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.

← Back to all clusters

Cluster 293

6 diseases · 11 shared-gene connections
6 Diseases
8 Unique genes
0.258 Avg. similarity score
Ataxia with vitamin e deficiency Most-connected disease (5 links)
Log in to save this analysis

Save This Analysis

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 ⇵
Ataxia with vitamin e deficiency 5 5 3
Aapoai amyloidosis 4 4 1
Apolipoprotein a-i amyloidosis 4 4 1
Apolipoprotein a-i deficiency 4 4 2
Hypoalphalipoproteinemia 4 4 7
Vitamin e deficiency 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
APOA1 5 / 6 Aapoai amyloidosis, Apolipoprotein a-i amyloidosis, Apolipoprotein a-i deficiency, Ataxia with vitamin e deficiency and 1 more
ABCA1 2 / 6 Apolipoprotein a-i deficiency, Hypoalphalipoproteinemia
APOB 2 / 6 Ataxia with vitamin e deficiency, Hypoalphalipoproteinemia
TTPA 2 / 6 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, ABCA1, APOB, ANGPTL3, PCSK9
 KEGG 5 / 51 147× 6.26e-11 9.37e-9 ✓ sig.
Defective ABCA1 causes Tangier disease
APOA1, ABCA1
 Reactome 2 / 2 1,501× 3.88e-7 2.15e-5 ✓ sig.
Fat digestion and absorption
APOA1, ABCA1, APOB
 KEGG 3 / 43 105× 2.36e-6 1.02e-4 ✓ sig.
Scavenging by Class B Receptors
APOA1, APOB
 Reactome 2 / 5 601× 3.88e-6 1.55e-4 ✓ sig.
HDL assembly
APOA1, ABCA1
 Reactome 2 / 8 375× 1.08e-5 3.59e-4 ✓ sig.
Chylomicron remodeling
APOA1, APOB
 Reactome 2 / 9 334× 1.39e-5 4.42e-4 ✓ sig.
Chylomicron assembly
APOA1, APOB
 Reactome 2 / 9 334× 1.39e-5 4.42e-4 ✓ sig.
Scavenging by Class A Receptors
APOA1, APOB
 Reactome 2 / 11 273× 2.13e-5 6.29e-4 ✓ sig.
Post-translational protein phosphorylation
APOA1, APOB, PCSK9
 Reactome 3 / 108 41.7× 3.83e-5 1.03e-3 ✓ sig.
LDL clearance
APOB, PCSK9
 Reactome 2 / 18 167× 5.91e-5 1.46e-3 ✓ sig.
Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)
APOA1, APOB, PCSK9
 Reactome 3 / 125 36.0× 5.93e-5 1.47e-3 ✓ sig.
Vitamin digestion and absorption
APOA1, APOB
 KEGG 2 / 26 115× 1.25e-4 2.69e-3 ✓ sig.
Lipid and atherosclerosis
APOA1, ABCA1, APOB
 KEGG 3 / 216 20.9× 3.01e-4 5.37e-3 ✓ sig.
Retinoid metabolism and transport
APOA1, APOB
 Reactome 2 / 41 73.2× 3.14e-4 5.56e-3 ✓ sig.
Vitamin E
TTPA
 Reactome 1 / 1 1,501× 6.66e-4 9.96e-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 ⇵
lipoprotein metabolic process
APOA1, ABCA1, APOB, PCSK9
 GO:0042157 4 / 26 359× 2.05e-10 5.46e-8 ✓ sig.
cholesterol metabolic process
APOA1, ABCA1, APOB, ANGPTL3, PCSK9
 GO:0008203 5 / 107 109× 3.09e-10 7.87e-8 ✓ sig.
cholesterol homeostasis
APOA1, ABCA1, APOB, ANGPTL3, PCSK9
 GO:0042632 5 / 112 104× 3.90e-10 9.61e-8 ✓ sig.
lipoprotein biosynthetic process
APOA1, ABCA1, APOB
 GO:0042158 3 / 6 1,168× 1.03e-9 2.29e-7 ✓ sig.
phospholipid homeostasis
APOA1, ABCA1, ANGPTL3
 GO:0055091 3 / 17 412× 3.49e-8 5.00e-6 ✓ sig.
cholesterol transport
APOA1, ABCA1, APOB
 GO:0030301 3 / 28 250× 1.68e-7 1.87e-5 ✓ sig.
steroid metabolic process
APOA1, ABCA1, APOB, PCSK9
 GO:0008202 4 / 135 69.2× 1.78e-7 1.96e-5 ✓ sig.
lipid metabolic process
APOA1, ABCA1, APOB, TTPA, ANGPTL3, PCSK9
 GO:0006629 6 / 840 16.7× 2.10e-7 2.26e-5 ✓ sig.
cholesterol efflux
APOA1, ABCA1, APOB
 GO:0033344 3 / 31 226× 2.30e-7 2.44e-5 ✓ sig.
acylglycerol homeostasis
APOA1, ANGPTL3
 GO:0055090 2 / 5 934× 1.60e-6 1.21e-4 ✓ sig.
cellular response to lipoprotein particle stimulus
APOA1, APOB
 GO:0071402 2 / 5 934× 1.60e-6 1.21e-4 ✓ sig.
phospholipid metabolic process
APOA1, ANGPTL3, PCSK9
 GO:0006644 3 / 66 106× 2.33e-6 1.63e-4 ✓ sig.
negative regulation of very-low-density lipoprotein particle remodeling
APOA1, ANGPTL3
 GO:0010903 2 / 6 779× 2.40e-6 1.67e-4 ✓ sig.
high-density lipoprotein particle assembly
APOA1, ABCA1
 GO:0034380 2 / 10 467× 7.20e-6 4.02e-4 ✓ sig.
vitamin transport
APOA1, TTPA
 GO:0051180 2 / 10 467× 7.20e-6 4.02e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Apolipoprotein a-i deficiency Hypoalphalipoproteinemia 0.250 2 1.77e-7 1.25e-6 ✓ sig.
Ataxia with vitamin e deficiency Hypoalphalipoproteinemia 0.222 2 5.31e-7 3.46e-6 ✓ sig.
Aapoai amyloidosis Apolipoprotein a-i amyloidosis 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Aapoai amyloidosis Apolipoprotein a-i deficiency 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Apolipoprotein a-i amyloidosis Apolipoprotein a-i deficiency 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Aapoai amyloidosis Ataxia with vitamin e deficiency 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Apolipoprotein a-i amyloidosis Ataxia with vitamin e deficiency 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Ataxia with vitamin e deficiency Vitamin e deficiency 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Apolipoprotein a-i deficiency Ataxia with vitamin e deficiency 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Aapoai amyloidosis Hypoalphalipoproteinemia 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Apolipoprotein a-i amyloidosis Hypoalphalipoproteinemia 0.125 1 4.55e-4 9.55e-4 ✓ sig.