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 140

9 diseases · 17 shared-gene connections
9 Diseases
19 Unique genes
0.198 Avg. similarity score
Ataxia with vitamin e deficiency Most-connected disease (6 links)
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Disease Searched: hypercholesterolemia, autosomal dominant, type B 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 ⇵
Ataxia with vitamin e deficiency 6 6 3
Hypobetalipoproteinemia 6 6 3
Isolated systolic hypertension 5 5 2
hypercholesterolemia, autosomal dominant, type B 5 5 1
Binge eating disorder 4 4 7
Hypoalphalipoproteinemia 3 3 7
Congenital stenosis of aortic valve 2 2 5
hypercholesterolemia, autosomal dominant, 3 2 2 1
Vitamin e deficiency 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
APOB 7 / 9 Ataxia with vitamin e deficiency, Binge eating disorder, Congenital stenosis of aortic valve, hypercholesterolemia, autosomal dominant, type B and 3 more
PCSK9 3 / 9 hypercholesterolemia, autosomal dominant, 3, Hypoalphalipoproteinemia, Hypobetalipoproteinemia
ANGPTL3 2 / 9 Hypoalphalipoproteinemia, Hypobetalipoproteinemia
APOA1 2 / 9 Ataxia with vitamin e deficiency, Hypoalphalipoproteinemia
TTPA 2 / 9 Ataxia with vitamin e deficiency, Vitamin e deficiency
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
APOA1, APOB, PCSK9, ANGPTL3, ABCA1
 KEGG 5 / 51 62.0× 1.26e-8 1.11e-6 ✓ sig.
Defective ABCA1 causes Tangier disease
APOA1, ABCA1
 Reactome 2 / 2 632× 2.37e-6 1.10e-4 ✓ sig.
Vitamin digestion and absorption
APOA1, APOB, CUBN
 KEGG 3 / 26 72.9× 8.53e-6 3.13e-4 ✓ sig.
Lipid and atherosclerosis
APOA1, APOB, MMP1, PPP3CB, ABCA1
 KEGG 5 / 216 14.6× 1.70e-5 5.51e-4 ✓ sig.
HDL clearance
APOA1, CUBN
 Reactome 2 / 5 253× 2.36e-5 7.26e-4 ✓ sig.
Scavenging by Class B Receptors
APOA1, APOB
 Reactome 2 / 5 253× 2.36e-5 7.26e-4 ✓ sig.
Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)
APOA1, APOB, MMP1, PCSK9
 Reactome 4 / 125 20.2× 3.84e-5 1.08e-3 ✓ sig.
Fat digestion and absorption
APOA1, APOB, ABCA1
 KEGG 3 / 43 44.1× 3.98e-5 1.11e-3 ✓ sig.
HDL assembly
APOA1, ABCA1
 Reactome 2 / 8 158× 6.60e-5 1.67e-3 ✓ sig.
Chylomicron remodeling
APOA1, APOB
 Reactome 2 / 9 140× 8.48e-5 2.03e-3 ✓ sig.
Chylomicron assembly
APOA1, APOB
 Reactome 2 / 9 140× 8.48e-5 2.03e-3 ✓ sig.
Scavenging by Class A Receptors
APOA1, APOB
 Reactome 2 / 11 115× 1.29e-4 2.84e-3 ✓ sig.
Vitamin D (calciferol) metabolism
CUBN, VDR
 Reactome 2 / 11 115× 1.29e-4 2.84e-3 ✓ sig.
LDL clearance
APOB, PCSK9
 Reactome 2 / 18 70.2× 3.57e-4 6.36e-3 ✓ sig.
Post-translational protein phosphorylation
APOA1, APOB, PCSK9
 Reactome 3 / 108 17.6× 6.17e-4 9.73e-3 ✓ 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
APOA1, APOB, CUBN, PCSK9, ANGPTL3, ABCA1
 GO:0008203 6 / 107 55.2× 7.81e-10 1.81e-7 ✓ sig.
lipoprotein metabolic process
APOA1, APOB, PCSK9, ABCA1
 GO:0042157 4 / 26 151× 1.12e-8 1.88e-6 ✓ sig.
lipoprotein biosynthetic process
APOA1, APOB, ABCA1
 GO:0042158 3 / 6 492× 1.78e-8 2.83e-6 ✓ sig.
cholesterol homeostasis
APOA1, APOB, PCSK9, ANGPTL3, ABCA1
 GO:0042632 5 / 112 43.9× 7.69e-8 9.82e-6 ✓ sig.
steroid metabolic process
APOA1, APOB, CUBN, PCSK9, ABCA1
 GO:0008202 5 / 135 36.4× 1.96e-7 2.19e-5 ✓ sig.
phospholipid homeostasis
APOA1, ANGPTL3, ABCA1
 GO:0055091 3 / 17 174× 6.01e-7 5.57e-5 ✓ sig.
lipid metabolic process
APOA1, APOB, TTPA, CUBN, PCSK9, ANGPTL3, ABCA1, BSCL2
 GO:0006629 8 / 840 9.4× 7.83e-7 6.94e-5 ✓ sig.
cholesterol transport
APOA1, APOB, ABCA1
 GO:0030301 3 / 28 105× 2.87e-6 1.98e-4 ✓ sig.
cholesterol efflux
APOA1, APOB, ABCA1
 GO:0033344 3 / 31 95.2× 3.93e-6 2.55e-4 ✓ sig.
lipid storage
APOA1, ANGPTL3, BSCL2
 GO:0019915 3 / 32 92.2× 4.34e-6 2.76e-4 ✓ sig.
cellular response to lipoprotein particle stimulus
APOA1, APOB
 GO:0071402 2 / 5 393× 9.78e-6 5.30e-4 ✓ sig.
acylglycerol homeostasis
APOA1, ANGPTL3
 GO:0055090 2 / 5 393× 9.78e-6 5.30e-4 ✓ sig.
negative regulation of very-low-density lipoprotein particle remodeling
APOA1, ANGPTL3
 GO:0010903 2 / 6 328× 1.47e-5 7.28e-4 ✓ sig.
phospholipid metabolic process
APOA1, PCSK9, ANGPTL3
 GO:0006644 3 / 66 44.7× 3.92e-5 1.55e-3 ✓ sig.
high-density lipoprotein particle assembly
APOA1, ABCA1
 GO:0034380 2 / 10 197× 4.39e-5 1.69e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Hypoalphalipoproteinemia Hypobetalipoproteinemia 0.375 3 5.75e-11 5.86e-10 ✓ sig.
Ataxia with vitamin e deficiency Hypoalphalipoproteinemia 0.222 2 5.31e-7 3.27e-6 ✓ sig.
hypercholesterolemia, autosomal dominant, type B Isolated systolic hypertension 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Ataxia with vitamin e deficiency Vitamin e deficiency 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Ataxia with vitamin e deficiency hypercholesterolemia, autosomal dominant, type B 0.250 1 1.95e-4 5.35e-4 ✓ sig.
hypercholesterolemia, autosomal dominant, type B Hypobetalipoproteinemia 0.250 1 1.95e-4 5.35e-4 ✓ sig.
hypercholesterolemia, autosomal dominant, 3 Hypobetalipoproteinemia 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Congenital stenosis of aortic valve hypercholesterolemia, autosomal dominant, type B 0.167 1 3.25e-4 7.71e-4 ✓ sig.
Ataxia with vitamin e deficiency Isolated systolic hypertension 0.200 1 3.90e-4 8.67e-4 ✓ sig.
Hypobetalipoproteinemia Isolated systolic hypertension 0.200 1 3.90e-4 8.67e-4 ✓ sig.
hypercholesterolemia, autosomal dominant, 3 Hypoalphalipoproteinemia 0.125 1 4.55e-4 9.73e-4 ✓ sig.
Binge eating disorder hypercholesterolemia, autosomal dominant, type B 0.125 1 4.55e-4 9.73e-4 ✓ sig.
Ataxia with vitamin e deficiency Hypobetalipoproteinemia 0.167 1 5.84e-4 1.16e-3 ✓ sig.
Congenital stenosis of aortic valve Isolated systolic hypertension 0.143 1 6.49e-4 1.24e-3 ✓ sig.
Binge eating disorder Isolated systolic hypertension 0.111 1 9.09e-4 1.58e-3 ✓ sig.
Binge eating disorder Hypobetalipoproteinemia 0.100 1 1.36e-3 2.15e-3 ✓ sig.
Ataxia with vitamin e deficiency Binge eating disorder 0.100 1 1.36e-3 2.15e-3 ✓ sig.