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 400
6
Diseases
13
Unique genes
0.224
Avg. similarity score
Abnormality of the cerebrum
Most-connected disease (5 links)
Disease
Searched: Abnormality of the cerebrum
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Abnormality of the cerebrum
Craniofacial neurological cardiovascular and skeletal features (turnpenny-fry syndrome)
Turnpenny-fry syndrome
Abnormality of the cardiovascular system
Abnormality of the skeletal system
Wolfram syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Abnormality of the cerebrum | 5 | 5 | 1 |
| Craniofacial neurological cardiovascular and skeletal features (turnpenny-fry syndrome) | 5 | 5 | 1 |
| Turnpenny-fry syndrome | 5 | 5 | 2 |
| Abnormality of the cardiovascular system | 4 | 4 | 5 |
| Abnormality of the skeletal system | 4 | 4 | 5 |
| Wolfram syndrome | 3 | 3 | 6 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| PCGF2 | 6 / 6 | Abnormality of the cardiovascular system, Abnormality of the cerebrum, Abnormality of the skeletal system, Craniofacial neurological cardiovascular and skeletal features (turnpenny-fry syndrome) and 2 more |
| CISD3 | 2 / 6 | Turnpenny-fry syndrome, Wolfram syndrome |
| ZMIZ1 | 2 / 6 | Abnormality of the cardiovascular system, Abnormality of the skeletal system |
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 ⇵ |
|---|---|---|---|---|---|
| TCF7L2 mutants don't bind CTBP | Reactome | 1 / 3 | 308× | 3.24e-3 | 2.69e-2 ✓ sig. |
| Transport and synthesis of PAPS | Reactome | 1 / 6 | 154× | 6.48e-3 | 4.32e-2 ✓ sig. |
| Binding of TCF/LEF:CTNNB1 to target gene promoters | Reactome | 1 / 8 | 115× | 8.63e-3 | 5.19e-2 |
| RUNX3 regulates WNT signaling | Reactome | 1 / 8 | 115× | 8.63e-3 | 5.19e-2 |
| Transport of nucleotide sugars | Reactome | 1 / 9 | 103× | 9.70e-3 | 5.59e-2 |
| Repression of WNT target genes | Reactome | 1 / 11 | 84.0× | 1.18e-2 | 6.31e-2 |
| Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) | Reactome | 1 / 14 | 66.0× | 1.51e-2 | 7.27e-2 |
| mRNA decay by 5' to 3' exoribonuclease | Reactome | 1 / 14 | 66.0× | 1.51e-2 | 7.27e-2 |
| Transcriptional Regulation by E2F6 | Reactome | 1 / 35 | 26.4× | 3.72e-2 | 1.22e-1 |
| Thyroid cancer | KEGG | 1 / 37 | 25.0× | 3.93e-2 | 1.26e-1 |
| Transcriptional Regulation by VENTX | Reactome | 1 / 38 | 24.3× | 4.04e-2 | 1.28e-1 |
| SUMOylation of transcription cofactors | Reactome | 1 / 41 | 22.5× | 4.35e-2 | 1.34e-1 |
| Deactivation of the beta-catenin transactivating complex | Reactome | 1 / 42 | 22.0× | 4.45e-2 | 1.36e-1 |
| SUMOylation of RNA binding proteins | Reactome | 1 / 47 | 19.7× | 4.97e-2 | 1.44e-1 |
| XBP1(S) activates chaperone genes | Reactome | 1 / 50 | 18.5× | 5.28e-2 | 1.49e-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 ⇵ |
|---|---|---|---|---|---|
| negative regulation of type B pancreatic cell apoptotic process | GO:2000675 | 2 / 6 | 479× | 6.69e-6 | 3.98e-4 ✓ sig. |
| pancreas development | GO:0031016 | 2 / 30 | 95.8× | 1.92e-4 | 4.95e-3 ✓ sig. |
| negative regulation of macromolecule biosynthetic process | GO:0010558 | 2 / 34 | 84.6× | 2.48e-4 | 5.91e-3 ✓ sig. |
| stem cell population maintenance | GO:0019827 | 2 / 47 | 61.2× | 4.74e-4 | 9.19e-3 ✓ sig. |
| positive regulation of epithelial to mesenchymal transition | GO:0010718 | 2 / 59 | 48.7× | 7.47e-4 | 1.23e-2 ✓ sig. |
| regulation of autophagy | GO:0010506 | 2 / 73 | 39.4× | 1.14e-3 | 1.57e-2 ✓ sig. |
| viral RNA genome packaging | GO:0019074 | 1 / 2 | 719× | 1.39e-3 | 1.75e-2 ✓ sig. |
| positive regulation of skeletal muscle satellite cell differentiation | GO:1902726 | 1 / 2 | 719× | 1.39e-3 | 1.75e-2 ✓ sig. |
| negative regulation of ATF6-mediated unfolded protein response | GO:1903892 | 1 / 2 | 719× | 1.39e-3 | 1.75e-2 ✓ sig. |
| 3'-phosphoadenosine 5'-phosphosulfate transport | GO:0046963 | 1 / 2 | 719× | 1.39e-3 | 1.75e-2 ✓ sig. |
| 5'-adenylyl sulfate transmembrane transport | GO:1902558 | 1 / 2 | 719× | 1.39e-3 | 1.75e-2 ✓ sig. |
| 3'-phospho-5'-adenylyl sulfate transmembrane transport | GO:1902559 | 1 / 2 | 719× | 1.39e-3 | 1.75e-2 ✓ sig. |
| negative regulation of translation | GO:0017148 | 2 / 98 | 29.3× | 2.04e-3 | 2.15e-2 ✓ sig. |
| pyramidal neuron migration to cerebral cortex | GO:0021852 | 1 / 3 | 479× | 2.09e-3 | 2.17e-2 ✓ sig. |
| positive regulation of heparan sulfate proteoglycan biosynthetic process | GO:0010909 | 1 / 3 | 479× | 2.09e-3 | 2.17e-2 ✓ sig. |