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 297
6
Diseases
16
Unique genes
0.213
Avg. similarity score
Cholesterol ester transfer protein deficiency
Most-connected disease (4 links)
Disease
Searched: Hyperalphalipoproteinemia
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.
Hyperalphalipoproteinemia
Cholesterol ester transfer protein deficiency
Malunion fracture
Follicular cyst
Apolipoprotein c-iii deficiency
Antecubital pterygium syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Cholesterol ester transfer protein deficiency | 4 | 4 | 3 |
| Hyperalphalipoproteinemia | 4 | 4 | 3 |
| Malunion fracture | 4 | 4 | 13 |
| Follicular cyst | 3 | 3 | 2 |
| Apolipoprotein c-iii deficiency | 2 | 2 | 1 |
| Antecubital pterygium syndrome | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| SCARB1 | 4 / 6 | Cholesterol ester transfer protein deficiency, Follicular cyst, Hyperalphalipoproteinemia, Malunion fracture |
| APOC3 | 3 / 6 | Apolipoprotein c-iii deficiency, Cholesterol ester transfer protein deficiency, Hyperalphalipoproteinemia |
| CETP | 2 / 6 | Cholesterol ester transfer protein deficiency, Hyperalphalipoproteinemia |
| PSD3 | 2 / 6 | Antecubital pterygium syndrome, Malunion fracture |
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 | 44.2× | 3.89e-5 | 1.05e-3 ✓ sig. |
| HDL remodeling | Reactome | 2 / 10 | 150× | 7.44e-5 | 1.78e-3 ✓ sig. |
| Notch-HLH transcription pathway | Reactome | 2 / 28 | 53.6× | 6.16e-4 | 9.58e-3 ✓ sig. |
| NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux | Reactome | 2 / 37 | 40.6× | 1.08e-3 | 1.47e-2 ✓ sig. |
| Notch signaling pathway | KEGG | 2 / 62 | 24.2× | 3.00e-3 | 3.12e-2 ✓ sig. |
| LDL remodeling | Reactome | 1 / 3 | 250× | 3.99e-3 | 3.82e-2 ✓ sig. |
| NOTCH2 Activation and Transmission of Signal to the Nucleus | Reactome | 1 / 3 | 250× | 3.99e-3 | 3.82e-2 ✓ sig. |
| HDL clearance | Reactome | 1 / 5 | 150× | 6.64e-3 | 5.40e-2 |
| Scavenging by Class B Receptors | Reactome | 1 / 5 | 150× | 6.64e-3 | 5.40e-2 |
| Defective LFNG causes SCDO3 | Reactome | 1 / 5 | 150× | 6.64e-3 | 5.40e-2 |
| Pre-NOTCH Processing in Golgi | Reactome | 1 / 6 | 125× | 7.97e-3 | 6.07e-2 |
| NOTCH2 intracellular domain regulates transcription | Reactome | 1 / 7 | 107× | 9.29e-3 | 6.69e-2 |
| NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis | Reactome | 1 / 9 | 83.4× | 1.19e-2 | 7.79e-2 |
| Chylomicron remodeling | Reactome | 1 / 9 | 83.4× | 1.19e-2 | 7.79e-2 |
| Chylomicron assembly | Reactome | 1 / 9 | 83.4× | 1.19e-2 | 7.79e-2 |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| reverse cholesterol transport | GO:0043691 | 3 / 17 | 206× | 3.48e-7 | 3.49e-5 ✓ sig. |
| high-density lipoprotein particle remodeling | GO:0034375 | 3 / 21 | 167× | 6.79e-7 | 6.08e-5 ✓ sig. |
| triglyceride homeostasis | GO:0070328 | 3 / 38 | 92.2× | 4.27e-6 | 2.69e-4 ✓ sig. |
| phospholipid homeostasis | GO:0055091 | 2 / 17 | 137× | 9.28e-5 | 2.93e-3 ✓ sig. |
| cholesterol homeostasis | GO:0042632 | 3 / 112 | 31.3× | 1.11e-4 | 3.33e-3 ✓ sig. |
| cholesterol transport | GO:0030301 | 2 / 28 | 83.4× | 2.56e-4 | 6.13e-3 ✓ sig. |
| cholesterol efflux | GO:0033344 | 2 / 31 | 75.4× | 3.15e-4 | 7.10e-3 ✓ sig. |
| triglyceride metabolic process | GO:0006641 | 2 / 39 | 59.9× | 5.00e-4 | 9.75e-3 ✓ sig. |
| lipid transport | GO:0006869 | 3 / 189 | 18.5× | 5.17e-4 | 9.98e-3 ✓ sig. |
| phospholipid transport | GO:0015914 | 2 / 47 | 49.7× | 7.26e-4 | 1.26e-2 ✓ sig. |
| high density lipoprotein particle mediated signaling | GO:0055097 | 1 / 1 | 1,168× | 8.56e-4 | 1.39e-2 ✓ sig. |
| positive regulation of endothelial cell migration | GO:0010595 | 2 / 66 | 35.4× | 1.43e-3 | 1.90e-2 ✓ sig. |
| regulation of phosphatidylcholine catabolic process | GO:0010899 | 1 / 2 | 584× | 1.71e-3 | 2.13e-2 ✓ sig. |
| cholangiocyte proliferation | GO:1990705 | 1 / 2 | 584× | 1.71e-3 | 2.13e-2 ✓ sig. |
| intrahepatic bile duct development | GO:0035622 | 1 / 2 | 584× | 1.71e-3 | 2.13e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Cholesterol ester transfer protein deficiency | Hyperalphalipoproteinemia | 0.750 | 3 | 1.64e-12 | 1.93e-11 ✓ sig. |
| Apolipoprotein c-iii deficiency | Cholesterol ester transfer protein deficiency | 0.250 | 1 | 1.95e-4 | 5.32e-4 ✓ sig. |
| Apolipoprotein c-iii deficiency | Hyperalphalipoproteinemia | 0.250 | 1 | 1.95e-4 | 5.32e-4 ✓ sig. |
| Cholesterol ester transfer protein deficiency | Follicular cyst | 0.200 | 1 | 3.90e-4 | 8.64e-4 ✓ sig. |
| Follicular cyst | Hyperalphalipoproteinemia | 0.200 | 1 | 3.90e-4 | 8.64e-4 ✓ sig. |
| Antecubital pterygium syndrome | Malunion fracture | 0.071 | 1 | 8.44e-4 | 1.50e-3 ✓ sig. |
| Follicular cyst | Malunion fracture | 0.067 | 1 | 1.69e-3 | 2.53e-3 ✓ sig. |
| Cholesterol ester transfer protein deficiency | Malunion fracture | 0.063 | 1 | 2.53e-3 | 3.45e-3 ✓ sig. |
| Hyperalphalipoproteinemia | Malunion fracture | 0.063 | 1 | 2.53e-3 | 3.45e-3 ✓ sig. |