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 415
6
Diseases
5
Unique genes
0.342
Avg. similarity score
Agnathia-holoprosencephaly-situs inversus syndrome
Most-connected disease (5 links)
Disease
Searched: Agnathia-holoprosencephaly-situs inversus syndrome
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Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Agnathia-holoprosencephaly-situs inversus syndrome
Butterfly-shaped pigmentary macular dystrophy
Ectopic posterior pituitary
Microphthalmia, syndromic 5
Patterned macular dystrophy
Retinal dystrophy, early-onset, with or without pituitary dysfunction
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Agnathia-holoprosencephaly-situs inversus syndrome | 5 | 5 | 1 |
| Butterfly-shaped pigmentary macular dystrophy | 5 | 5 | 5 |
| Ectopic posterior pituitary | 5 | 5 | 1 |
| Microphthalmia, syndromic 5 | 5 | 5 | 1 |
| Patterned macular dystrophy | 5 | 5 | 4 |
| Retinal dystrophy, early-onset, with or without pituitary dysfunction | 5 | 5 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| OTX2 | 6 / 6 | Agnathia-holoprosencephaly-situs inversus syndrome, Butterfly-shaped pigmentary macular dystrophy, Ectopic posterior pituitary, Microphthalmia, syndromic 5 and 2 more |
| CTNNA1 | 2 / 6 | Butterfly-shaped pigmentary macular dystrophy, Patterned macular dystrophy |
| MAPKAPK3 | 2 / 6 | Butterfly-shaped pigmentary macular dystrophy, Patterned macular dystrophy |
| PRPH2 | 2 / 6 | Butterfly-shaped pigmentary macular dystrophy, Patterned macular dystrophy |
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 ⇵ |
|---|---|---|---|---|---|
| p38MAPK events | Reactome | 1 / 8 | 300× | 3.33e-3 | 2.74e-2 ✓ sig. |
| activated TAK1 mediates p38 MAPK activation | Reactome | 1 / 24 | 100× | 9.95e-3 | 5.67e-2 |
| Myogenesis | Reactome | 1 / 27 | 89.0× | 1.12e-2 | 6.09e-2 |
| VEGFR2 mediated vascular permeability | Reactome | 1 / 29 | 82.8× | 1.20e-2 | 6.35e-2 |
| Adherens junctions interactions | Reactome | 1 / 32 | 75.1× | 1.33e-2 | 6.74e-2 |
| RHO GTPases activate IQGAPs | Reactome | 1 / 32 | 75.1× | 1.33e-2 | 6.74e-2 |
| Endometrial cancer | KEGG | 1 / 59 | 40.7× | 2.43e-2 | 9.60e-2 |
| VEGF signaling pathway | KEGG | 1 / 60 | 40.0× | 2.47e-2 | 9.68e-2 |
| VEGFA-VEGFR2 Pathway | Reactome | 1 / 62 | 38.7× | 2.56e-2 | 9.87e-2 |
| Degradation of the extracellular matrix | Reactome | 1 / 70 | 34.3× | 2.88e-2 | 1.06e-1 |
| Bacterial invasion of epithelial cells | KEGG | 1 / 78 | 30.8× | 3.21e-2 | 1.12e-1 |
| Arrhythmogenic right ventricular cardiomyopathy | KEGG | 1 / 86 | 27.9× | 3.53e-2 | 1.19e-1 |
| Adherens junction | KEGG | 1 / 93 | 25.8× | 3.81e-2 | 1.24e-1 |
| Leukocyte transendothelial migration | KEGG | 1 / 116 | 20.7× | 4.74e-2 | 1.40e-1 |
| Oxidative Stress Induced Senescence | Reactome | 1 / 125 | 19.2× | 5.10e-2 | 1.46e-1 |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| response to low light intensity stimulus | GO:0009645 | 1 / 1 | 3,737× | 2.68e-4 | 6.25e-3 ✓ sig. |
| cellular response to indole-3-methanol | GO:0071681 | 1 / 5 | 747× | 1.34e-3 | 1.71e-2 ✓ sig. |
| negative regulation of integrin-mediated signaling pathway | GO:2001045 | 1 / 5 | 747× | 1.34e-3 | 1.71e-2 ✓ sig. |
| chorionic trophoblast cell differentiation | GO:0060718 | 1 / 6 | 623× | 1.60e-3 | 1.88e-2 ✓ sig. |
| regulation of fibroblast growth factor receptor signaling pathway | GO:0040036 | 1 / 7 | 534× | 1.87e-3 | 2.05e-2 ✓ sig. |
| positive regulation of gastrulation | GO:2000543 | 1 / 7 | 534× | 1.87e-3 | 2.05e-2 ✓ sig. |
| gap junction assembly | GO:0016264 | 1 / 8 | 467× | 2.14e-3 | 2.19e-2 ✓ sig. |
| apical junction assembly | GO:0043297 | 1 / 8 | 467× | 2.14e-3 | 2.19e-2 ✓ sig. |
| macropinocytosis | GO:0044351 | 1 / 8 | 467× | 2.14e-3 | 2.19e-2 ✓ sig. |
| positive regulation of extrinsic apoptotic signaling pathway in absence of ligand | GO:2001241 | 1 / 11 | 340× | 2.94e-3 | 2.58e-2 ✓ sig. |
| primitive streak formation | GO:0090009 | 1 / 11 | 340× | 2.94e-3 | 2.58e-2 ✓ sig. |
| epithelial cell-cell adhesion | GO:0090136 | 1 / 12 | 311× | 3.21e-3 | 2.69e-2 ✓ sig. |
| negative regulation of cell motility | GO:2000146 | 1 / 14 | 267× | 3.74e-3 | 2.90e-2 ✓ sig. |
| negative regulation of neuroblast proliferation | GO:0007406 | 1 / 14 | 267× | 3.74e-3 | 2.90e-2 ✓ sig. |
| protein heterooligomerization | GO:0051291 | 1 / 15 | 249× | 4.01e-3 | 3.01e-2 ✓ sig. |