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 200
8
Diseases
8
Unique genes
0.279
Avg. similarity score
Blepharophimosis syndrome
Most-connected disease (5 links)
Disease
Searched: KAT6B-related multiple congenital anomalies syndrome
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KAT6B-related multiple congenital anomalies syndrome
Blepharophimosis syndrome
Blepharophimosis-intellectual disability syndrome
Cholestasis-pigmentary retinopathy-cleft palate syndrome
MED12-related intellectual disability syndrome
Simpson syndrome
Simpson-golabi-behmel syndrome
Nasodigitoacoustic syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Blepharophimosis syndrome | 5 | 5 | 3 |
| Blepharophimosis-intellectual disability syndrome | 5 | 5 | 3 |
| Cholestasis-pigmentary retinopathy-cleft palate syndrome | 4 | 4 | 1 |
| MED12-related intellectual disability syndrome | 4 | 4 | 1 |
| KAT6B-related multiple congenital anomalies syndrome | 3 | 3 | 1 |
| Simpson syndrome | 3 | 3 | 1 |
| Simpson-golabi-behmel syndrome | 3 | 3 | 5 |
| Nasodigitoacoustic syndrome | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| MED12 | 5 / 8 | Blepharophimosis syndrome, Blepharophimosis-intellectual disability syndrome, Cholestasis-pigmentary retinopathy-cleft palate syndrome, MED12-related intellectual disability syndrome and 1 more |
| KAT6B | 4 / 8 | Blepharophimosis syndrome, Blepharophimosis-intellectual disability syndrome, KAT6B-related multiple congenital anomalies syndrome, Simpson syndrome |
| GPC4 | 2 / 8 | Nasodigitoacoustic syndrome, Simpson-golabi-behmel 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 ⇵ |
|---|---|---|---|---|---|
| Defective EXT2 causes exostoses 2 | Reactome | 2 / 14 | 214× | 3.52e-5 | 1.00e-3 ✓ sig. |
| Defective EXT1 causes exostoses 1, TRPS2 and CHDS | Reactome | 2 / 14 | 214× | 3.52e-5 | 1.00e-3 ✓ sig. |
| Defective B4GALT7 causes EDS, progeroid type | Reactome | 2 / 20 | 150× | 7.33e-5 | 1.81e-3 ✓ sig. |
| Defective B3GAT3 causes JDSSDHD | Reactome | 2 / 20 | 150× | 7.33e-5 | 1.81e-3 ✓ sig. |
| Defective B3GALT6 causes EDSP2 and SEMDJL1 | Reactome | 2 / 20 | 150× | 7.33e-5 | 1.81e-3 ✓ sig. |
| HS-GAG degradation | Reactome | 2 / 22 | 136× | 8.91e-5 | 2.12e-3 ✓ sig. |
| A tetrasaccharide linker sequence is required for GAG synthesis | Reactome | 2 / 26 | 115× | 1.25e-4 | 2.77e-3 ✓ sig. |
| HS-GAG biosynthesis | Reactome | 2 / 30 | 100× | 1.67e-4 | 3.49e-3 ✓ sig. |
| Retinoid metabolism and transport | Reactome | 2 / 41 | 73.2× | 3.14e-4 | 5.72e-3 ✓ sig. |
| SUMOylation of transcription factors | Reactome | 1 / 18 | 83.4× | 1.19e-2 | 7.90e-2 |
| RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known | Reactome | 1 / 38 | 39.5× | 2.50e-2 | 1.22e-1 |
| Hedgehog 'off' state | Reactome | 1 / 56 | 26.8× | 3.67e-2 | 1.49e-1 |
| Transcriptional regulation of white adipocyte differentiation | Reactome | 1 / 67 | 22.4× | 4.38e-2 | 1.64e-1 |
| Retinol metabolism | KEGG | 1 / 68 | 22.1× | 4.44e-2 | 1.65e-1 |
| Loss of Nlp from mitotic centrosomes | Reactome | 1 / 70 | 21.4× | 4.57e-2 | 1.68e-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 ⇵ |
|---|---|---|---|---|---|
| Wnt signaling pathway, planar cell polarity pathway | GO:0060071 | 2 / 34 | 137× | 8.94e-5 | 2.89e-3 ✓ sig. |
| positive regulation of DNA-templated transcription | GO:0045893 | 4 / 778 | 12.0× | 1.82e-4 | 4.90e-3 ✓ sig. |
| female somatic sex determination | GO:0019101 | 1 / 1 | 2,336× | 4.28e-4 | 8.87e-3 ✓ sig. |
| granulosa cell differentiation | GO:0060014 | 1 / 1 | 2,336× | 4.28e-4 | 8.87e-3 ✓ sig. |
| body morphogenesis | GO:0010171 | 1 / 1 | 2,336× | 4.28e-4 | 8.87e-3 ✓ sig. |
| regulation of signal transduction | GO:0009966 | 2 / 101 | 46.3× | 7.93e-4 | 1.35e-2 ✓ sig. |
| mesenchymal cell proliferation involved in ureteric bud development | GO:0072138 | 1 / 2 | 1,168× | 8.56e-4 | 1.41e-2 ✓ sig. |
| axis elongation involved in somitogenesis | GO:0090245 | 1 / 2 | 1,168× | 8.56e-4 | 1.41e-2 ✓ sig. |
| cell proliferation involved in metanephros development | GO:0072203 | 1 / 2 | 1,168× | 8.56e-4 | 1.41e-2 ✓ sig. |
| negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation | GO:2000314 | 1 / 2 | 1,168× | 8.56e-4 | 1.41e-2 ✓ sig. |
| mesonephric duct morphogenesis | GO:0072180 | 1 / 2 | 1,168× | 8.56e-4 | 1.41e-2 ✓ sig. |
| positive regulation of transcription by RNA polymerase II | GO:0045944 | 4 / 1,208 | 7.7× | 9.85e-4 | 1.54e-2 ✓ sig. |
| cell proliferation involved in kidney development | GO:0072111 | 1 / 3 | 779× | 1.28e-3 | 1.80e-2 ✓ sig. |
| regulation of non-canonical Wnt signaling pathway | GO:2000050 | 1 / 3 | 779× | 1.28e-3 | 1.80e-2 ✓ sig. |
| oocyte growth | GO:0001555 | 1 / 4 | 584× | 1.71e-3 | 2.14e-2 ✓ sig. |