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 223
7
Diseases
20
Unique genes
0.228
Avg. similarity score
Corneal opacity
Most-connected disease (4 links)
Disease
Searched: Hepatic ductular hypoplasia
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Hepatic ductular hypoplasia
Corneal opacity
Deafness with congenital heart defects and posterior embryotoxon
Alagille syndrome
Eye abnormalities
Proximal renal tubular acidosis
frank-ter haar syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Corneal opacity | 4 | 4 | 3 |
| Deafness with congenital heart defects and posterior embryotoxon | 4 | 4 | 1 |
| Hepatic ductular hypoplasia | 4 | 4 | 1 |
| Alagille syndrome | 3 | 3 | 2 |
| Eye abnormalities | 3 | 3 | 17 |
| Proximal renal tubular acidosis | 1 | 1 | 1 |
| frank-ter haar syndrome | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| JAG1 | 5 / 7 | Alagille syndrome, Corneal opacity, Deafness with congenital heart defects and posterior embryotoxon, Eye abnormalities and 1 more |
| SH3PXD2B | 2 / 7 | Eye abnormalities, frank-ter haar syndrome |
| SLC4A4 | 2 / 7 | Corneal opacity, Proximal renal tubular acidosis |
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 ⇵ |
|---|---|---|---|---|---|
| Pathways in cancer | KEGG | 9 / 533 | 10.1× | 6.77e-8 | 4.51e-6 ✓ sig. |
| Hippo signaling pathway | KEGG | 5 / 157 | 19.1× | 4.74e-6 | 1.76e-4 ✓ sig. |
| TGF-beta signaling pathway | KEGG | 4 / 108 | 22.2× | 2.68e-5 | 7.44e-4 ✓ sig. |
| Gastric cancer | KEGG | 4 / 150 | 16.0× | 9.69e-5 | 2.13e-3 ✓ sig. |
| Colorectal cancer | KEGG | 3 / 87 | 20.7× | 3.83e-4 | 6.40e-3 ✓ sig. |
| AGE-RAGE signaling pathway in diabetic complications | KEGG | 3 / 101 | 17.8× | 5.93e-4 | 8.99e-3 ✓ sig. |
| Signaling by BMP | Reactome | 2 / 28 | 42.9× | 9.70e-4 | 1.31e-2 ✓ sig. |
| Cytokine-cytokine receptor interaction | KEGG | 4 / 298 | 8.1× | 1.31e-3 | 1.66e-2 ✓ sig. |
| Signaling pathways regulating pluripotency of stem cells | KEGG | 3 / 144 | 12.5× | 1.66e-3 | 1.99e-2 ✓ sig. |
| MPS IV - Morquio syndrome B | Reactome | 1 / 1 | 601× | 1.67e-3 | 1.99e-2 ✓ sig. |
| APC truncation mutants are not K63 polyubiquitinated | Reactome | 1 / 1 | 601× | 1.67e-3 | 1.99e-2 ✓ sig. |
| Defective SLC4A4 causes renal tubular acidosis, proximal, with ocular abnormalities and mental retardation (pRTA-OA) | Reactome | 1 / 1 | 601× | 1.67e-3 | 1.99e-2 ✓ sig. |
| Breast cancer | KEGG | 3 / 148 | 12.2× | 1.79e-3 | 2.11e-2 ✓ sig. |
| Human papillomavirus infection | KEGG | 4 / 333 | 7.2× | 1.98e-3 | 2.26e-2 ✓ sig. |
| Hepatitis B | KEGG | 3 / 163 | 11.1× | 2.36e-3 | 2.57e-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 ⇵ |
|---|---|---|---|---|---|
| cardiac right ventricle morphogenesis | GO:0003215 | 3 / 13 | 216× | 2.98e-7 | 3.02e-5 ✓ sig. |
| heart development | GO:0007507 | 6 / 273 | 20.5× | 3.00e-7 | 3.05e-5 ✓ sig. |
| roof of mouth development | GO:0060021 | 4 / 70 | 53.4× | 8.36e-7 | 7.15e-5 ✓ sig. |
| pulmonary valve morphogenesis | GO:0003184 | 3 / 18 | 156× | 8.47e-7 | 7.23e-5 ✓ sig. |
| endocardial cushion morphogenesis | GO:0003203 | 3 / 19 | 148× | 1.00e-6 | 8.30e-5 ✓ sig. |
| cellular response to growth factor stimulus | GO:0071363 | 4 / 76 | 49.2× | 1.16e-6 | 9.42e-5 ✓ sig. |
| regulation of cell population proliferation | GO:0042127 | 5 / 201 | 23.2× | 1.86e-6 | 1.38e-4 ✓ sig. |
| nervous system development | GO:0007399 | 7 / 631 | 10.4× | 2.56e-6 | 1.76e-4 ✓ sig. |
| positive regulation of mesenchymal cell proliferation | GO:0002053 | 3 / 26 | 108× | 2.68e-6 | 1.83e-4 ✓ sig. |
| outflow tract septum morphogenesis | GO:0003148 | 3 / 28 | 100× | 3.38e-6 | 2.21e-4 ✓ sig. |
| embryonic forelimb morphogenesis | GO:0035115 | 3 / 33 | 84.9× | 5.60e-6 | 3.31e-4 ✓ sig. |
| cell surface receptor protein serine/threonine kinase signaling pathway | GO:0007178 | 3 / 33 | 84.9× | 5.60e-6 | 3.31e-4 ✓ sig. |
| branching involved in blood vessel morphogenesis | GO:0001569 | 3 / 33 | 84.9× | 5.60e-6 | 3.31e-4 ✓ sig. |
| ciliary body morphogenesis | GO:0061073 | 2 / 4 | 467× | 6.52e-6 | 3.74e-4 ✓ sig. |
| positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation | GO:1905007 | 2 / 4 | 467× | 6.52e-6 | 3.74e-4 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Deafness with congenital heart defects and posterior embryotoxon | Hepatic ductular hypoplasia | 0.500 | 1 | 6.49e-5 | 2.33e-4 ✓ sig. |
| Alagille syndrome | Deafness with congenital heart defects and posterior embryotoxon | 0.333 | 1 | 1.30e-4 | 3.93e-4 ✓ sig. |
| Alagille syndrome | Hepatic ductular hypoplasia | 0.333 | 1 | 1.30e-4 | 3.93e-4 ✓ sig. |
| Corneal opacity | Deafness with congenital heart defects and posterior embryotoxon | 0.250 | 1 | 1.95e-4 | 5.35e-4 ✓ sig. |
| Corneal opacity | Hepatic ductular hypoplasia | 0.250 | 1 | 1.95e-4 | 5.35e-4 ✓ sig. |
| Corneal opacity | Proximal renal tubular acidosis | 0.250 | 1 | 1.95e-4 | 5.35e-4 ✓ sig. |
| Alagille syndrome | Corneal opacity | 0.200 | 1 | 3.90e-4 | 8.66e-4 ✓ sig. |
| Deafness with congenital heart defects and posterior embryotoxon | Eye abnormalities | 0.056 | 1 | 1.10e-3 | 1.83e-3 ✓ sig. |
| Eye abnormalities | frank-ter haar syndrome | 0.056 | 1 | 1.10e-3 | 1.83e-3 ✓ sig. |
| Eye abnormalities | Hepatic ductular hypoplasia | 0.056 | 1 | 1.10e-3 | 1.83e-3 ✓ sig. |