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 11
28
Diseases
35
Unique genes
0.364
Avg. similarity score
Endometrial cyst
Most-connected disease (23 links)
Disease
Searched: Endometrial cyst
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Endometrial cyst
Low grade vulvar intraepithelial neoplasia
PTEN hamartoma tumor syndrome
Atypical ductal hyperplasia
Cervical endometrioid adenocarcinoma
Anisometropia
Lipomatosis
Atrophy
Bannayan-riley-ruvalcaba syndrome
Breast and ovarian cancer
Concussion
Cowden syndrome 1
Extragonadal germ cell cancer
Gangliocytoma
Glioma susceptibility 2
Lacrimal duct cancer
Lhermitte-duclos disease
Malignant melanoma, somatic
Primary effusion lymphoma
Proteus syndrome
Squamous cell carcinoma, head and neck, somatic
Vater association with macrocephaly and ventriculomegaly
Calcifying epithelial odontogenic tumor
Papillary tumor of the pineal region
Ceroid lipofuscinosis, neuronal, 4a (kufs type), autosomal recessive
Dicarboxylic aminoaciduria
Maturity-onset diabetes of the young type 8
Trichiasis
Member diseases (most connected first ‐ the cluster's core)
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| PTEN | 24 / 28 | Anisometropia, Atrophy, Atypical ductal hyperplasia, Bannayan-riley-ruvalcaba syndrome and 20 more |
| CDKN2A | 2 / 28 | Calcifying epithelial odontogenic tumor, Primary effusion lymphoma |
| CEL | 2 / 28 | Lipomatosis, Maturity-onset diabetes of the young type 8 |
| CLN6 | 2 / 28 | Atrophy, Ceroid lipofuscinosis, neuronal, 4a (kufs type), autosomal recessive |
| KRAS | 2 / 28 | Atypical ductal hyperplasia, Cervical endometrioid adenocarcinoma |
| MCM7 | 2 / 28 | Anisometropia, Trichiasis |
| SLC1A1 | 2 / 28 | Atrophy, Dicarboxylic aminoaciduria |
| TP53 | 2 / 28 | Cervical endometrioid adenocarcinoma, Papillary tumor of the pineal region |
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 ⇵ |
|---|---|---|---|---|---|
| Non-small cell lung cancer | KEGG | 11 / 73 | 51.7× | 7.08e-17 | 3.07e-14 ✓ sig. |
| Central carbon metabolism in cancer | KEGG | 10 / 71 | 48.3× | 4.40e-15 | 1.35e-12 ✓ sig. |
| Melanoma | KEGG | 10 / 73 | 47.0× | 5.90e-15 | 1.75e-12 ✓ sig. |
| EGFR tyrosine kinase inhibitor resistance | KEGG | 10 / 80 | 42.9× | 1.54e-14 | 4.22e-12 ✓ sig. |
| Glioma | KEGG | 9 / 76 | 40.6× | 6.18e-13 | 1.24e-10 ✓ sig. |
| Pancreatic cancer | KEGG | 9 / 77 | 40.1× | 6.98e-13 | 1.40e-10 ✓ sig. |
| Hepatocellular carcinoma | KEGG | 11 / 170 | 22.2× | 1.03e-12 | 1.95e-10 ✓ sig. |
| PD-L1 expression and PD-1 checkpoint pathway in cancer | KEGG | 9 / 90 | 34.3× | 2.98e-12 | 5.08e-10 ✓ sig. |
| Endometrial cancer | KEGG | 8 / 59 | 46.5× | 4.40e-12 | 7.24e-10 ✓ sig. |
| Endocrine resistance | KEGG | 9 / 99 | 31.2× | 7.18e-12 | 1.13e-9 ✓ sig. |
| Proteoglycans in cancer | KEGG | 11 / 204 | 18.5× | 7.58e-12 | 1.18e-9 ✓ sig. |
| Acute myeloid leukemia | KEGG | 8 / 68 | 40.4× | 1.44e-11 | 2.10e-9 ✓ sig. |
| Cellular senescence | KEGG | 10 / 157 | 21.9× | 1.51e-11 | 2.20e-9 ✓ sig. |
| Autophagy - animal | KEGG | 10 / 169 | 20.3× | 3.16e-11 | 4.27e-9 ✓ sig. |
| Chronic myeloid leukemia | KEGG | 8 / 77 | 35.7× | 4.03e-11 | 5.29e-9 ✓ 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 ⇵ |
|---|---|---|---|---|---|
| phosphatidylinositol 3-kinase/protein kinase B signal transduction | GO:0043491 | 6 / 92 | 34.8× | 1.75e-8 | 2.86e-6 ✓ sig. |
| negative regulation of autophagy | GO:0010507 | 5 / 73 | 36.6× | 2.35e-7 | 2.58e-5 ✓ sig. |
| Ras protein signal transduction | GO:0007265 | 5 / 79 | 33.8× | 3.49e-7 | 3.60e-5 ✓ sig. |
| insulin receptor signaling pathway | GO:0008286 | 5 / 80 | 33.4× | 3.72e-7 | 3.79e-5 ✓ sig. |
| apoptotic process | GO:0006915 | 10 / 747 | 7.1× | 7.26e-7 | 6.60e-5 ✓ sig. |
| anoikis | GO:0043276 | 3 / 12 | 133× | 1.31e-6 | 1.07e-4 ✓ sig. |
| phosphorylation | GO:0016310 | 3 / 14 | 114× | 2.16e-6 | 1.61e-4 ✓ sig. |
| glucose homeostasis | GO:0042593 | 5 / 134 | 19.9× | 4.80e-6 | 3.07e-4 ✓ sig. |
| cytokine-mediated signaling pathway | GO:0019221 | 5 / 145 | 18.4× | 7.06e-6 | 4.15e-4 ✓ sig. |
| TORC1 signaling | GO:0038202 | 4 / 67 | 31.9× | 7.27e-6 | 4.25e-4 ✓ sig. |
| cell population proliferation | GO:0008283 | 6 / 263 | 12.2× | 8.46e-6 | 4.79e-4 ✓ sig. |
| negative regulation of TORC1 signaling | GO:1904262 | 4 / 71 | 30.1× | 9.16e-6 | 5.09e-4 ✓ sig. |
| insulin-like growth factor receptor signaling pathway | GO:0048009 | 3 / 33 | 48.5× | 3.16e-5 | 1.30e-3 ✓ sig. |
| central nervous system myelin maintenance | GO:0032286 | 2 / 5 | 214× | 3.40e-5 | 1.38e-3 ✓ sig. |
| positive regulation of gene expression | GO:0010628 | 7 / 504 | 7.4× | 3.48e-5 | 1.40e-3 ✓ sig. |