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 201

8 diseases · 14 shared-gene connections
8 Diseases
14 Unique genes
0.226 Avg. similarity score
Hypobetalipoproteinemia 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 ⇵
Hypobetalipoproteinemia 6 6 3
familial hypobetalipoproteinemia 1 5 5 1
hypercholesterolemia, autosomal dominant, type B 5 5 1
Binge eating disorder 4 4 7
Isolated systolic hypertension 4 4 2
Congenital stenosis of aortic valve 2 2 5
familial hypobetalipoproteinemia 2 1 1 1
hypercholesterolemia, autosomal dominant, 3 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
APOB 6 / 8 Binge eating disorder, Congenital stenosis of aortic valve, familial hypobetalipoproteinemia 1, hypercholesterolemia, autosomal dominant, type B and 2 more
ANGPTL3 2 / 8 familial hypobetalipoproteinemia 2, Hypobetalipoproteinemia
PCSK9 2 / 8 hypercholesterolemia, autosomal dominant, 3, Hypobetalipoproteinemia
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 ⇵
Cholesterol metabolism
APOB, PCSK9, ANGPTL3
 KEGG 3 / 51 50.5× 2.54e-5 7.26e-4 ✓ sig.
Vitamin D (calciferol) metabolism
CUBN, VDR
 Reactome 2 / 11 156× 6.90e-5 1.65e-3 ✓ sig.
LDL clearance
APOB, PCSK9
 Reactome 2 / 18 95.3× 1.91e-4 3.77e-3 ✓ sig.
Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)
APOB, MMP1, PCSK9
 Reactome 3 / 125 20.6× 3.68e-4 6.29e-3 ✓ sig.
Vitamin digestion and absorption
APOB, CUBN
 KEGG 2 / 26 66.0× 4.04e-4 6.76e-3 ✓ sig.
Lipid and atherosclerosis
APOB, MMP1, PPP3CB
 KEGG 3 / 216 11.9× 1.80e-3 2.12e-2 ✓ sig.
Degradation of the extracellular matrix
ELN, MMP1
 Reactome 2 / 70 24.5× 2.91e-3 3.01e-2 ✓ sig.
LDL remodeling
APOB
 Reactome 1 / 3 286× 3.49e-3 3.42e-2 ✓ sig.
Defective AMN causes hereditary megaloblastic anemia 1
CUBN
 Reactome 1 / 3 286× 3.49e-3 3.42e-2 ✓ sig.
Defective CUBN causes hereditary megaloblastic anemia 1
CUBN
 Reactome 1 / 3 286× 3.49e-3 3.42e-2 ✓ sig.
Scavenging by Class H Receptors
APOB
 Reactome 1 / 4 214× 4.66e-3 4.18e-2 ✓ sig.
Chylomicron clearance
APOB
 Reactome 1 / 5 172× 5.82e-3 4.84e-2 ✓ sig.
HDL clearance
CUBN
 Reactome 1 / 5 172× 5.82e-3 4.84e-2 ✓ sig.
Scavenging by Class B Receptors
APOB
 Reactome 1 / 5 172× 5.82e-3 4.84e-2 ✓ sig.
VLDL assembly
APOB
 Reactome 1 / 5 172× 5.82e-3 4.84e-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 ⇵
cholesterol metabolic process
APOB, CUBN, PCSK9, ANGPTL3
 GO:0008203 4 / 107 49.9× 9.73e-7 8.11e-5 ✓ sig.
cholesterol homeostasis
APOB, PCSK9, ANGPTL3
 GO:0042632 3 / 112 35.8× 7.27e-5 2.39e-3 ✓ sig.
lipoprotein transport
APOB, CUBN
 GO:0042953 2 / 20 133× 9.83e-5 2.98e-3 ✓ sig.
steroid metabolic process
APOB, CUBN, PCSK9
 GO:0008202 3 / 135 29.7× 1.27e-4 3.61e-3 ✓ sig.
lipoprotein metabolic process
APOB, PCSK9
 GO:0042157 2 / 26 103× 1.68e-4 4.45e-3 ✓ sig.
artery morphogenesis
APOB, ANGPTL3
 GO:0048844 2 / 27 98.9× 1.81e-4 4.71e-3 ✓ sig.
lipid storage
ANGPTL3, BSCL2
 GO:0019915 2 / 32 83.4× 2.55e-4 5.99e-3 ✓ sig.
lipid metabolic process
APOB, CUBN, PCSK9, ANGPTL3, BSCL2
 GO:0006629 5 / 840 7.9× 2.59e-4 6.06e-3 ✓ sig.
S-adenosyl-L-methionine transport
SLC25A26
 GO:0015805 1 / 1 1,335× 7.49e-4 1.25e-2 ✓ sig.
macromolecule methylation
SLC25A26
 GO:0043414 1 / 1 1,335× 7.49e-4 1.25e-2 ✓ sig.
mitochondrial S-adenosyl-L-methionine transmembrane transport
SLC25A26
 GO:1990543 1 / 1 1,335× 7.49e-4 1.25e-2 ✓ sig.
low-density lipoprotein receptor particle metabolic process
PCSK9
 GO:0032799 1 / 1 1,335× 7.49e-4 1.25e-2 ✓ sig.
low-density lipoprotein particle receptor catabolic process
PCSK9
 GO:0032802 1 / 1 1,335× 7.49e-4 1.25e-2 ✓ sig.
phospholipid metabolic process
PCSK9, ANGPTL3
 GO:0006644 2 / 66 40.4× 1.09e-3 1.59e-2 ✓ sig.
nuclear receptor-mediated bile acid signaling pathway
VDR
 GO:0038185 1 / 2 667× 1.50e-3 1.91e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
familial hypobetalipoproteinemia 1 hypercholesterolemia, autosomal dominant, type B 0.500 1 6.49e-5 2.34e-4 ✓ sig.
familial hypobetalipoproteinemia 1 Isolated systolic hypertension 0.333 1 1.30e-4 3.90e-4 ✓ sig.
hypercholesterolemia, autosomal dominant, type B Isolated systolic hypertension 0.333 1 1.30e-4 3.90e-4 ✓ sig.
familial hypobetalipoproteinemia 1 Hypobetalipoproteinemia 0.250 1 1.95e-4 5.28e-4 ✓ sig.
familial hypobetalipoproteinemia 2 Hypobetalipoproteinemia 0.250 1 1.95e-4 5.28e-4 ✓ sig.
hypercholesterolemia, autosomal dominant, 3 Hypobetalipoproteinemia 0.250 1 1.95e-4 5.28e-4 ✓ sig.
hypercholesterolemia, autosomal dominant, type B Hypobetalipoproteinemia 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Congenital stenosis of aortic valve familial hypobetalipoproteinemia 1 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Congenital stenosis of aortic valve hypercholesterolemia, autosomal dominant, type B 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Hypobetalipoproteinemia Isolated systolic hypertension 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Binge eating disorder familial hypobetalipoproteinemia 1 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Binge eating disorder hypercholesterolemia, autosomal dominant, type B 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Binge eating disorder Isolated systolic hypertension 0.111 1 9.09e-4 1.56e-3 ✓ sig.
Binge eating disorder Hypobetalipoproteinemia 0.100 1 1.36e-3 2.13e-3 ✓ sig.