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 644
5
Diseases
5
Unique genes
0.233
Avg. similarity score
Thrombocytopenia with normal platelets
Most-connected disease (4 links)
Disease
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Thrombocytopenia with normal platelets
Thrombocytopenia 7
Thrombocytopenia, reduced platelet alpha granules
Thrombocytopenia 2
Thrombocytopenia 4
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Thrombocytopenia with normal platelets | 4 | 4 | 5 |
| Thrombocytopenia 7 | 2 | 2 | 1 |
| Thrombocytopenia, reduced platelet alpha granules | 2 | 2 | 1 |
| Thrombocytopenia 2 | 1 | 1 | 1 |
| Thrombocytopenia 4 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| IKZF5 | 3 / 5 | Thrombocytopenia 7, Thrombocytopenia with normal platelets, Thrombocytopenia, reduced platelet alpha granules |
| ANKRD26 | 2 / 5 | Thrombocytopenia 2, Thrombocytopenia with normal platelets |
| CYCS | 2 / 5 | Thrombocytopenia 4, Thrombocytopenia with normal platelets |
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 ⇵ |
|---|---|---|---|---|---|
| MASTL Facilitates Mitotic Progression | Reactome | 1 / 3 | 801× | 1.25e-3 | 1.34e-2 ✓ sig. |
| Signaling by membrane-tethered fusions of PDGFRA or PDGFRB | Reactome | 1 / 5 | 480× | 2.08e-3 | 1.96e-2 ✓ sig. |
| Release of apoptotic factors from the mitochondria | Reactome | 1 / 5 | 480× | 2.08e-3 | 1.96e-2 ✓ sig. |
| Formation of apoptosome | Reactome | 1 / 6 | 400× | 2.50e-3 | 2.23e-2 ✓ sig. |
| Activation of caspases through apoptosome-mediated cleavage | Reactome | 1 / 6 | 400× | 2.50e-3 | 2.23e-2 ✓ sig. |
| Regulation of the apoptosome activity | Reactome | 1 / 10 | 240× | 4.16e-3 | 3.21e-2 ✓ sig. |
| Apoptosis - multiple species | KEGG | 1 / 32 | 75.1× | 1.33e-2 | 6.74e-2 |
| Detoxification of Reactive Oxygen Species | Reactome | 1 / 34 | 70.6× | 1.41e-2 | 6.99e-2 |
| Transcriptional activation of mitochondrial biogenesis | Reactome | 1 / 51 | 47.1× | 2.11e-2 | 8.82e-2 |
| Legionellosis | KEGG | 1 / 56 | 42.9× | 2.31e-2 | 9.30e-2 |
| Viral myocarditis | KEGG | 1 / 70 | 34.3× | 2.88e-2 | 1.06e-1 |
| Platinum drug resistance | KEGG | 1 / 75 | 32.0× | 3.08e-2 | 1.10e-1 |
| p53 signaling pathway | KEGG | 1 / 75 | 32.0× | 3.08e-2 | 1.10e-1 |
| Respiratory electron transport | Reactome | 1 / 83 | 28.9× | 3.41e-2 | 1.16e-1 |
| TP53 Regulates Metabolic Genes | Reactome | 1 / 86 | 27.9× | 3.53e-2 | 1.19e-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 ⇵ |
|---|---|---|---|---|---|
| female meiosis II | GO:0007147 | 1 / 2 | 1,869× | 5.35e-4 | 9.88e-3 ✓ sig. |
| vitellogenesis | GO:0007296 | 1 / 4 | 934× | 1.07e-3 | 1.51e-2 ✓ sig. |
| mesenchymal cell apoptotic process | GO:0097152 | 1 / 10 | 374× | 2.67e-3 | 2.46e-2 ✓ sig. |
| mitochondrial electron transport, ubiquinol to cytochrome c | GO:0006122 | 1 / 14 | 267× | 3.74e-3 | 2.90e-2 ✓ sig. |
| mitochondrial electron transport, cytochrome c to oxygen | GO:0006123 | 1 / 23 | 162× | 6.14e-3 | 3.68e-2 ✓ sig. |
| hematopoietic stem cell proliferation | GO:0071425 | 1 / 25 | 149× | 6.67e-3 | 3.84e-2 ✓ sig. |
| execution phase of apoptosis | GO:0097194 | 1 / 25 | 149× | 6.67e-3 | 3.84e-2 ✓ sig. |
| cellular respiration | GO:0045333 | 1 / 41 | 91.2× | 1.09e-2 | 4.84e-2 ✓ sig. |
| intrinsic apoptotic signaling pathway | GO:0097193 | 1 / 45 | 83.1× | 1.20e-2 | 5.06e-2 |
| G2/M transition of mitotic cell cycle | GO:0000086 | 1 / 53 | 70.5× | 1.41e-2 | 5.48e-2 |
| negative regulation of fat cell differentiation | GO:0045599 | 1 / 57 | 65.6× | 1.52e-2 | 5.69e-2 |
| regulation of mitotic cell cycle | GO:0007346 | 1 / 77 | 48.5× | 2.04e-2 | 6.59e-2 |
| apoptotic signaling pathway | GO:0097190 | 1 / 84 | 44.5× | 2.23e-2 | 6.88e-2 |
| negative regulation of transcription by RNA polymerase II | GO:0000122 | 2 / 1,002 | 7.5× | 2.58e-2 | 7.48e-2 |
| neurogenesis | GO:0022008 | 1 / 102 | 36.6× | 2.70e-2 | 7.66e-2 |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Thrombocytopenia 7 | Thrombocytopenia, reduced platelet alpha granules | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Thrombocytopenia 2 | Thrombocytopenia with normal platelets | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |
| Thrombocytopenia 4 | Thrombocytopenia with normal platelets | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |
| Thrombocytopenia 7 | Thrombocytopenia with normal platelets | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |
| Thrombocytopenia with normal platelets | Thrombocytopenia, reduced platelet alpha granules | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |