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 273

8 diseases · 25 shared-gene connections
8 Diseases
4 Unique genes
0.440 Avg. similarity score
Arterial calcification, generalized, of infancy, 1 Most-connected disease (7 links)
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Disease Searched: Hypophosphatemic rickets, autosomal recessive, 2 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 ⇵
Arterial calcification, generalized, of infancy, 1 7 7 1
Cole disease 7 7 1
Coronary medial sclerosis of infancy 7 7 1
Generalised arterial calcification of infancy and hypophosphatemic rickets 7 7 1
Hypopigmentation-punctate palmoplantar keratoderma syndrome 7 7 1
Crystal arthropathy 5 5 4
Hypophosphatemic rickets, autosomal recessive, 2 5 5 1
Ossification of the posterior longitudinal ligament of the spine 5 5 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
ENPP1 8 / 8 Arterial calcification, generalized, of infancy, 1, Cole disease, Coronary medial sclerosis of infancy, Crystal arthropathy and 4 more
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 ⇵
Vitamin B2 (riboflavin) metabolism
ENPP1
 Reactome 1 / 7 429× 2.33e-3 2.13e-2 ✓ sig.
Riboflavin metabolism
ENPP1
 KEGG 1 / 8 375× 2.66e-3 2.34e-2 ✓ sig.
Vitamin B5 (pantothenate) metabolism
ENPP1
 Reactome 1 / 9 334× 2.99e-3 2.54e-2 ✓ sig.
Heme degradation
ABCG2
 Reactome 1 / 14 214× 4.66e-3 3.48e-2 ✓ sig.
Heme biosynthesis
ABCG2
 Reactome 1 / 14 214× 4.66e-3 3.48e-2 ✓ sig.
Pantothenate and CoA biosynthesis
ENPP1
 KEGG 1 / 21 143× 6.98e-3 4.53e-2 ✓ sig.
Iron uptake and transport
ABCG2
 Reactome 1 / 28 107× 9.29e-3 5.43e-2
Antifolate resistance
ABCG2
 KEGG 1 / 30 100× 9.96e-3 5.67e-2
Folate transport and metabolism
ABCG2
 KEGG 1 / 31 96.9× 1.03e-2 5.79e-2
Starch and sucrose metabolism
ENPP1
 KEGG 1 / 36 83.4× 1.19e-2 6.32e-2
Nicotinate and nicotinamide metabolism
ENPP1
 KEGG 1 / 38 79.0× 1.26e-2 6.55e-2
ABC transporters
ABCG2
 KEGG 1 / 45 66.7× 1.49e-2 7.22e-2
Pyrimidine metabolism
ENPP1
 KEGG 1 / 58 51.8× 1.92e-2 8.36e-2
Nucleotide metabolism
ENPP1
 KEGG 1 / 85 35.3× 2.80e-2 1.04e-1
Bile secretion
ABCG2
 KEGG 1 / 90 33.4× 2.96e-2 1.07e-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 ⇵
negative regulation of hh target transcription factor activity
ENPP1
 GO:1990787 1 / 1 4,672× 2.14e-4 5.31e-3 ✓ sig.
biotin transport
ABCG2
 GO:0015878 1 / 3 1,557× 6.42e-4 1.11e-2 ✓ sig.
renal urate salt excretion
ABCG2
 GO:0097744 1 / 3 1,557× 6.42e-4 1.11e-2 ✓ sig.
inorganic diphosphate transport
ENPP1
 GO:0030505 1 / 4 1,168× 8.56e-4 1.33e-2 ✓ sig.
riboflavin transport
ABCG2
 GO:0032218 1 / 6 779× 1.28e-3 1.67e-2 ✓ sig.
xenobiotic transport across blood-brain barrier
ABCG2
 GO:1990962 1 / 6 779× 1.28e-3 1.67e-2 ✓ sig.
nucleoside triphosphate catabolic process
ENPP1
 GO:0009143 1 / 6 779× 1.28e-3 1.67e-2 ✓ sig.
nucleic acid metabolic process
ENPP1
 GO:0090304 1 / 6 779× 1.28e-3 1.67e-2 ✓ sig.
export across plasma membrane
ABCG2
 GO:0140115 1 / 10 467× 2.14e-3 2.19e-2 ✓ sig.
urate metabolic process
ABCG2
 GO:0046415 1 / 10 467× 2.14e-3 2.19e-2 ✓ sig.
negative regulation of glycogen biosynthetic process
ENPP1
 GO:0045719 1 / 10 467× 2.14e-3 2.19e-2 ✓ sig.
intracellular phosphate ion homeostasis
ENPP1
 GO:0030643 1 / 10 467× 2.14e-3 2.19e-2 ✓ sig.
urate transport
ABCG2
 GO:0015747 1 / 11 425× 2.35e-3 2.30e-2 ✓ sig.
transepithelial transport
ABCG2
 GO:0070633 1 / 13 359× 2.78e-3 2.51e-2 ✓ sig.
cellular detoxification
ABCG2
 GO:1990748 1 / 14 334× 2.99e-3 2.59e-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 6.46e-5 1.98e-4 ✓ sig.
Generalised arterial calcification of infancy and hypophosphatemic rickets Ossification of the posterior longitudinal ligament of the spine 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Arterial calcification, generalized, of infancy, 1 Ossification of the posterior longitudinal ligament of the spine 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hypopigmentation-punctate palmoplantar keratoderma syndrome Ossification of the posterior longitudinal ligament of the spine 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Coronary medial sclerosis of infancy Ossification of the posterior longitudinal ligament of the spine 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cole disease Ossification of the posterior longitudinal ligament of the spine 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hypophosphatemic rickets, autosomal recessive, 2 Hypopigmentation-punctate palmoplantar keratoderma syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Generalised arterial calcification of infancy and hypophosphatemic rickets Hypophosphatemic rickets, autosomal recessive, 2 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Generalised arterial calcification of infancy and hypophosphatemic rickets Hypopigmentation-punctate palmoplantar keratoderma syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Coronary medial sclerosis of infancy Hypophosphatemic rickets, autosomal recessive, 2 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Coronary medial sclerosis of infancy Generalised arterial calcification of infancy and hypophosphatemic rickets 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Coronary medial sclerosis of infancy Hypopigmentation-punctate palmoplantar keratoderma syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cole disease Hypophosphatemic rickets, autosomal recessive, 2 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cole disease Generalised arterial calcification of infancy and hypophosphatemic rickets 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cole disease Hypopigmentation-punctate palmoplantar keratoderma syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cole disease Coronary medial sclerosis of infancy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Arterial calcification, generalized, of infancy, 1 Hypophosphatemic rickets, autosomal recessive, 2 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Arterial calcification, generalized, of infancy, 1 Generalised arterial calcification of infancy and hypophosphatemic rickets 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Arterial calcification, generalized, of infancy, 1 Hypopigmentation-punctate palmoplantar keratoderma syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Arterial calcification, generalized, of infancy, 1 Cole disease 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cole disease Crystal arthropathy 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Coronary medial sclerosis of infancy Crystal arthropathy 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Crystal arthropathy Hypopigmentation-punctate palmoplantar keratoderma syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Arterial calcification, generalized, of infancy, 1 Crystal arthropathy 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Crystal arthropathy Generalised arterial calcification of infancy and hypophosphatemic rickets 0.200 1 2.58e-4 5.38e-4 ✓ sig.