism disorder 4 4 5
MPI-congenital disorder of glycosylation 2 2 1
Transaldolase deficiency 2 2 1
Triose phosphate isomerase deficiency 2 2 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
MPI 3 / 5 Carbohydrate metabolism disease, Carbohydrate metabolism disorder, MPI-congenital disorder of glycosylation
TALDO1 3 / 5 Carbohydrate metabolism disease, Carbohydrate metabolism disorder, Transaldolase deficiency
TPI1 3 / 5 Carbohydrate metabolism disease, Carbohydrate metabolism disorder, Triose phosphate isomerase deficiency
ACAT1 2 / 5 Carbohydrate metabolism disease, Carbohydrate metabolism disorder
PRKAG3 2 / 5 Carbohydrate metabolism disease, Carbohydrate metabolism disorder
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 ⇵
Carbon metabolism
GCK, HK1, ACAT1, TALDO1, TPI1
 KEGG 5 / 115 52.2× 1.79e-8 1.45e-6 ✓ sig.
Glycolysis / Gluconeogenesis
G6PC2, GCK, HK1, TPI1
 KEGG 4 / 67 71.7× 1.81e-7 1.10e-5 ✓ sig.
Glycolysis
GCK, HK1, TPI1
 Reactome 3 / 28 129× 1.35e-6 6.33e-5 ✓ sig.
Galactose metabolism
G6PC2, GCK, HK1
 KEGG 3 / 32 113× 2.04e-6 8.92e-5 ✓ sig.
Fructose and mannose metabolism
HK1, MPI, TPI1
 KEGG 3 / 34 106× 2.45e-6 1.05e-4 ✓ sig.
Starch and sucrose metabolism
G6PC2, GCK, HK1
 KEGG 3 / 36 100× 2.93e-6 1.22e-4 ✓ sig.
Biosynthesis of nucleotide sugars
GCK, HK1, MPI
 KEGG 3 / 37 97.4× 3.18e-6 1.30e-4 ✓ sig.
Insulin signaling pathway
G6PC2, GCK, HK1, PRKAG3
 KEGG 4 / 138 34.8× 3.32e-6 1.35e-4 ✓ sig.
Amino sugar and nucleotide sugar metabolism
GCK, HK1, MPI
 KEGG 3 / 38 94.8× 3.45e-6 1.40e-4 ✓ sig.
Neomycin, kanamycin and gentamicin biosynthesis
GCK, HK1
 KEGG 2 / 5 480× 6.23e-6 2.26e-4 ✓ sig.
Metabolic pathways
G6PC2, GCK, HK1, ACAT1, MPI, TALDO1, TPI1
 KEGG 7 / 1,563 5.4× 5.23e-5 1.33e-3 ✓ sig.
Glucagon signaling pathway
G6PC2, GCK, PRKAG3
 KEGG 3 / 107 33.7× 7.88e-5 1.85e-3 ✓ sig.
Gluconeogenesis
G6PC2, TPI1
 Reactome 2 / 34 70.6× 3.45e-4 5.98e-3 ✓ sig.
Type II diabetes mellitus
GCK, HK1
 KEGG 2 / 47 51.1× 6.61e-4 9.91e-3 ✓ sig.
Carbohydrate digestion and absorption
G6PC2, HK1
 KEGG 2 / 48 50.0× 6.90e-4 1.02e-2 ✓ 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 ⇵
glucose 6-phosphate metabolic process
G6PC2, GCK, HK1
 GO:0051156 3 / 11 510× 1.82e-8 2.87e-6 ✓ sig.
canonical glycolysis
GCK, HK1, TPI1
 GO:0061621 3 / 22 255× 1.69e-7 1.88e-5 ✓ sig.
glyceraldehyde-3-phosphate metabolic process
TALDO1, TPI1
 GO:0019682 2 / 3 1,246× 7.73e-7 6.73e-5 ✓ sig.
carbohydrate metabolic process
GCK, HK1, MPI, TALDO1
 GO:0005975 4 / 175 42.7× 1.49e-6 1.14e-4 ✓ sig.
glycolytic process
GCK, HK1, TPI1
 GO:0006096 3 / 49 114× 2.01e-6 1.45e-4 ✓ sig.
hexose metabolic process
GCK, HK1
 GO:0019318 2 / 6 623× 3.86e-6 2.44e-4 ✓ sig.
GDP-mannose biosynthetic process
HK1, MPI
 GO:0009298 2 / 6 623× 3.86e-6 2.44e-4 ✓ sig.
glucose metabolic process
GCK, HK1, TPI1
 GO:0006006 3 / 66 84.9× 4.96e-6 2.98e-4 ✓ sig.
fructose 6-phosphate metabolic process
HK1, TALDO1
 GO:0006002 2 / 13 287× 2.00e-5 8.99e-4 ✓ sig.
regulation of glycolytic process
GCK, PRKAG3
 GO:0006110 2 / 13 287× 2.00e-5 8.99e-4 ✓ sig.
carbohydrate phosphorylation
GCK, HK1
 GO:0046835 2 / 24 156× 7.07e-5 2.34e-3 ✓ sig.
intracellular glucose homeostasis
GCK, HK1
 GO:0001678 2 / 27 138× 8.98e-5 2.79e-3 ✓ sig.
regulation of insulin secretion
G6PC2, GCK
 GO:0050796 2 / 46 81.2× 2.63e-4 6.14e-3 ✓ sig.
gluconeogenesis
G6PC2, TPI1
 GO:0006094 2 / 56 66.7× 3.91e-4 8.07e-3 ✓ sig.
methylglyoxal biosynthetic process
TPI1
 GO:0019242 1 / 1 1,869× 5.35e-4 9.98e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Carbohydrate metabolism disease Carbohydrate metabolism disorder 0.455 5 3.50e-17 6.09e-16 ✓ sig.
Carbohydrate metabolism disorder Triose phosphate isomerase deficiency 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Carbohydrate metabolism disorder MPI-congenital disorder of glycosylation 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Carbohydrate metabolism disorder Transaldolase deficiency 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Carbohydrate metabolism disease Triose phosphate isomerase deficiency 0.091 1 6.49e-4 1.22e-3 ✓ sig.
Carbohydrate metabolism disease MPI-congenital disorder of glycosylation 0.091 1 6.49e-4 1.22e-3 ✓ sig.
Carbohydrate metabolism disease Transaldolase deficiency 0.091 1 6.49e-4 1.22e-3 ✓ sig.