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 152
10
Diseases
7
Unique genes
0.348
Avg. similarity score
Abnormality of the genitourinary system
Most-connected disease (7 links)
Disease
Searched: Intellectual developmental disorder with impaired language and dysmorphic facies
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Intellectual developmental disorder with impaired language and dysmorphic facies
Abnormality of the genitourinary system
Abnormality of the ear
Abnormality of the vertebrae
Abnormality of vision
Iris coloboma
Preauricular skin tag
Abnormality of limbs
Unsteady gait
Li-ghorgani-weisz-hubshman syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Abnormality of the genitourinary system | 7 | 7 | 2 |
| Abnormality of the ear | 5 | 5 | 1 |
| Abnormality of the vertebrae | 5 | 5 | 1 |
| Abnormality of vision | 5 | 5 | 4 |
| Iris coloboma | 5 | 5 | 1 |
| Preauricular skin tag | 5 | 5 | 1 |
| Abnormality of limbs | 3 | 3 | 4 |
| Intellectual developmental disorder with impaired language and dysmorphic facies | 3 | 3 | 1 |
| Unsteady gait | 3 | 3 | 1 |
| Li-ghorgani-weisz-hubshman syndrome | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| CDK9 | 7 / 10 | Abnormality of limbs, Abnormality of the ear, Abnormality of the genitourinary system, Abnormality of the vertebrae and 3 more |
| DDX6 | 4 / 10 | Abnormality of limbs, Abnormality of the genitourinary system, Intellectual developmental disorder with impaired language and dysmorphic facies, Unsteady gait |
| KAT8 | 2 / 10 | Abnormality of vision, Li-ghorgani-weisz-hubshman 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 ⇵ |
|---|---|---|---|---|---|
| Interactions of Tat with host cellular proteins | Reactome | 1 / 2 | 858× | 1.17e-3 | 1.27e-2 ✓ sig. |
| mRNA decay by 5' to 3' exoribonuclease | Reactome | 1 / 14 | 123× | 8.13e-3 | 5.01e-2 |
| Formation of HIV-1 elongation complex containing HIV-1 Tat | Reactome | 1 / 23 | 74.6× | 1.33e-2 | 6.77e-2 |
| SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription | Reactome | 1 / 32 | 53.6× | 1.85e-2 | 8.20e-2 |
| Hedgehog signaling pathway | KEGG | 1 / 56 | 30.6× | 3.22e-2 | 1.13e-1 |
| RNA Polymerase II Transcription Elongation | Reactome | 1 / 59 | 29.1× | 3.39e-2 | 1.16e-1 |
| Formation of RNA Pol II elongation complex | Reactome | 1 / 61 | 28.1× | 3.50e-2 | 1.18e-1 |
| Viral life cycle - HIV-1 | KEGG | 1 / 64 | 26.8× | 3.67e-2 | 1.21e-1 |
| TP53 Regulates Transcription of DNA Repair Genes | Reactome | 1 / 65 | 26.4× | 3.73e-2 | 1.22e-1 |
| RNA polymerase II transcribes snRNA genes | Reactome | 1 / 74 | 23.2× | 4.24e-2 | 1.32e-1 |
| RNA degradation | KEGG | 1 / 78 | 22.0× | 4.46e-2 | 1.36e-1 |
| RNA Polymerase II Pre-transcription Events | Reactome | 1 / 84 | 20.4× | 4.80e-2 | 1.41e-1 |
| HATs acetylate histones | Reactome | 1 / 93 | 18.4× | 5.30e-2 | 1.49e-1 |
| Estrogen-dependent gene expression | Reactome | 1 / 150 | 11.4× | 8.42e-2 | 1.95e-1 |
| Transcriptional misregulation in cancer | KEGG | 1 / 198 | 8.7× | 1.10e-1 | 2.29e-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 transcription elongation by RNA polymerase II | GO:0032968 | 2 / 57 | 93.7× | 1.90e-4 | 4.91e-3 ✓ sig. |
| viral RNA genome packaging | GO:0019074 | 1 / 2 | 1,335× | 7.49e-4 | 1.23e-2 ✓ sig. |
| positive regulation of skeletal muscle satellite cell differentiation | GO:1902726 | 1 / 2 | 1,335× | 7.49e-4 | 1.23e-2 ✓ sig. |
| positive regulation of protein localization to chromatin | GO:0120187 | 1 / 3 | 890× | 1.12e-3 | 1.55e-2 ✓ sig. |
| regulation of mRNA 3'-end processing | GO:0031440 | 1 / 4 | 667× | 1.50e-3 | 1.82e-2 ✓ sig. |
| regulation of postsynaptic density protein 95 clustering | GO:1902897 | 1 / 4 | 667× | 1.50e-3 | 1.82e-2 ✓ sig. |
| positive regulation of dendritic spine maintenance | GO:1902952 | 1 / 5 | 534× | 1.87e-3 | 2.05e-2 ✓ sig. |
| post-embryonic hemopoiesis | GO:0035166 | 1 / 5 | 534× | 1.87e-3 | 2.05e-2 ✓ sig. |
| nucleus localization | GO:0051647 | 1 / 5 | 534× | 1.87e-3 | 2.05e-2 ✓ sig. |
| transcription pausing by RNA polymerase II | GO:0160239 | 1 / 5 | 534× | 1.87e-3 | 2.05e-2 ✓ sig. |
| negative regulation of protein localization to chromatin | GO:0120186 | 1 / 6 | 445× | 2.25e-3 | 2.24e-2 ✓ sig. |
| transcription elongation-coupled chromatin remodeling | GO:0140673 | 1 / 8 | 334× | 2.99e-3 | 2.59e-2 ✓ sig. |
| regulation of mitochondrial transcription | GO:1903108 | 1 / 8 | 334× | 2.99e-3 | 2.59e-2 ✓ sig. |
| modulation of excitatory postsynaptic potential | GO:0098815 | 1 / 9 | 297× | 3.37e-3 | 2.76e-2 ✓ sig. |
| skeletal muscle satellite cell differentiation | GO:0014816 | 1 / 9 | 297× | 3.37e-3 | 2.76e-2 ✓ sig. |