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 478
6
Diseases
6
Unique genes
0.332
Avg. similarity score
Cerebral arterial disease
Most-connected disease (5 links)
Disease
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Cerebral arterial disease
CBL-related disorder
Early onset vitamin b6 dependent epilepsy
Juvenile myelomonocytic leukemia
Noonan syndrome-like disorder with or without juvenile myelomonocytic leukemia
Cerebral artery occlusion
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Cerebral arterial disease | 5 | 5 | 2 |
| CBL-related disorder | 4 | 4 | 1 |
| Early onset vitamin b6 dependent epilepsy | 4 | 4 | 3 |
| Juvenile myelomonocytic leukemia | 4 | 4 | 1 |
| Noonan syndrome-like disorder with or without juvenile myelomonocytic leukemia | 4 | 4 | 1 |
| Cerebral artery occlusion | 1 | 1 | 3 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| CBL | 5 / 6 | CBL-related disorder, Cerebral arterial disease, Early onset vitamin b6 dependent epilepsy, Juvenile myelomonocytic leukemia and 1 more |
| ADGRE3 | 2 / 6 | Cerebral arterial disease, Cerebral artery occlusion |
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 ⇵ |
|---|---|---|---|---|---|
| Choline catabolism | Reactome | 1 / 6 | 334× | 2.99e-3 | 2.54e-2 ✓ sig. |
| InlB-mediated entry of Listeria monocytogenes into host cell | Reactome | 1 / 7 | 286× | 3.49e-3 | 2.83e-2 ✓ sig. |
| PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 | Reactome | 1 / 9 | 222× | 4.49e-3 | 3.39e-2 ✓ sig. |
| Interleukin-6 signaling | Reactome | 1 / 11 | 182× | 5.48e-3 | 3.87e-2 ✓ sig. |
| Lysine catabolism | Reactome | 1 / 12 | 167× | 5.98e-3 | 4.10e-2 ✓ sig. |
| TGF-beta receptor signaling activates SMADs | Reactome | 1 / 12 | 167× | 5.98e-3 | 4.10e-2 ✓ sig. |
| Regulation of KIT signaling | Reactome | 1 / 14 | 143× | 6.98e-3 | 4.53e-2 ✓ sig. |
| Constitutive Signaling by EGFRvIII | Reactome | 1 / 15 | 133× | 7.47e-3 | 4.73e-2 ✓ sig. |
| Spry regulation of FGF signaling | Reactome | 1 / 16 | 125× | 7.97e-3 | 4.94e-2 ✓ sig. |
| Class B/2 (Secretin family receptors) | Reactome | 1 / 18 | 111× | 8.96e-3 | 5.31e-2 |
| Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants | Reactome | 1 / 19 | 105× | 9.46e-3 | 5.49e-2 |
| Negative regulation of MET activity | Reactome | 1 / 21 | 95.3× | 1.04e-2 | 5.84e-2 |
| Regulation of signaling by CBL | Reactome | 1 / 21 | 95.3× | 1.04e-2 | 5.84e-2 |
| Histidine metabolism | KEGG | 1 / 22 | 91.0× | 1.09e-2 | 6.01e-2 |
| Negative regulation of FGFR3 signaling | Reactome | 1 / 22 | 91.0× | 1.09e-2 | 6.01e-2 |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| vitamin B6 metabolic process | GO:0042816 | 1 / 1 | 3,115× | 3.21e-4 | 7.04e-3 ✓ sig. |
| glycine betaine biosynthetic process from choline | GO:0019285 | 1 / 2 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| regulation of platelet-derived growth factor receptor-alpha signaling pathway | GO:2000583 | 1 / 3 | 1,038× | 9.63e-4 | 1.42e-2 ✓ sig. |
| choline catabolic process | GO:0042426 | 1 / 4 | 779× | 1.28e-3 | 1.67e-2 ✓ sig. |
| regulation of Rap protein signal transduction | GO:0032487 | 1 / 4 | 779× | 1.28e-3 | 1.67e-2 ✓ sig. |
| positive regulation of chemokine (C-C motif) ligand 5 production | GO:0071651 | 1 / 7 | 445× | 2.25e-3 | 2.24e-2 ✓ sig. |
| ubiquitin-dependent endocytosis | GO:0070086 | 1 / 7 | 445× | 2.25e-3 | 2.24e-2 ✓ sig. |
| positive regulation of growth hormone secretion | GO:0060124 | 1 / 9 | 346× | 2.89e-3 | 2.55e-2 ✓ sig. |
| aldehyde metabolic process | GO:0006081 | 1 / 13 | 240× | 4.17e-3 | 3.06e-2 ✓ sig. |
| regulation of signaling | GO:0023051 | 1 / 15 | 208× | 4.81e-3 | 3.27e-2 ✓ sig. |
| activation of adenylate cyclase activity | GO:0007190 | 1 / 15 | 208× | 4.81e-3 | 3.27e-2 ✓ sig. |
| positive regulation of cAMP/PKA signal transduction | GO:0141163 | 1 / 16 | 195× | 5.13e-3 | 3.37e-2 ✓ sig. |
| cell surface receptor signaling pathway | GO:0007166 | 2 / 373 | 16.7× | 5.65e-3 | 3.53e-2 ✓ sig. |
| negative regulation of epidermal growth factor receptor signaling pathway | GO:0042059 | 1 / 21 | 148× | 6.72e-3 | 3.84e-2 ✓ sig. |
| positive regulation of receptor-mediated endocytosis | GO:0048260 | 1 / 21 | 148× | 6.72e-3 | 3.84e-2 ✓ sig. |