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 540
5
Diseases
7
Unique genes
0.264
Avg. similarity score
Familial hypobetalipoproteinemia 1
Most-connected disease (3 links)
Disease
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Familial hypobetalipoproteinemia 1
Hypercholesterolemia, autosomal dominant, type B
Hypobetalipoproteinemia
Congenital stenosis of aortic valve
Hypobetalipoproteinemia, familial, 2
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Familial hypobetalipoproteinemia 1 | 3 | 3 | 1 |
| Hypercholesterolemia, autosomal dominant, type B | 3 | 3 | 1 |
| Hypobetalipoproteinemia | 3 | 3 | 3 |
| Congenital stenosis of aortic valve | 2 | 2 | 5 |
| Hypobetalipoproteinemia, familial, 2 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| APOB | 4 / 5 | Congenital stenosis of aortic valve, Familial hypobetalipoproteinemia 1, Hypercholesterolemia, autosomal dominant, type B, Hypobetalipoproteinemia |
| ANGPTL3 | 2 / 5 | Hypobetalipoproteinemia, Hypobetalipoproteinemia, familial, 2 |
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 | KEGG | 3 / 51 | 101× | 2.49e-6 | 9.12e-5 ✓ sig. |
| Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) | Reactome | 3 / 125 | 41.2× | 3.74e-5 | 8.66e-4 ✓ sig. |
| LDL clearance | Reactome | 2 / 18 | 191× | 4.44e-5 | 9.94e-4 ✓ sig. |
| Lipid and atherosclerosis | KEGG | 3 / 216 | 23.8× | 1.90e-4 | 3.16e-3 ✓ sig. |
| Degradation of the extracellular matrix | Reactome | 2 / 70 | 49.0× | 6.90e-4 | 8.56e-3 ✓ sig. |
| Post-translational protein phosphorylation | Reactome | 2 / 108 | 31.8× | 1.63e-3 | 1.64e-2 ✓ sig. |
| LDL remodeling | Reactome | 1 / 3 | 572× | 1.75e-3 | 1.73e-2 ✓ sig. |
| Scavenging by Class H Receptors | Reactome | 1 / 4 | 429× | 2.33e-3 | 2.13e-2 ✓ sig. |
| Chylomicron clearance | Reactome | 1 / 5 | 343× | 2.91e-3 | 2.49e-2 ✓ sig. |
| Scavenging by Class B Receptors | Reactome | 1 / 5 | 343× | 2.91e-3 | 2.49e-2 ✓ sig. |
| VLDL assembly | Reactome | 1 / 5 | 343× | 2.91e-3 | 2.49e-2 ✓ sig. |
| VLDL clearance | Reactome | 1 / 5 | 343× | 2.91e-3 | 2.49e-2 ✓ sig. |
| Scavenging by Class F Receptors | Reactome | 1 / 6 | 286× | 3.49e-3 | 2.83e-2 ✓ sig. |
| Tuberculosis | KEGG | 2 / 181 | 19.0× | 4.51e-3 | 3.41e-2 ✓ sig. |
| NR1H2 & NR1H3 regulate gene expression linked to lipogenesis | Reactome | 1 / 9 | 191× | 5.24e-3 | 3.76e-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 | GO:0008203 | 3 / 107 | 74.8× | 6.28e-6 | 3.80e-4 ✓ sig. |
| cholesterol homeostasis | GO:0042632 | 3 / 112 | 71.5× | 7.21e-6 | 4.22e-4 ✓ sig. |
| lipoprotein metabolic process | GO:0042157 | 2 / 26 | 205× | 3.89e-5 | 1.53e-3 ✓ sig. |
| artery morphogenesis | GO:0048844 | 2 / 27 | 198× | 4.20e-5 | 1.62e-3 ✓ sig. |
| phospholipid metabolic process | GO:0006644 | 2 / 66 | 80.9× | 2.55e-4 | 6.04e-3 ✓ sig. |
| low-density lipoprotein receptor particle metabolic process | GO:0032799 | 1 / 1 | 2,670× | 3.75e-4 | 7.81e-3 ✓ sig. |
| low-density lipoprotein particle receptor catabolic process | GO:0032802 | 1 / 1 | 2,670× | 3.75e-4 | 7.81e-3 ✓ sig. |
| nuclear receptor-mediated bile acid signaling pathway | GO:0038185 | 1 / 2 | 1,335× | 7.49e-4 | 1.23e-2 ✓ sig. |
| negative regulation of phosphate transmembrane transport | GO:2000186 | 1 / 2 | 1,335× | 7.49e-4 | 1.23e-2 ✓ sig. |
| regulation of low-density lipoprotein particle receptor catabolic process | GO:0032803 | 1 / 2 | 1,335× | 7.49e-4 | 1.23e-2 ✓ sig. |
| regulation of chylomicron remodeling | GO:0090318 | 1 / 2 | 1,335× | 7.49e-4 | 1.23e-2 ✓ sig. |
| animal organ morphogenesis | GO:0009887 | 2 / 130 | 41.1× | 9.86e-4 | 1.45e-2 ✓ sig. |
| steroid metabolic process | GO:0008202 | 2 / 135 | 39.5× | 1.06e-3 | 1.51e-2 ✓ sig. |
| positive regulation of low-density lipoprotein particle receptor catabolic process | GO:0032805 | 1 / 3 | 890× | 1.12e-3 | 1.55e-2 ✓ sig. |
| negative regulation of signaling | GO:0023057 | 1 / 3 | 890× | 1.12e-3 | 1.55e-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 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Familial hypobetalipoproteinemia 1 | Hypobetalipoproteinemia | 0.250 | 1 | 1.94e-4 | 4.41e-4 ✓ sig. |
| Hypercholesterolemia, autosomal dominant, type B | Hypobetalipoproteinemia | 0.250 | 1 | 1.94e-4 | 4.41e-4 ✓ sig. |
| Hypobetalipoproteinemia | Hypobetalipoproteinemia, familial, 2 | 0.250 | 1 | 1.94e-4 | 4.41e-4 ✓ sig. |
| Congenital stenosis of aortic valve | Hypercholesterolemia, autosomal dominant, type B | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |
| Congenital stenosis of aortic valve | Familial hypobetalipoproteinemia 1 | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |