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 459
6
Diseases
7
Unique genes
0.315
Avg. similarity score
Cervical carcinosarcoma
Most-connected disease (4 links)
Disease
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Cervical carcinosarcoma
Conjunctival telangiectasis
Benign smooth muscle neoplasm
Primary peritoneal serous adenocarcinoma
Splenic mantle cell lymphoma
Rauch-steindl syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Cervical carcinosarcoma | 4 | 4 | 2 |
| Conjunctival telangiectasis | 4 | 4 | 1 |
| Benign smooth muscle neoplasm | 3 | 3 | 2 |
| Primary peritoneal serous adenocarcinoma | 3 | 3 | 4 |
| Splenic mantle cell lymphoma | 3 | 3 | 4 |
| Rauch-steindl syndrome | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| ATM | 5 / 6 | Benign smooth muscle neoplasm, Cervical carcinosarcoma, Conjunctival telangiectasis, Primary peritoneal serous adenocarcinoma and 1 more |
| TP53 | 3 / 6 | Cervical carcinosarcoma, Primary peritoneal serous adenocarcinoma, Splenic mantle cell lymphoma |
| NSD2 | 2 / 6 | Rauch-steindl syndrome, Splenic mantle cell lymphoma |
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 ⇵ |
|---|---|---|---|---|---|
| Breast cancer | KEGG | 4 / 148 | 46.4× | 7.53e-7 | 3.26e-5 ✓ sig. |
| DNA Damage/Telomere Stress Induced Senescence | Reactome | 3 / 66 | 78.0× | 5.46e-6 | 1.77e-4 ✓ sig. |
| Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks | Reactome | 3 / 76 | 67.7× | 8.37e-6 | 2.52e-4 ✓ sig. |
| Pancreatic cancer | KEGG | 3 / 77 | 66.8× | 8.71e-6 | 2.60e-4 ✓ sig. |
| G2/M DNA damage checkpoint | Reactome | 3 / 84 | 61.3× | 1.13e-5 | 3.23e-4 ✓ sig. |
| MicroRNAs in cancer | KEGG | 4 / 311 | 22.1× | 1.45e-5 | 3.98e-4 ✓ sig. |
| Stabilization of p53 | Reactome | 2 / 11 | 312× | 1.60e-5 | 4.32e-4 ✓ sig. |
| Endocrine resistance | KEGG | 3 / 99 | 52.0× | 1.86e-5 | 4.90e-4 ✓ sig. |
| Human papillomavirus infection | KEGG | 4 / 333 | 20.6× | 1.90e-5 | 5.00e-4 ✓ sig. |
| TP53 Regulates Transcription of Caspase Activators and Caspases | Reactome | 2 / 12 | 286× | 1.92e-5 | 5.02e-4 ✓ sig. |
| Thyroid hormone signaling pathway | KEGG | 3 / 122 | 42.2× | 3.47e-5 | 8.18e-4 ✓ sig. |
| Apoptosis | KEGG | 3 / 137 | 37.6× | 4.92e-5 | 1.08e-3 ✓ sig. |
| Regulation of TP53 Activity through Methylation | Reactome | 2 / 19 | 181× | 4.96e-5 | 1.08e-3 ✓ sig. |
| TP53 Regulates Transcription of Genes Involved in Cytochrome C Release | Reactome | 2 / 20 | 172× | 5.51e-5 | 1.18e-3 ✓ sig. |
| Cellular senescence | KEGG | 3 / 157 | 32.8× | 7.38e-5 | 1.49e-3 ✓ 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 ⇵ |
|---|---|---|---|---|---|
| double-strand break repair | GO:0006302 | 4 / 87 | 123× | 1.52e-8 | 2.54e-6 ✓ sig. |
| DNA damage response, signal transduction by p53 class mediator | GO:0030330 | 3 / 48 | 167× | 5.53e-7 | 5.29e-5 ✓ sig. |
| cellular senescence | GO:0090398 | 3 / 57 | 141× | 9.34e-7 | 8.13e-5 ✓ sig. |
| cell population proliferation | GO:0008283 | 4 / 263 | 40.6× | 1.30e-6 | 1.06e-4 ✓ sig. |
| regulation of telomere maintenance via telomerase | GO:0032210 | 2 / 6 | 890× | 1.80e-6 | 1.39e-4 ✓ sig. |
| establishment of protein localization to telomere | GO:0070200 | 2 / 7 | 763× | 2.52e-6 | 1.83e-4 ✓ sig. |
| regulation of double-strand break repair via nonhomologous end joining | GO:2001032 | 2 / 8 | 667× | 3.36e-6 | 2.30e-4 ✓ sig. |
| neuron apoptotic process | GO:0051402 | 3 / 98 | 81.7× | 4.82e-6 | 3.08e-4 ✓ sig. |
| multicellular organism growth | GO:0035264 | 3 / 115 | 69.6× | 7.81e-6 | 4.51e-4 ✓ sig. |
| replicative senescence | GO:0090399 | 2 / 16 | 334× | 1.44e-5 | 7.22e-4 ✓ sig. |
| cardiac septum morphogenesis | GO:0060411 | 2 / 16 | 334× | 1.44e-5 | 7.22e-4 ✓ sig. |
| glial cell proliferation | GO:0014009 | 2 / 18 | 297× | 1.84e-5 | 8.67e-4 ✓ sig. |
| response to X-ray | GO:0010165 | 2 / 19 | 281× | 2.05e-5 | 9.42e-4 ✓ sig. |
| positive regulation of cellular senescence | GO:2000774 | 2 / 20 | 267× | 2.28e-5 | 1.02e-3 ✓ sig. |
| negative regulation of telomere maintenance via telomerase | GO:0032211 | 2 / 22 | 243× | 2.77e-5 | 1.18e-3 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Cervical carcinosarcoma | Conjunctival telangiectasis | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Benign smooth muscle neoplasm | Conjunctival telangiectasis | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Benign smooth muscle neoplasm | Cervical carcinosarcoma | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Cervical carcinosarcoma | Primary peritoneal serous adenocarcinoma | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Conjunctival telangiectasis | Primary peritoneal serous adenocarcinoma | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Cervical carcinosarcoma | Splenic mantle cell lymphoma | 0.250 | 1 | 1.94e-4 | 4.41e-4 ✓ sig. |
| Conjunctival telangiectasis | Splenic mantle cell lymphoma | 0.250 | 1 | 1.94e-4 | 4.41e-4 ✓ sig. |
| Rauch-steindl syndrome | Splenic mantle cell lymphoma | 0.250 | 1 | 1.94e-4 | 4.41e-4 ✓ sig. |
| Benign smooth muscle neoplasm | Primary peritoneal serous adenocarcinoma | 0.250 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |