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 318
6
Diseases
4
Unique genes
0.309
Avg. similarity score
Blepharophimosis syndrome
Most-connected disease (5 links)
Disease
Searched: MED12-related intellectual disability syndrome
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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MED12-related intellectual disability syndrome
Blepharophimosis syndrome
Blepharophimosis-intellectual disability syndrome
Cholestasis-pigmentary retinopathy-cleft palate syndrome
KAT6B-related multiple congenital anomalies syndrome
Simpson 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 | 3 | 3 | 1 |
| KAT6B-related multiple congenital anomalies syndrome | 3 | 3 | 1 |
| MED12-related intellectual disability syndrome | 3 | 3 | 1 |
| Simpson syndrome | 3 | 3 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| KAT6B | 4 / 6 | Blepharophimosis syndrome, Blepharophimosis-intellectual disability syndrome, KAT6B-related multiple congenital anomalies syndrome, Simpson syndrome |
| MED12 | 4 / 6 | Blepharophimosis syndrome, Blepharophimosis-intellectual disability syndrome, Cholestasis-pigmentary retinopathy-cleft palate syndrome, MED12-related intellectual disability 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 ⇵ |
|---|---|---|---|---|---|
| SUMOylation of transcription factors | Reactome | 1 / 18 | 167× | 5.98e-3 | 4.93e-2 ✓ sig. |
| RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known | Reactome | 1 / 38 | 79.0× | 1.26e-2 | 8.00e-2 |
| Transcriptional regulation of white adipocyte differentiation | Reactome | 1 / 67 | 44.8× | 2.21e-2 | 1.11e-1 |
| RMTs methylate histone arginines | Reactome | 1 / 79 | 38.0× | 2.61e-2 | 1.22e-1 |
| HATs acetylate histones | Reactome | 1 / 93 | 32.3× | 3.06e-2 | 1.34e-1 |
| PPARA activates gene expression | Reactome | 1 / 115 | 26.1× | 3.78e-2 | 1.50e-1 |
| ATP-dependent chromatin remodeling | KEGG | 1 / 117 | 25.7× | 3.84e-2 | 1.52e-1 |
| Thyroid hormone signaling pathway | KEGG | 1 / 122 | 24.6× | 4.00e-2 | 1.55e-1 |
| Hepatocellular carcinoma | KEGG | 1 / 170 | 17.7× | 5.54e-2 | 1.86e-1 |
| Thermogenesis | KEGG | 1 / 234 | 12.8× | 7.57e-2 | 2.18e-1 |
| Generic Transcription Pathway | Reactome | 1 / 346 | 8.7× | 1.10e-1 | 2.67e-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 ⇵ |
|---|---|---|---|---|---|
| positive regulation of DNA-templated transcription | GO:0045893 | 4 / 778 | 24.0× | 2.98e-6 | 1.99e-4 ✓ sig. |
| positive regulation of transcription by RNA polymerase II | GO:0045944 | 4 / 1,208 | 15.5× | 1.74e-5 | 8.07e-4 ✓ sig. |
| regulation of transcription by RNA polymerase II | GO:0006357 | 4 / 1,602 | 11.7× | 5.38e-5 | 1.91e-3 ✓ sig. |
| negative regulation of DNA-templated transcription | GO:0045892 | 3 / 631 | 22.2× | 1.49e-4 | 4.10e-3 ✓ sig. |
| female somatic sex determination | GO:0019101 | 1 / 1 | 4,672× | 2.14e-4 | 5.29e-3 ✓ sig. |
| granulosa cell differentiation | GO:0060014 | 1 / 1 | 4,672× | 2.14e-4 | 5.29e-3 ✓ sig. |
| axis elongation involved in somitogenesis | GO:0090245 | 1 / 2 | 2,336× | 4.28e-4 | 8.64e-3 ✓ sig. |
| oocyte growth | GO:0001555 | 1 / 4 | 1,168× | 8.56e-4 | 1.38e-2 ✓ sig. |
| positive regulation of luteinizing hormone secretion | GO:0033686 | 1 / 4 | 1,168× | 8.56e-4 | 1.38e-2 ✓ sig. |
| positive regulation of follicle-stimulating hormone secretion | GO:0046881 | 1 / 6 | 779× | 1.28e-3 | 1.76e-2 ✓ sig. |
| extraocular skeletal muscle development | GO:0002074 | 1 / 6 | 779× | 1.28e-3 | 1.76e-2 ✓ sig. |
| embryonic neurocranium morphogenesis | GO:0048702 | 1 / 8 | 584× | 1.71e-3 | 2.10e-2 ✓ sig. |
| regulation of DNA-templated transcription | GO:0006355 | 3 / 1,454 | 9.6× | 1.77e-3 | 2.15e-2 ✓ sig. |
| embryonic eye morphogenesis | GO:0048048 | 1 / 11 | 425× | 2.35e-3 | 2.52e-2 ✓ sig. |
| apoptotic DNA fragmentation | GO:0006309 | 1 / 12 | 389× | 2.57e-3 | 2.64e-2 ✓ sig. |