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 361
5
Diseases
9
Unique genes
0.227
Avg. similarity score
Well-differentiated liposarcoma
Most-connected disease (4 links)
Disease
Pinned (dragged)
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Well-differentiated liposarcoma
Liposarcoma
silver-russell syndrome 5
Benign epithelial tumor of salivary glands
melanoma, cutaneous malignant, susceptibility to, 3
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Well-differentiated liposarcoma | 4 | 4 | 3 |
| Liposarcoma | 3 | 3 | 8 |
| silver-russell syndrome 5 | 3 | 3 | 1 |
| Benign epithelial tumor of salivary glands | 2 | 2 | 2 |
| melanoma, cutaneous malignant, susceptibility to, 3 | 2 | 2 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| HMGA2 | 4 / 5 | Benign epithelial tumor of salivary glands, Liposarcoma, silver-russell syndrome 5, Well-differentiated liposarcoma |
| CDK4 | 3 / 5 | Liposarcoma, melanoma, cutaneous malignant, susceptibility to, 3, Well-differentiated liposarcoma |
| MDM2 | 2 / 5 | Liposarcoma, Well-differentiated liposarcoma |
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 ⇵ |
|---|---|---|---|---|---|
| Transcriptional misregulation in cancer | KEGG | 4 / 198 | 27.0× | 8.46e-6 | 2.92e-4 ✓ sig. |
| Oncogene Induced Senescence | Reactome | 2 / 33 | 80.9× | 2.60e-4 | 4.80e-3 ✓ sig. |
| Bladder cancer | KEGG | 2 / 41 | 65.1× | 4.03e-4 | 6.75e-3 ✓ sig. |
| Melanoma | KEGG | 2 / 73 | 36.6× | 1.28e-3 | 1.63e-2 ✓ sig. |
| p53 signaling pathway | KEGG | 2 / 75 | 35.6× | 1.35e-3 | 1.69e-2 ✓ sig. |
| Glioma | KEGG | 2 / 76 | 35.1× | 1.38e-3 | 1.73e-2 ✓ sig. |
| Chronic myeloid leukemia | KEGG | 2 / 77 | 34.7× | 1.42e-3 | 1.77e-2 ✓ sig. |
| Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 | Reactome | 1 / 2 | 667× | 1.50e-3 | 1.85e-2 ✓ sig. |
| Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 | Reactome | 1 / 2 | 667× | 1.50e-3 | 1.85e-2 ✓ sig. |
| Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 | Reactome | 1 / 3 | 445× | 2.25e-3 | 2.48e-2 ✓ sig. |
| Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 | Reactome | 1 / 3 | 445× | 2.25e-3 | 2.48e-2 ✓ sig. |
| Endocrine resistance | KEGG | 2 / 99 | 27.0× | 2.33e-3 | 2.55e-2 ✓ sig. |
| Oxidative Stress Induced Senescence | Reactome | 2 / 125 | 21.4× | 3.69e-3 | 3.56e-2 ✓ sig. |
| PTK6 Regulates Cell Cycle | Reactome | 1 / 6 | 222× | 4.49e-3 | 4.08e-2 ✓ sig. |
| ChREBP activates metabolic gene expression | Reactome | 1 / 7 | 191× | 5.24e-3 | 4.50e-2 ✓ sig. |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| vascular associated smooth muscle cell migration | GO:1904738 | 2 / 3 | 1,384× | 6.18e-7 | 5.59e-5 ✓ sig. |
| vascular associated smooth muscle cell proliferation | GO:1990874 | 2 / 6 | 692× | 3.09e-6 | 2.04e-4 ✓ sig. |
| regulation of cell cycle | GO:0051726 | 4 / 262 | 31.7× | 4.50e-6 | 2.76e-4 ✓ sig. |
| response to caloric restriction | GO:0061771 | 2 / 10 | 415× | 9.26e-6 | 4.92e-4 ✓ sig. |
| negative regulation of astrocyte differentiation | GO:0048712 | 2 / 11 | 378× | 1.13e-5 | 5.73e-4 ✓ sig. |
| regulation of gene expression | GO:0010468 | 4 / 402 | 20.7× | 2.44e-5 | 1.04e-3 ✓ sig. |
| adrenal gland development | GO:0030325 | 2 / 24 | 173× | 5.66e-5 | 1.97e-3 ✓ sig. |
| cellular response to interleukin-4 | GO:0071353 | 2 / 24 | 173× | 5.66e-5 | 1.97e-3 ✓ sig. |
| astrocyte differentiation | GO:0048708 | 2 / 25 | 166× | 6.15e-5 | 2.10e-3 ✓ sig. |
| amyloid fibril formation | GO:1990000 | 2 / 29 | 143× | 8.32e-5 | 2.64e-3 ✓ sig. |
| fibroblast proliferation | GO:0048144 | 2 / 42 | 98.9× | 1.76e-4 | 4.61e-3 ✓ sig. |
| positive regulation of double-strand break repair via homologous recombination | GO:1905168 | 2 / 46 | 90.3× | 2.11e-4 | 5.24e-3 ✓ sig. |
| regulation of DNA-templated transcription | GO:0006355 | 5 / 1,454 | 7.1× | 2.74e-4 | 6.29e-3 ✓ sig. |
| positive regulation of vascular associated smooth muscle cell proliferation | GO:1904707 | 2 / 53 | 78.4× | 2.81e-4 | 6.40e-3 ✓ sig. |
| stem cell proliferation | GO:0072089 | 2 / 54 | 76.9× | 2.91e-4 | 6.57e-3 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Liposarcoma | Well-differentiated liposarcoma | 0.333 | 3 | 9.21e-11 | 9.69e-10 ✓ sig. |
| Benign epithelial tumor of salivary glands | silver-russell syndrome 5 | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| melanoma, cutaneous malignant, susceptibility to, 3 | Well-differentiated liposarcoma | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |
| silver-russell syndrome 5 | Well-differentiated liposarcoma | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |
| Benign epithelial tumor of salivary glands | Well-differentiated liposarcoma | 0.200 | 1 | 3.90e-4 | 8.52e-4 ✓ sig. |
| Liposarcoma | silver-russell syndrome 5 | 0.111 | 1 | 5.20e-4 | 1.04e-3 ✓ sig. |
| Liposarcoma | melanoma, cutaneous malignant, susceptibility to, 3 | 0.111 | 1 | 5.20e-4 | 1.04e-3 ✓ sig. |