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 189
8
Diseases
47
Unique genes
0.102
Avg. similarity score
Retinopathy of prematurity
Most-connected disease (5 links)
Disease
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Retinopathy of prematurity
Exudative retinopathy
Exudative vitreoretinopathy
FZD4-related exudative vitreoretinopathy
Syndactyly
Acrocapitofemoral dysplasia
RCBTB1-related retinopathy
Cernunnos-XLF deficiency
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Retinopathy of prematurity | 5 | 5 | 20 |
| Exudative retinopathy | 4 | 4 | 7 |
| Exudative vitreoretinopathy | 4 | 4 | 9 |
| FZD4-related exudative vitreoretinopathy | 4 | 4 | 1 |
| Syndactyly | 4 | 4 | 22 |
| Acrocapitofemoral dysplasia | 2 | 2 | 1 |
| RCBTB1-related retinopathy | 2 | 2 | 1 |
| Cernunnos-XLF deficiency | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| FZD4 | 5 / 8 | Exudative retinopathy, Exudative vitreoretinopathy, FZD4-related exudative vitreoretinopathy, Retinopathy of prematurity and 1 more |
| IHH | 3 / 8 | Acrocapitofemoral dysplasia, Retinopathy of prematurity, Syndactyly |
| NDP | 3 / 8 | Exudative retinopathy, Exudative vitreoretinopathy, Retinopathy of prematurity |
| PRSS23 | 3 / 8 | Exudative retinopathy, Exudative vitreoretinopathy, Retinopathy of prematurity |
| RCBTB1 | 3 / 8 | Exudative retinopathy, Exudative vitreoretinopathy, RCBTB1-related retinopathy |
| GLI3 | 2 / 8 | Retinopathy of prematurity, Syndactyly |
| LRP5 | 2 / 8 | Exudative vitreoretinopathy, Retinopathy of prematurity |
| NHEJ1 | 2 / 8 | Cernunnos-XLF deficiency, Syndactyly |
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 ⇵ |
|---|---|---|---|---|---|
| Breast cancer | KEGG | 8 / 148 | 13.8× | 9.21e-8 | 6.11e-6 ✓ sig. |
| Gastric cancer | KEGG | 7 / 150 | 11.9× | 1.71e-6 | 7.70e-5 ✓ sig. |
| RNF mutants show enhanced WNT signaling and proliferation | Reactome | 3 / 8 | 95.8× | 3.10e-6 | 1.28e-4 ✓ sig. |
| Basal cell carcinoma | KEGG | 5 / 63 | 20.3× | 4.38e-6 | 1.70e-4 ✓ sig. |
| Pathways in cancer | KEGG | 11 / 533 | 5.3× | 4.82e-6 | 1.85e-4 ✓ sig. |
| Disassembly of the destruction complex and recruitment of AXIN to the membrane | Reactome | 4 / 30 | 34.1× | 5.24e-6 | 1.97e-4 ✓ sig. |
| Activation of SMO | Reactome | 3 / 18 | 42.6× | 4.40e-5 | 1.15e-3 ✓ sig. |
| Wnt signaling pathway | KEGG | 6 / 174 | 8.8× | 5.57e-5 | 1.40e-3 ✓ sig. |
| Hedgehog signaling pathway | KEGG | 4 / 56 | 18.3× | 6.51e-5 | 1.58e-3 ✓ sig. |
| Regulation of FZD by ubiquitination | Reactome | 3 / 21 | 36.5× | 7.11e-5 | 1.70e-3 ✓ sig. |
| HHAT G278V abrogates palmitoylation of Hh-Np | Reactome | 2 / 4 | 128× | 8.95e-5 | 2.05e-3 ✓ sig. |
| Release of Hh-Np from the secreting cell | Reactome | 2 / 7 | 73.0× | 3.11e-4 | 5.52e-3 ✓ sig. |
| Ligand-receptor interactions | Reactome | 2 / 7 | 73.0× | 3.11e-4 | 5.52e-3 ✓ sig. |
| Cell adhesion molecules | KEGG | 5 / 160 | 8.0× | 3.85e-4 | 6.52e-3 ✓ sig. |
| Negative regulation of TCF-dependent signaling by WNT ligand antagonists | Reactome | 2 / 8 | 63.9× | 4.13e-4 | 6.88e-3 ✓ 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 ⇵ |
|---|---|---|---|---|---|
| embryonic digit morphogenesis | GO:0042733 | 9 / 57 | 62.8× | 1.47e-14 | 9.29e-12 ✓ sig. |
| Norrin signaling pathway | GO:0110135 | 4 / 4 | 398× | 3.51e-11 | 1.12e-8 ✓ sig. |
| Wnt signaling pathway | GO:0016055 | 9 / 232 | 15.4× | 5.43e-9 | 1.00e-6 ✓ sig. |
| establishment of blood-brain barrier | GO:0060856 | 4 / 11 | 145× | 1.14e-8 | 1.92e-6 ✓ sig. |
| limb morphogenesis | GO:0035108 | 5 / 31 | 64.1× | 1.31e-8 | 2.16e-6 ✓ sig. |
| negative regulation of alpha-beta T cell differentiation | GO:0046639 | 3 / 3 | 398× | 1.49e-8 | 2.42e-6 ✓ sig. |
| extracellular matrix-cell signaling | GO:0035426 | 3 / 4 | 298× | 5.95e-8 | 7.85e-6 ✓ sig. |
| canonical Wnt signaling pathway | GO:0060070 | 6 / 105 | 22.7× | 2.43e-7 | 2.55e-5 ✓ sig. |
| odontogenesis of dentin-containing tooth | GO:0042475 | 5 / 56 | 35.5× | 2.81e-7 | 2.88e-5 ✓ sig. |
| limb development | GO:0060173 | 5 / 56 | 35.5× | 2.81e-7 | 2.88e-5 ✓ sig. |
| retinal blood vessel morphogenesis | GO:0061304 | 3 / 6 | 199× | 2.97e-7 | 3.02e-5 ✓ sig. |
| establishment of blood-retinal barrier | GO:1990963 | 3 / 6 | 199× | 2.97e-7 | 3.02e-5 ✓ sig. |
| pattern specification process | GO:0007389 | 5 / 60 | 33.1× | 3.98e-7 | 3.86e-5 ✓ sig. |
| positive regulation of mesenchymal cell proliferation | GO:0002053 | 4 / 26 | 61.2× | 5.04e-7 | 4.71e-5 ✓ sig. |
| retina vasculature morphogenesis in camera-type eye | GO:0061299 | 3 / 7 | 170× | 5.18e-7 | 4.81e-5 ✓ sig. |