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 570
5
Diseases
64
Unique genes
0.300
Avg. similarity score
Parotid gland pleomorphic adenoma
Most-connected disease (4 links)
Disease
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Parotid gland pleomorphic adenoma
Salivary gland basal cell adenocarcinoma
Salivary gland carcinoma ex pleomorphic adenoma
Salivary gland mucoepidermoid carcinoma
Salivary gland pleomorphic adenoma
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Parotid gland pleomorphic adenoma | 4 | 4 | 9 |
| Salivary gland basal cell adenocarcinoma | 4 | 4 | 18 |
| Salivary gland carcinoma ex pleomorphic adenoma | 4 | 4 | 36 |
| Salivary gland mucoepidermoid carcinoma | 4 | 4 | 34 |
| Salivary gland pleomorphic adenoma | 4 | 4 | 15 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| CHCHD7 | 5 / 5 | Parotid gland pleomorphic adenoma, Salivary gland basal cell adenocarcinoma, Salivary gland carcinoma ex pleomorphic adenoma, Salivary gland mucoepidermoid carcinoma and 1 more |
| FHIT | 5 / 5 | Parotid gland pleomorphic adenoma, Salivary gland basal cell adenocarcinoma, Salivary gland carcinoma ex pleomorphic adenoma, Salivary gland mucoepidermoid carcinoma and 1 more |
| HMGA2 | 5 / 5 | Parotid gland pleomorphic adenoma, Salivary gland basal cell adenocarcinoma, Salivary gland carcinoma ex pleomorphic adenoma, Salivary gland mucoepidermoid carcinoma and 1 more |
| LIFR | 5 / 5 | Parotid gland pleomorphic adenoma, Salivary gland basal cell adenocarcinoma, Salivary gland carcinoma ex pleomorphic adenoma, Salivary gland mucoepidermoid carcinoma and 1 more |
| PLAG1 | 5 / 5 | Parotid gland pleomorphic adenoma, Salivary gland basal cell adenocarcinoma, Salivary gland carcinoma ex pleomorphic adenoma, Salivary gland mucoepidermoid carcinoma and 1 more |
| TCEA1 | 5 / 5 | Parotid gland pleomorphic adenoma, Salivary gland basal cell adenocarcinoma, Salivary gland carcinoma ex pleomorphic adenoma, Salivary gland mucoepidermoid carcinoma and 1 more |
| CTNNB1 | 4 / 5 | Parotid gland pleomorphic adenoma, Salivary gland basal cell adenocarcinoma, Salivary gland carcinoma ex pleomorphic adenoma, Salivary gland pleomorphic adenoma |
| NFIB | 4 / 5 | Salivary gland basal cell adenocarcinoma, Salivary gland carcinoma ex pleomorphic adenoma, Salivary gland mucoepidermoid carcinoma, Salivary gland pleomorphic adenoma |
| WIF1 | 4 / 5 | Salivary gland basal cell adenocarcinoma, Salivary gland carcinoma ex pleomorphic adenoma, Salivary gland mucoepidermoid carcinoma, Salivary gland pleomorphic adenoma |
| HRAS | 3 / 5 | Salivary gland carcinoma ex pleomorphic adenoma, Salivary gland mucoepidermoid carcinoma, Salivary gland pleomorphic adenoma |
| KRAS | 3 / 5 | Salivary gland carcinoma ex pleomorphic adenoma, Salivary gland mucoepidermoid carcinoma, Salivary gland pleomorphic adenoma |
| TP53 | 3 / 5 | Parotid gland pleomorphic adenoma, Salivary gland carcinoma ex pleomorphic adenoma, Salivary gland pleomorphic adenoma |
| CDKN2A | 2 / 5 | Salivary gland carcinoma ex pleomorphic adenoma, Salivary gland mucoepidermoid carcinoma |
| CRTC1 | 2 / 5 | Salivary gland basal cell adenocarcinoma, Salivary gland pleomorphic adenoma |
| CRTC3 | 2 / 5 | Salivary gland mucoepidermoid carcinoma, Salivary gland pleomorphic adenoma |
| FBXW7 | 2 / 5 | Salivary gland basal cell adenocarcinoma, Salivary gland carcinoma ex pleomorphic adenoma |
