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 319
6
Diseases
34
Unique genes
0.121
Avg. similarity score
Intrahepatic cholestasis
Most-connected disease (5 links)
Disease
Searched: Intrahepatic cholestasis
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Intrahepatic cholestasis
Intrahepatic cholestasis of pregnancy
Progressive intrahepatic cholestasis
Benign recurrent intrahepatic cholestasis
progressive familial intrahepatic cholestasis type 3
mednik syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Intrahepatic cholestasis | 5 | 5 | 9 |
| Intrahepatic cholestasis of pregnancy | 4 | 4 | 20 |
| Progressive intrahepatic cholestasis | 4 | 4 | 13 |
| Benign recurrent intrahepatic cholestasis | 3 | 3 | 2 |
| progressive familial intrahepatic cholestasis type 3 | 3 | 3 | 1 |
| mednik syndrome | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| ABCB11 | 4 / 6 | Benign recurrent intrahepatic cholestasis, Intrahepatic cholestasis, Intrahepatic cholestasis of pregnancy, Progressive intrahepatic cholestasis |
| ABCB4 | 4 / 6 | Intrahepatic cholestasis, Intrahepatic cholestasis of pregnancy, progressive familial intrahepatic cholestasis type 3, Progressive intrahepatic cholestasis |
| ATP8B1 | 4 / 6 | Benign recurrent intrahepatic cholestasis, Intrahepatic cholestasis, Intrahepatic cholestasis of pregnancy, Progressive intrahepatic cholestasis |
| AP1S1 | 2 / 6 | Intrahepatic cholestasis, mednik syndrome |
| NR1H4 | 2 / 6 | Intrahepatic cholestasis of pregnancy, Progressive intrahepatic cholestasis |
| TJP2 | 2 / 6 | Intrahepatic cholestasis, Progressive intrahepatic cholestasis |
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 ⇵ |
|---|---|---|---|---|---|
| Bile secretion | KEGG | 9 / 90 | 35.3× | 2.23e-12 | 4.54e-10 ✓ sig. |
| Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol | Reactome | 4 / 24 | 58.9× | 5.46e-7 | 3.07e-5 ✓ sig. |
| ABC transporters | KEGG | 4 / 45 | 31.4× | 7.35e-6 | 2.77e-4 ✓ sig. |
| Synthesis of bile acids and bile salts via 27-hydroxycholesterol | Reactome | 3 / 15 | 70.6× | 9.22e-6 | 3.33e-4 ✓ sig. |
| Recycling of bile acids and salts | Reactome | 3 / 16 | 66.2× | 1.13e-5 | 3.93e-4 ✓ sig. |
| PPARA activates gene expression | Reactome | 4 / 115 | 12.3× | 2.96e-4 | 5.47e-3 ✓ sig. |
| Cholesterol metabolism | KEGG | 3 / 51 | 20.8× | 3.93e-4 | 6.86e-3 ✓ sig. |
| Synthesis of bile acids and bile salts | Reactome | 2 / 14 | 50.5× | 6.93e-4 | 1.06e-2 ✓ sig. |
| Primary bile acid biosynthesis | KEGG | 2 / 17 | 41.6× | 1.03e-3 | 1.44e-2 ✓ sig. |
| Endogenous sterols | Reactome | 2 / 25 | 28.3× | 2.24e-3 | 2.58e-2 ✓ sig. |
| MPS IV - Morquio syndrome B | Reactome | 1 / 1 | 353× | 2.83e-3 | 3.03e-2 ✓ sig. |
| Defective ABCB4 causes progressive familial intrahepatic cholestasis 3, intrahepatic cholestasis of pregnancy 3 and gallbladder disease 1 | Reactome | 1 / 1 | 353× | 2.83e-3 | 3.03e-2 ✓ sig. |
| Defective ABCB11 causes progressive familial intrahepatic cholestasis 2 and benign recurrent intrahepatic cholestasis 2 | Reactome | 1 / 1 | 353× | 2.83e-3 | 3.03e-2 ✓ sig. |
| AGE-RAGE signaling pathway in diabetic complications | KEGG | 3 / 101 | 10.5× | 2.86e-3 | 3.05e-2 ✓ sig. |
| African trypanosomiasis | KEGG | 2 / 37 | 19.1× | 4.87e-3 | 4.45e-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 ⇵ |
|---|---|---|---|---|---|
| bile acid and bile salt transport | GO:0015721 | 5 / 26 | 106× | 9.39e-10 | 2.13e-7 ✓ sig. |
| lipid transport | GO:0006869 | 7 / 189 | 20.4× | 4.14e-8 | 5.80e-6 ✓ sig. |
| triglyceride homeostasis | GO:0070328 | 4 / 38 | 57.9× | 6.45e-7 | 5.91e-5 ✓ sig. |
| cholesterol homeostasis | GO:0042632 | 5 / 112 | 24.5× | 1.71e-6 | 1.32e-4 ✓ sig. |
| bile acid metabolic process | GO:0008206 | 3 / 17 | 97.0× | 3.68e-6 | 2.42e-4 ✓ sig. |
| ceramide translocation | GO:0099040 | 2 / 3 | 366× | 9.63e-6 | 5.25e-4 ✓ sig. |
| response to nutrient levels | GO:0031667 | 4 / 79 | 27.8× | 1.25e-5 | 6.40e-4 ✓ sig. |
| phospholipid translocation | GO:0045332 | 3 / 27 | 61.1× | 1.56e-5 | 7.65e-4 ✓ sig. |
| bile acid biosynthetic process | GO:0006699 | 3 / 27 | 61.1× | 1.56e-5 | 7.65e-4 ✓ sig. |
| cellular response to bile acid | GO:1903413 | 2 / 4 | 275× | 1.92e-5 | 9.02e-4 ✓ sig. |
| regulation of chloride transport | GO:2001225 | 2 / 4 | 275× | 1.92e-5 | 9.02e-4 ✓ sig. |
| regulation of bile acid biosynthetic process | GO:0070857 | 2 / 5 | 220× | 3.20e-5 | 1.33e-3 ✓ sig. |
| response to ethanol | GO:0045471 | 4 / 110 | 20.0× | 4.60e-5 | 1.75e-3 ✓ sig. |
| bile acid secretion | GO:0032782 | 2 / 6 | 183× | 4.80e-5 | 1.80e-3 ✓ sig. |
| xenobiotic metabolic process | GO:0006805 | 4 / 120 | 18.3× | 6.46e-5 | 2.25e-3 ✓ sig. |