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 272
7
Diseases
30
Unique genes
0.212
Avg. similarity score
Congenital ocular coloboma
Most-connected disease (5 links)
Disease
Searched: microphthalmia, isolated, with coloboma 7
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microphthalmia, isolated, with coloboma 7
Congenital ocular coloboma
Cleft eyelid
Coloboma
Congenital iris coloboma
Cataract-microcornea-metabolic syndrome
Neurooculocardio-genitourinary syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Congenital ocular coloboma | 5 | 5 | 26 |
| Cleft eyelid | 4 | 4 | 4 |
| Coloboma | 4 | 4 | 15 |
| Congenital iris coloboma | 4 | 4 | 5 |
| microphthalmia, isolated, with coloboma 7 | 3 | 3 | 1 |
| Cataract-microcornea-metabolic syndrome | 1 | 1 | 1 |
| Neurooculocardio-genitourinary syndrome | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| ABCB6 | 4 / 7 | Cleft eyelid, Coloboma, Congenital iris coloboma, microphthalmia, isolated, with coloboma 7 |
| FZD5 | 4 / 7 | Cleft eyelid, Coloboma, Congenital iris coloboma, Congenital ocular coloboma |
| PAX6 | 4 / 7 | Cleft eyelid, Coloboma, Congenital iris coloboma, Congenital ocular coloboma |
| SALL2 | 4 / 7 | Cleft eyelid, Coloboma, Congenital iris coloboma, Congenital ocular coloboma |
| ACTG1 | 3 / 7 | Coloboma, Congenital iris coloboma, Congenital ocular coloboma |
| ACTB | 2 / 7 | Coloboma, Congenital ocular coloboma |
| ALDH7A1 | 2 / 7 | Coloboma, Congenital ocular coloboma |
| ELP4 | 2 / 7 | Coloboma, Congenital ocular coloboma |
| LAMB1 | 2 / 7 | Coloboma, Congenital ocular coloboma |
| MYH10 | 2 / 7 | Coloboma, Congenital ocular coloboma |
| RAX | 2 / 7 | Coloboma, Congenital ocular coloboma |
| SLBP | 2 / 7 | Coloboma, Congenital ocular coloboma |
| SLC16A12 | 2 / 7 | Cataract-microcornea-metabolic syndrome, Congenital ocular coloboma |
| WDR37 | 2 / 7 | Congenital ocular coloboma, Neurooculocardio-genitourinary syndrome |
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 ⇵ |
|---|---|---|---|---|---|
| Hippo signaling pathway | KEGG | 5 / 157 | 12.7× | 3.92e-5 | 1.10e-3 ✓ sig. |
| Formation of annular gap junctions | Reactome | 2 / 11 | 72.8× | 3.27e-4 | 5.93e-3 ✓ sig. |
| Cell-extracellular matrix interactions | Reactome | 2 / 12 | 66.7× | 3.92e-4 | 6.83e-3 ✓ sig. |
| Gap junction degradation | Reactome | 2 / 12 | 66.7× | 3.92e-4 | 6.83e-3 ✓ sig. |
| Interaction between L1 and Ankyrins | Reactome | 2 / 13 | 61.6× | 4.63e-4 | 7.80e-3 ✓ sig. |
| Defective ABCB6 causes isolated colobomatous microphthalmia 7 (MCOPCB7) | Reactome | 1 / 1 | 400× | 2.50e-3 | 2.77e-2 ✓ sig. |
| Defective CYP1B1 causes Glaucoma | Reactome | 1 / 1 | 400× | 2.50e-3 | 2.77e-2 ✓ sig. |
| Retinoid metabolism disease events | Reactome | 1 / 1 | 400× | 2.50e-3 | 2.77e-2 ✓ sig. |
| Adherens junctions interactions | Reactome | 2 / 32 | 25.0× | 2.86e-3 | 3.05e-2 ✓ sig. |
| RHO GTPases activate IQGAPs | Reactome | 2 / 32 | 25.0× | 2.86e-3 | 3.05e-2 ✓ sig. |
| RHO GTPases Activate WASPs and WAVEs | Reactome | 2 / 36 | 22.2× | 3.60e-3 | 3.60e-2 ✓ sig. |
