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 285
6
Diseases
5
Unique genes
0.313
Avg. similarity score
17p11.2 microduplication syndrome
Most-connected disease (4 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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17p11.2 microduplication syndrome
Potocki-lupski syndrome
Birt-hogg-dube syndrome
Smith-magenis syndrome
obsolete Birt-Hogg-Dube syndrome
syndromic X-linked intellectual disability Snyder type
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| 17p11.2 microduplication syndrome | 4 | 4 | 2 |
| Potocki-lupski syndrome | 4 | 4 | 2 |
| Birt-hogg-dube syndrome | 3 | 3 | 2 |
| Smith-magenis syndrome | 3 | 3 | 3 |
| obsolete Birt-Hogg-Dube syndrome | 3 | 3 | 1 |
| syndromic X-linked intellectual disability Snyder type | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| FLCN | 4 / 6 | 17p11.2 microduplication syndrome, Birt-hogg-dube syndrome, obsolete Birt-Hogg-Dube syndrome, Potocki-lupski syndrome |
| RAI1 | 3 / 6 | 17p11.2 microduplication syndrome, Potocki-lupski syndrome, Smith-magenis syndrome |
| SMS | 2 / 6 | Smith-magenis syndrome, syndromic X-linked intellectual disability Snyder type |
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 ⇵ |
|---|---|---|---|---|---|
| Metabolism of polyamines | Reactome | 1 / 4 | 601× | 1.66e-3 | 2.00e-2 ✓ sig. |
| Arginine and proline metabolism | KEGG | 1 / 50 | 48.0× | 2.06e-2 | 1.05e-1 |
| Cysteine and methionine metabolism | KEGG | 1 / 52 | 46.2× | 2.15e-2 | 1.07e-1 |
| Amino acids regulate mTORC1 | Reactome | 1 / 55 | 43.7× | 2.27e-2 | 1.10e-1 |
| Glutathione metabolism | KEGG | 1 / 59 | 40.7× | 2.43e-2 | 1.15e-1 |
| Renal cell carcinoma | KEGG | 1 / 70 | 34.3× | 2.88e-2 | 1.26e-1 |
| mTOR signaling pathway | KEGG | 1 / 158 | 15.2× | 6.41e-2 | 1.95e-1 |
| Endocytosis | KEGG | 1 / 250 | 9.6× | 9.99e-2 | 2.48e-1 |
| Metabolic pathways | KEGG | 1 / 1,563 | 1.5× | 5.02e-1 | 6.44e-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 ⇵ |
|---|---|---|---|---|---|
| negative regulation of cell proliferation involved in kidney development | GO:1901723 | 1 / 1 | 3,737× | 2.68e-4 | 6.20e-3 ✓ sig. |
| spermine biosynthetic process | GO:0006597 | 1 / 2 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| spermine metabolic process | GO:0008215 | 1 / 2 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| cell proliferation involved in kidney development | GO:0072111 | 1 / 3 | 1,246× | 8.03e-4 | 1.30e-2 ✓ sig. |
| negative regulation of post-translational protein modification | GO:1901874 | 1 / 4 | 934× | 1.07e-3 | 1.57e-2 ✓ sig. |
| negative regulation of lysosome organization | GO:1905672 | 1 / 4 | 934× | 1.07e-3 | 1.57e-2 ✓ sig. |
| regulation of pro-B cell differentiation | GO:2000973 | 1 / 4 | 934× | 1.07e-3 | 1.57e-2 ✓ sig. |
| negative regulation of brown fat cell differentiation | GO:1903444 | 1 / 5 | 747× | 1.34e-3 | 1.79e-2 ✓ sig. |
| polyamine metabolic process | GO:0006595 | 1 / 5 | 747× | 1.34e-3 | 1.79e-2 ✓ sig. |
| methionine metabolic process | GO:0006555 | 1 / 6 | 623× | 1.60e-3 | 1.98e-2 ✓ sig. |
| positive regulation of long-term synaptic depression | GO:1900454 | 1 / 7 | 534× | 1.87e-3 | 2.19e-2 ✓ sig. |
| regulation of Ras protein signal transduction | GO:0046578 | 1 / 8 | 467× | 2.14e-3 | 2.34e-2 ✓ sig. |
| polyamine biosynthetic process | GO:0006596 | 1 / 12 | 311× | 3.21e-3 | 2.91e-2 ✓ sig. |
| negative regulation of multicellular organism growth | GO:0040015 | 1 / 13 | 287× | 3.47e-3 | 3.06e-2 ✓ sig. |
| negative regulation of glycolytic process | GO:0045820 | 1 / 16 | 234× | 4.27e-3 | 3.38e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| 17p11.2 microduplication syndrome | Potocki-lupski syndrome | 0.667 | 2 | 8.44e-9 | 7.20e-8 ✓ sig. |
| 17p11.2 microduplication syndrome | obsolete Birt-Hogg-Dube syndrome | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Birt-hogg-dube syndrome | obsolete Birt-Hogg-Dube syndrome | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| obsolete Birt-Hogg-Dube syndrome | Potocki-lupski syndrome | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Smith-magenis syndrome | syndromic X-linked intellectual disability Snyder type | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |
| 17p11.2 microduplication syndrome | Birt-hogg-dube syndrome | 0.250 | 1 | 2.60e-4 | 6.40e-4 ✓ sig. |
| Birt-hogg-dube syndrome | Potocki-lupski syndrome | 0.250 | 1 | 2.60e-4 | 6.40e-4 ✓ sig. |
| 17p11.2 microduplication syndrome | Smith-magenis syndrome | 0.200 | 1 | 3.90e-4 | 8.52e-4 ✓ sig. |
| Potocki-lupski syndrome | Smith-magenis syndrome | 0.200 | 1 | 3.90e-4 | 8.52e-4 ✓ sig. |