| FGFR2 | 2 / 5 | Salivary gland basal cell adenocarcinoma, Salivary gland carcinoma ex pleomorphic adenoma |
| MAML2 | 2 / 5 | Salivary gland basal cell adenocarcinoma, Salivary gland pleomorphic adenoma |
| MYB | 2 / 5 | Salivary gland carcinoma ex pleomorphic adenoma, Salivary gland mucoepidermoid carcinoma |
| PIK3CA | 2 / 5 | Salivary gland basal cell adenocarcinoma, Salivary gland carcinoma ex pleomorphic adenoma |
| PTEN | 2 / 5 | Salivary gland carcinoma ex pleomorphic adenoma, Salivary gland mucoepidermoid carcinoma |
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 ⇵ |
|---|---|---|---|---|---|
| Prostate cancer | KEGG | 11 / 98 | 21.1× | 3.13e-12 | 5.32e-10 ✓ sig. |
| Melanoma | KEGG | 10 / 73 | 25.7× | 4.24e-12 | 7.00e-10 ✓ sig. |
| Bladder cancer | KEGG | 8 / 41 | 36.6× | 3.44e-11 | 4.61e-9 ✓ sig. |
| Hepatocellular carcinoma | KEGG | 12 / 170 | 13.2× | 7.60e-11 | 9.21e-9 ✓ sig. |
| Endocrine resistance | KEGG | 10 / 99 | 19.0× | 9.55e-11 | 1.13e-8 ✓ sig. |
| Breast cancer | KEGG | 11 / 148 | 13.9× | 2.91e-10 | 3.06e-8 ✓ sig. |
| Endometrial cancer | KEGG | 8 / 59 | 25.4× | 7.41e-10 | 7.08e-8 ✓ sig. |
| Pathways in cancer | KEGG | 17 / 533 | 6.0× | 1.55e-9 | 1.38e-7 ✓ sig. |
| Human papillomavirus infection | KEGG | 14 / 333 | 7.9× | 1.65e-9 | 1.46e-7 ✓ sig. |
| Central carbon metabolism in cancer | KEGG | 8 / 71 | 21.1× | 3.38e-9 | 2.81e-7 ✓ sig. |
| Non-small cell lung cancer | KEGG | 8 / 73 | 20.6× | 4.24e-9 | 3.43e-7 ✓ sig. |
| Glioma | KEGG | 8 / 76 | 19.8× | 5.87e-9 | 4.60e-7 ✓ sig. |
| Rap1 signaling pathway | KEGG | 11 / 211 | 9.8× | 1.25e-8 | 9.02e-7 ✓ sig. |
| Thyroid hormone signaling pathway | KEGG | 9 / 122 | 13.8× | 1.47e-8 | 1.05e-6 ✓ sig. |
| Human T-cell leukemia virus 1 infection | KEGG | 11 / 224 | 9.2× | 2.32e-8 | 1.56e-6 ✓ 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 ⇵ |
|---|---|---|---|---|---|
| positive regulation of transcription by RNA polymerase II | GO:0045944 | 23 / 1,208 | 5.6× | 4.04e-12 | 1.68e-9 ✓ sig. |
| negative regulation of transcription by RNA polymerase II | GO:0000122 | 20 / 1,002 | 5.8× | 6.61e-11 | 2.11e-8 ✓ sig. |
| chromatin remodeling | GO:0006338 | 12 / 320 | 10.9× | 7.67e-10 | 1.85e-7 ✓ sig. |
| regulation of gene expression | GO:0010468 | 13 / 402 | 9.4× | 8.47e-10 | 2.01e-7 ✓ sig. |
| negative regulation of DNA-templated transcription | GO:0045892 | 14 / 631 | 6.5× | 2.18e-8 | 3.48e-6 ✓ sig. |
| chromatin organization | GO:0006325 | 12 / 449 | 7.8× | 3.39e-8 | 5.11e-6 ✓ sig. |
| chondrocyte differentiation | GO:0002062 | 6 / 61 | 28.7× | 6.08e-8 | 8.37e-6 ✓ sig. |
| positive regulation of phospholipase activity | GO:0010518 | 3 / 4 | 219× | 1.53e-7 | 1.82e-5 ✓ sig. |
| negative regulation of gene expression | GO:0010629 | 10 / 339 | 8.6× | 2.15e-7 | 2.39e-5 ✓ sig. |
| cell population proliferation | GO:0008283 | 9 / 263 | 10.0× | 2.65e-7 | 2.86e-5 ✓ sig. |
| glial cell proliferation | GO:0014009 | 4 / 18 | 64.9× | 3.69e-7 | 3.77e-5 ✓ sig. |
| stem cell proliferation | GO:0072089 | 5 / 54 | 27.0× | 1.12e-6 | 9.40e-5 ✓ sig. |
| oncogene-induced cell senescence | GO:0090402 | 3 / 7 | 125× | 1.33e-6 | 1.08e-4 ✓ sig. |
| regulation of G1/S transition of mitotic cell cycle | GO:2000045 | 5 / 57 | 25.6× | 1.47e-6 | 1.18e-4 ✓ sig. |
| positive regulation of cell population proliferation | GO:0008284 | 11 / 532 | 6.0× | 1.70e-6 | 1.33e-4 ✓ sig. |