| Signaling by high-kinase activity BRAF mutants | Reactome | 2 / 36 | 22.2× | 3.60e-3 | 3.60e-2 ✓ sig. |
| EPHB-mediated forward signaling | Reactome | 2 / 39 | 20.5× | 4.22e-3 | 4.03e-2 ✓ sig. |
| MAP2K and MAPK activation | Reactome | 2 / 40 | 20.0× | 4.44e-3 | 4.18e-2 ✓ sig. |
| Recycling pathway of L1 | Reactome | 2 / 40 | 20.0× | 4.44e-3 | 4.18e-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 ⇵ |
|---|---|---|---|---|---|
| eye development | GO:0001654 | 5 / 49 | 63.6× | 1.36e-8 | 2.23e-6 ✓ sig. |
| camera-type eye development | GO:0043010 | 5 / 74 | 42.1× | 1.12e-7 | 1.35e-5 ✓ sig. |
| axonogenesis | GO:0007409 | 5 / 125 | 24.9× | 1.54e-6 | 1.21e-4 ✓ sig. |
| brain development | GO:0007420 | 6 / 244 | 15.3× | 2.13e-6 | 1.56e-4 ✓ sig. |
| postsynaptic actin cytoskeleton organization | GO:0098974 | 3 / 20 | 93.4× | 4.18e-6 | 2.68e-4 ✓ sig. |
| retina development in camera-type eye | GO:0060041 | 4 / 85 | 29.3× | 9.98e-6 | 5.39e-4 ✓ sig. |
| positive regulation of transcription by RNA polymerase II | GO:0045944 | 10 / 1,208 | 5.2× | 1.12e-5 | 5.89e-4 ✓ sig. |
| regulation of transepithelial transport | GO:0150111 | 2 / 4 | 311× | 1.49e-5 | 7.38e-4 ✓ sig. |
| regulation of neuron differentiation | GO:0045664 | 3 / 32 | 58.4× | 1.79e-5 | 8.52e-4 ✓ sig. |
| neural precursor cell proliferation | GO:0061351 | 3 / 33 | 56.6× | 1.97e-5 | 9.18e-4 ✓ sig. |
| regulation of metanephric nephron tubule epithelial cell differentiation | GO:0072307 | 2 / 5 | 249× | 2.48e-5 | 1.09e-3 ✓ sig. |
| morphogenesis of a polarized epithelium | GO:0001738 | 2 / 6 | 208× | 3.72e-5 | 1.49e-3 ✓ sig. |
| embryonic retina morphogenesis in camera-type eye | GO:0060059 | 2 / 7 | 178× | 5.21e-5 | 1.92e-3 ✓ sig. |
| platelet aggregation | GO:0070527 | 3 / 49 | 38.1× | 6.54e-5 | 2.27e-3 ✓ sig. |
| regulation of neurogenesis | GO:0050767 | 3 / 49 | 38.1× | 6.54e-5 | 2.27e-3 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Coloboma | Congenital ocular coloboma | 0.355 | 11 | 3.65e-29 | 1.08e-27 ✓ sig. |
| Coloboma | Congenital iris coloboma | 0.313 | 5 | 4.17e-16 | 6.40e-15 ✓ sig. |
| Cleft eyelid | Congenital iris coloboma | 0.667 | 4 | 2.14e-15 | 3.12e-14 ✓ sig. |
| Cleft eyelid | Coloboma | 0.250 | 4 | 5.83e-13 | 7.18e-12 ✓ sig. |
| Congenital iris coloboma | Congenital ocular coloboma | 0.143 | 4 | 3.19e-11 | 3.33e-10 ✓ sig. |
| Cleft eyelid | Congenital ocular coloboma | 0.107 | 3 | 1.71e-8 | 1.34e-7 ✓ sig. |
| Cleft eyelid | microphthalmia, isolated, with coloboma 7 | 0.200 | 1 | 2.60e-4 | 6.51e-4 ✓ sig. |
| Congenital iris coloboma | microphthalmia, isolated, with coloboma 7 | 0.167 | 1 | 3.25e-4 | 7.71e-4 ✓ sig. |
| Coloboma | microphthalmia, isolated, with coloboma 7 | 0.063 | 1 | 9.74e-4 | 1.67e-3 ✓ sig. |
| Cataract-microcornea-metabolic syndrome | Congenital ocular coloboma | 0.037 | 1 | 1.69e-3 | 2.53e-3 ✓ sig. |
| Congenital ocular coloboma | Neurooculocardio-genitourinary syndrome | 0.037 | 1 | 1.69e-3 | 2.53e-3 ✓ sig. |