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 393
5
Diseases
4
Unique genes
0.329
Avg. similarity score
Brain stem neoplasms
Most-connected disease (4 links)
Disease
Searched: Brain stem neoplasms
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Brain stem neoplasms
Atypical multiple mole melanoma syndrome
Trisomy
melanoma-pancreatic cancer syndrome
Intellectual developmental disorder growth other organ
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Brain stem neoplasms | 4 | 4 | 4 |
| Atypical multiple mole melanoma syndrome | 3 | 3 | 1 |
| Trisomy | 3 | 3 | 1 |
| melanoma-pancreatic cancer syndrome | 3 | 3 | 1 |
| Intellectual developmental disorder growth other organ | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| CDKN2A | 4 / 5 | Atypical multiple mole melanoma syndrome, Brain stem neoplasms, melanoma-pancreatic cancer syndrome, Trisomy |
| PPM1D | 2 / 5 | Brain stem neoplasms, Intellectual developmental disorder growth other organ |
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 ⇵ |
|---|---|---|---|---|---|
| Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 | Reactome | 3 / 3 | 3,003× | 1.39e-11 | 2.29e-9 ✓ sig. |
| Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 | Reactome | 3 / 3 | 3,003× | 1.39e-11 | 2.29e-9 ✓ sig. |
| p53 signaling pathway | KEGG | 4 / 75 | 160× | 1.40e-9 | 1.44e-7 ✓ sig. |
| Oncogene Induced Senescence | Reactome | 3 / 33 | 273× | 7.55e-8 | 5.12e-6 ✓ sig. |
| Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 | Reactome | 2 / 2 | 3,003× | 8.32e-8 | 5.59e-6 ✓ sig. |
| Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 | Reactome | 2 / 2 | 3,003× | 8.32e-8 | 5.59e-6 ✓ sig. |
| Cyclin D associated events in G1 | Reactome | 3 / 44 | 205× | 1.83e-7 | 1.11e-5 ✓ sig. |
| Melanoma | KEGG | 3 / 73 | 123× | 8.58e-7 | 4.25e-5 ✓ sig. |
| Non-small cell lung cancer | KEGG | 3 / 73 | 123× | 8.58e-7 | 4.25e-5 ✓ sig. |
| Glioma | KEGG | 3 / 76 | 119× | 9.70e-7 | 4.75e-5 ✓ sig. |
| Pancreatic cancer | KEGG | 3 / 77 | 117× | 1.01e-6 | 4.90e-5 ✓ sig. |
| Chronic myeloid leukemia | KEGG | 3 / 77 | 117× | 1.01e-6 | 4.90e-5 ✓ sig. |
| Senescence-Associated Secretory Phenotype (SASP) | Reactome | 3 / 111 | 81.1× | 3.05e-6 | 1.28e-4 ✓ sig. |
| Oxidative Stress Induced Senescence | Reactome | 3 / 125 | 72.1× | 4.37e-6 | 1.73e-4 ✓ sig. |
| Transcriptional regulation by RUNX2 | Reactome | 2 / 12 | 500× | 5.49e-6 | 2.09e-4 ✓ 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 ⇵ |
|---|---|---|---|---|---|
| regulation of transcription initiation by RNA polymerase II | GO:0060260 | 2 / 3 | 3,115× | 1.03e-7 | 1.25e-5 ✓ sig. |
| regulation of G2/M transition of mitotic cell cycle | GO:0010389 | 2 / 15 | 623× | 3.61e-6 | 2.35e-4 ✓ sig. |
| regulation of cell cycle | GO:0051726 | 3 / 262 | 53.5× | 1.08e-5 | 5.62e-4 ✓ sig. |
| regulation of gene expression | GO:0010468 | 3 / 402 | 34.9× | 3.89e-5 | 1.52e-3 ✓ sig. |
| positive regulation of fibroblast proliferation | GO:0048146 | 2 / 55 | 170× | 5.08e-5 | 1.86e-3 ✓ sig. |
| negative regulation of cell population proliferation | GO:0008285 | 3 / 444 | 31.6× | 5.24e-5 | 1.90e-3 ✓ sig. |
| negative regulation of cell cycle | GO:0045786 | 2 / 59 | 158× | 5.86e-5 | 2.06e-3 ✓ sig. |
| G1/S transition of mitotic cell cycle | GO:0000082 | 2 / 85 | 110× | 1.22e-4 | 3.57e-3 ✓ sig. |
| positive regulation of macrophage apoptotic process | GO:2000111 | 1 / 3 | 1,557× | 6.42e-4 | 1.15e-2 ✓ sig. |
| apoptotic process involved in mammary gland involution | GO:0060057 | 1 / 3 | 1,557× | 6.42e-4 | 1.15e-2 ✓ sig. |
| nuclear body organization | GO:0030575 | 1 / 3 | 1,557× | 6.42e-4 | 1.15e-2 ✓ sig. |
| negative regulation of proteolysis involved in protein catabolic process | GO:1903051 | 1 / 4 | 1,168× | 8.56e-4 | 1.39e-2 ✓ sig. |
| positive regulation of apoptotic process involved in mammary gland involution | GO:0060058 | 1 / 4 | 1,168× | 8.56e-4 | 1.39e-2 ✓ sig. |
| cell dedifferentiation | GO:0043697 | 1 / 5 | 934× | 1.07e-3 | 1.60e-2 ✓ sig. |
| negative regulation of mammary gland epithelial cell proliferation | GO:0033600 | 1 / 5 | 934× | 1.07e-3 | 1.60e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Atypical multiple mole melanoma syndrome | Trisomy | 0.500 | 1 | 6.49e-5 | 2.32e-4 ✓ sig. |
| Atypical multiple mole melanoma syndrome | melanoma-pancreatic cancer syndrome | 0.500 | 1 | 6.49e-5 | 2.32e-4 ✓ sig. |
| melanoma-pancreatic cancer syndrome | Trisomy | 0.500 | 1 | 6.49e-5 | 2.32e-4 ✓ sig. |
| Atypical multiple mole melanoma syndrome | Brain stem neoplasms | 0.200 | 1 | 2.60e-4 | 6.48e-4 ✓ sig. |
| Brain stem neoplasms | Trisomy | 0.200 | 1 | 2.60e-4 | 6.48e-4 ✓ sig. |
| Brain stem neoplasms | melanoma-pancreatic cancer syndrome | 0.200 | 1 | 2.60e-4 | 6.48e-4 ✓ sig. |
| Brain stem neoplasms | Intellectual developmental disorder growth other organ | 0.200 | 1 | 2.60e-4 | 6.48e-4 ✓ sig. |