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 138
10
Diseases
70
Unique genes
0.149
Avg. similarity score
Lipoma
Most-connected disease (5 links)
Disease
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Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Lipoma
Coats plus syndrome
Benign prostatic hyperplasia
Cerebroretinal microangiopathy with calcifications and cysts
cerebroretinal microangiopathy with calcifications and cysts 2
Uterine benign neoplasm
Uterine polyp
cerebroretinal microangiopathy with calcifications and cysts 1
Cervical polyp
Periventricular leukomalacia
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Lipoma | 5 | 5 | 12 |
| Coats plus syndrome | 4 | 4 | 2 |
| Benign prostatic hyperplasia | 3 | 3 | 35 |
| Cerebroretinal microangiopathy with calcifications and cysts | 3 | 3 | 4 |
| cerebroretinal microangiopathy with calcifications and cysts 2 | 3 | 3 | 1 |
| Uterine benign neoplasm | 2 | 2 | 1 |
| Uterine polyp | 2 | 2 | 24 |
| cerebroretinal microangiopathy with calcifications and cysts 1 | 2 | 2 | 1 |
| Cervical polyp | 1 | 1 | 2 |
| Periventricular leukomalacia | 1 | 1 | 2 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| STN1 | 5 / 10 | Benign prostatic hyperplasia, Cerebroretinal microangiopathy with calcifications and cysts, cerebroretinal microangiopathy with calcifications and cysts 2, Coats plus syndrome and 1 more |
| BET1L | 3 / 10 | Benign prostatic hyperplasia, Lipoma, Uterine benign neoplasm |
| CTC1 | 3 / 10 | Cerebroretinal microangiopathy with calcifications and cysts, cerebroretinal microangiopathy with calcifications and cysts 1, Coats plus syndrome |
| TERT | 3 / 10 | Benign prostatic hyperplasia, Lipoma, Uterine polyp |
| ACTRT3 | 2 / 10 | Lipoma, Uterine polyp |
| IRAK1BP1 | 2 / 10 | Benign prostatic hyperplasia, Cervical polyp |
| MEI4 | 2 / 10 | Benign prostatic hyperplasia, Cervical polyp |
| PLEKHG1 | 2 / 10 | Periventricular leukomalacia, Uterine polyp |
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 ⇵ |
|---|---|---|---|---|---|
| Telomere C-strand synthesis initiation | Reactome | 3 / 7 | 73.5× | 6.53e-6 | 2.34e-4 ✓ sig. |
| Telomere Extension By Telomerase | Reactome | 2 / 16 | 21.4× | 3.81e-3 | 3.64e-2 ✓ sig. |
| Signaling by FGFR2 amplification mutants | Reactome | 1 / 1 | 172× | 5.83e-3 | 4.84e-2 ✓ sig. |
| Signaling by FGFR2 fusions | Reactome | 1 / 1 | 172× | 5.83e-3 | 4.84e-2 ✓ sig. |
| PTEN Loss of Function in Cancer | Reactome | 1 / 1 | 172× | 5.83e-3 | 4.84e-2 ✓ sig. |
| Central carbon metabolism in cancer | KEGG | 3 / 71 | 7.2× | 8.17e-3 | 6.06e-2 |
| Defective GCLC causes Hemolytic anemia due to gamma-glutamylcysteine synthetase deficiency (HAGGSD) | Reactome | 1 / 2 | 85.8× | 1.16e-2 | 7.51e-2 |
| Biosynthesis of cofactors | KEGG | 4 / 154 | 4.5× | 1.24e-2 | 7.78e-2 |
| DNA replication | KEGG | 2 / 36 | 9.5× | 1.86e-2 | 9.86e-2 |
| Invadopodia formation | Reactome | 1 / 4 | 42.9× | 2.31e-2 | 1.12e-1 |
| Vitamin B1 (thiamin) metabolism | Reactome | 1 / 5 | 34.3× | 2.88e-2 | 1.26e-1 |
| Mineralocorticoid biosynthesis | Reactome | 1 / 6 | 28.6× | 3.45e-2 | 1.39e-1 |
| Thyroxine biosynthesis | Reactome | 1 / 7 | 24.5× | 4.01e-2 | 1.52e-1 |
| Regulation of FOXO transcriptional activity by acetylation | Reactome | 1 / 7 | 24.5× | 4.01e-2 | 1.52e-1 |
| Synthesis of 12-eicosatetraenoic acid derivatives | Reactome | 1 / 7 | 24.5× | 4.01e-2 | 1.52e-1 |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| intestinal epithelial cell differentiation | GO:0060575 | 3 / 11 | 72.8× | 8.13e-6 | 4.44e-4 ✓ sig. |
| telomere capping | GO:0016233 | 3 / 12 | 66.7× | 1.08e-5 | 5.53e-4 ✓ sig. |
| hepatoblast differentiation | GO:0061017 | 2 / 2 | 267× | 1.38e-5 | 6.73e-4 ✓ sig. |
| follicle-stimulating hormone secretion | GO:0046884 | 2 / 2 | 267× | 1.38e-5 | 6.73e-4 ✓ sig. |
| positive regulation of Wnt signaling pathway | GO:0030177 | 4 / 48 | 22.2× | 3.10e-5 | 1.25e-3 ✓ sig. |
| smooth muscle cell differentiation | GO:0051145 | 3 / 18 | 44.5× | 3.95e-5 | 1.51e-3 ✓ sig. |
| negative regulation of telomere maintenance via telomerase | GO:0032211 | 3 / 22 | 36.4× | 7.37e-5 | 2.41e-3 ✓ sig. |
| protein lipidation | GO:0006497 | 2 / 4 | 133× | 8.26e-5 | 2.62e-3 ✓ sig. |
| luteinizing hormone secretion | GO:0032275 | 2 / 4 | 133× | 8.26e-5 | 2.62e-3 ✓ sig. |
| cardiac vascular smooth muscle cell differentiation | GO:0060947 | 2 / 4 | 133× | 8.26e-5 | 2.62e-3 ✓ sig. |
| telomere maintenance | GO:0000723 | 4 / 66 | 16.2× | 1.09e-4 | 3.23e-3 ✓ sig. |
| positive regulation of transcription by RNA polymerase II | GO:0045944 | 14 / 1,208 | 3.1× | 1.31e-4 | 3.71e-3 ✓ sig. |
| regulation of smooth muscle cell differentiation | GO:0051150 | 2 / 5 | 107× | 1.37e-4 | 3.83e-3 ✓ sig. |
| cardiac muscle cell differentiation | GO:0055007 | 3 / 30 | 26.7× | 1.90e-4 | 4.88e-3 ✓ sig. |
| cellular response to BMP stimulus | GO:0071773 | 3 / 33 | 24.3× | 2.53e-4 | 5.98e-3 ✓ sig. |