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 126

10 diseases · 20 shared-gene connections
10 Diseases
16 Unique genes
0.261 Avg. similarity score
Pseudoxanthoma elasticum Most-connected disease (9 links)
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Disease Searched: inherited pseudoxanthoma elasticum 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 ⇵
Pseudoxanthoma elasticum 9 9 5
Cole disease 5 5 1
Coronary medial sclerosis of infancy 5 5 1
Crystal arthropathy 5 5 4
arterial calcification, generalized, of infancy, 1 5 5 1
hypopigmentation-punctate palmoplantar keratoderma syndrome 5 5 1
Desbuquois dysplasia 2 2 3
Graft versus host disease 2 2 7
Dubin-johnson syndrome 1 1 1
inherited pseudoxanthoma elasticum 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
ENPP1 6 / 10 arterial calcification, generalized, of infancy, 1, Cole disease, Coronary medial sclerosis of infancy, Crystal arthropathy and 2 more
XYLT1 3 / 10 Desbuquois dysplasia, Graft versus host disease, Pseudoxanthoma elasticum
ABCC2 2 / 10 Dubin-johnson syndrome, Pseudoxanthoma elasticum
ABCC6 2 / 10 inherited pseudoxanthoma elasticum, Pseudoxanthoma elasticum
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 ⇵
ABC transporters
ABCC2, ABCC6, ABCG2
 KEGG 3 / 45 50.0× 2.66e-5 7.39e-4 ✓ sig.
Heme degradation
ABCC2, ABCG2
 Reactome 2 / 14 107× 1.50e-4 3.02e-3 ✓ sig.
Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate
XYLT1, XYLT2
 KEGG 2 / 21 71.5× 3.44e-4 5.88e-3 ✓ sig.
Glycosaminoglycan biosynthesis - heparan sulfate / heparin
XYLT1, XYLT2
 KEGG 2 / 24 62.6× 4.51e-4 7.28e-3 ✓ sig.
A tetrasaccharide linker sequence is required for GAG synthesis
XYLT1, XYLT2
 Reactome 2 / 26 57.7× 5.31e-4 8.25e-3 ✓ sig.
Antifolate resistance
ABCC2, ABCG2
 KEGG 2 / 30 50.0× 7.08e-4 1.03e-2 ✓ sig.
Folate transport and metabolism
ABCC2, ABCG2
 KEGG 2 / 31 48.4× 7.57e-4 1.08e-2 ✓ sig.
Defective ABCC2 causes Dubin-Johnson syndrome
ABCC2
 Reactome 1 / 1 751× 1.33e-3 1.67e-2 ✓ sig.
Defective ABCC6 causes pseudoxanthoma elasticum (PXE)
ABCC6
 Reactome 1 / 1 751× 1.33e-3 1.67e-2 ✓ sig.
Pyrimidine metabolism
ENPP1, CANT1
 KEGG 2 / 58 25.9× 2.63e-3 2.79e-2 ✓ sig.
ABC-family proteins mediated transport
ABCC2, ABCC6
 Reactome 2 / 81 18.5× 5.07e-3 4.42e-2 ✓ sig.
Nucleotide metabolism
ENPP1, CANT1
 KEGG 2 / 85 17.7× 5.57e-3 4.71e-2 ✓ sig.
Bile secretion
ABCC2, ABCG2
 KEGG 2 / 90 16.7× 6.22e-3 5.08e-2
Vitamin B2 (riboflavin) metabolism
ENPP1
 Reactome 1 / 7 107× 9.29e-3 6.61e-2
Riboflavin metabolism
ENPP1
 KEGG 1 / 8 93.8× 1.06e-2 7.20e-2

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
proteoglycan biosynthetic process
XYLT1, XYLT2, CANT1, FAM20B
 GO:0030166 4 / 21 222× 2.13e-9 4.36e-7 ✓ sig.
phosphate ion homeostasis
ABCC6, ENPP1, TMEM174
 GO:0055062 3 / 15 234× 2.33e-7 2.45e-5 ✓ sig.
inorganic diphosphate transport
ABCC6, ENPP1
 GO:0030505 2 / 4 584× 4.12e-6 2.59e-4 ✓ sig.
carboxylic acid transport
ABCC2, ABCC6
 GO:0046942 2 / 5 467× 6.86e-6 3.90e-4 ✓ sig.
xenobiotic transport across blood-brain barrier
ABCC2, ABCG2
 GO:1990962 2 / 6 389× 1.03e-5 5.37e-4 ✓ sig.
leukotriene transport
ABCC2, ABCC6
 GO:0071716 2 / 7 334× 1.44e-5 6.99e-4 ✓ sig.
intracellular phosphate ion homeostasis
ABCC6, ENPP1
 GO:0030643 2 / 10 234× 3.08e-5 1.25e-3 ✓ sig.
glycosaminoglycan metabolic process
XYLT1, XYLT2
 GO:0030203 2 / 12 195× 4.51e-5 1.67e-3 ✓ sig.
transepithelial transport
ABCC2, ABCG2
 GO:0070633 2 / 13 180× 5.33e-5 1.90e-3 ✓ sig.
glycosaminoglycan biosynthetic process
XYLT1, XYLT2
 GO:0006024 2 / 20 117× 1.29e-4 3.69e-3 ✓ sig.
glycoprotein biosynthetic process
XYLT1, XYLT2
 GO:0009101 2 / 21 111× 1.43e-4 3.96e-3 ✓ sig.
chondroitin sulfate proteoglycan biosynthetic process
XYLT1, XYLT2
 GO:0050650 2 / 26 89.8× 2.21e-4 5.40e-3 ✓ sig.
heparan sulfate proteoglycan biosynthetic process
XYLT1, XYLT2
 GO:0015012 2 / 30 77.9× 2.95e-4 6.67e-3 ✓ sig.
ATP metabolic process
ABCC6, ENPP1
 GO:0046034 2 / 36 64.9× 4.26e-4 8.64e-3 ✓ sig.
monoatomic anion transmembrane transport
ABCC2, ABCC6
 GO:0098656 2 / 40 58.4× 5.26e-4 1.00e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
arterial calcification, generalized, of infancy, 1 Coronary medial sclerosis of infancy 0.500 1 6.49e-5 2.33e-4 ✓ sig.
arterial calcification, generalized, of infancy, 1 hypopigmentation-punctate palmoplantar keratoderma syndrome 0.500 1 6.49e-5 2.33e-4 ✓ sig.
arterial calcification, generalized, of infancy, 1 Cole disease 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Cole disease Coronary medial sclerosis of infancy 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Cole disease hypopigmentation-punctate palmoplantar keratoderma syndrome 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Coronary medial sclerosis of infancy hypopigmentation-punctate palmoplantar keratoderma syndrome 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Coronary medial sclerosis of infancy Crystal arthropathy 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Crystal arthropathy hypopigmentation-punctate palmoplantar keratoderma syndrome 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Cole disease Crystal arthropathy 0.200 1 2.60e-4 6.51e-4 ✓ sig.
arterial calcification, generalized, of infancy, 1 Crystal arthropathy 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Cole disease Pseudoxanthoma elasticum 0.167 1 3.25e-4 7.70e-4 ✓ sig.
arterial calcification, generalized, of infancy, 1 Pseudoxanthoma elasticum 0.167 1 3.25e-4 7.70e-4 ✓ sig.
Coronary medial sclerosis of infancy Pseudoxanthoma elasticum 0.167 1 3.25e-4 7.70e-4 ✓ sig.
Dubin-johnson syndrome Pseudoxanthoma elasticum 0.167 1 3.25e-4 7.70e-4 ✓ sig.
hypopigmentation-punctate palmoplantar keratoderma syndrome Pseudoxanthoma elasticum 0.167 1 3.25e-4 7.70e-4 ✓ sig.
inherited pseudoxanthoma elasticum Pseudoxanthoma elasticum 0.167 1 3.25e-4 7.70e-4 ✓ sig.
Desbuquois dysplasia Pseudoxanthoma elasticum 0.125 1 9.74e-4 1.66e-3 ✓ sig.
Crystal arthropathy Pseudoxanthoma elasticum 0.111 1 1.30e-3 2.06e-3 ✓ sig.
Desbuquois dysplasia Graft versus host disease 0.100 1 1.36e-3 2.15e-3 ✓ sig.
Graft versus host disease Pseudoxanthoma elasticum 0.083 1 2.27e-3 3.19e-3 ✓ sig.