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 324
6
Diseases
6
Unique genes
0.301
Avg. similarity score
Facioscapulohumeral muscular dystrophy
Most-connected disease (5 links)
Disease
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Facioscapulohumeral muscular dystrophy
Arhinia-choanal atresia-microphthalmia syndrome
Bosma arhinia microphthalmia syndrome
Chediak-higashi syndrome
arhinia, choanal atresia, and microphthalmia
immunodeficiency-centromeric instability-facial anomalies syndrome 1
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Facioscapulohumeral muscular dystrophy | 5 | 5 | 5 |
| Arhinia-choanal atresia-microphthalmia syndrome | 4 | 4 | 1 |
| Bosma arhinia microphthalmia syndrome | 4 | 4 | 1 |
| Chediak-higashi syndrome | 4 | 4 | 2 |
| arhinia, choanal atresia, and microphthalmia | 4 | 4 | 1 |
| immunodeficiency-centromeric instability-facial anomalies syndrome 1 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| SMCHD1 | 5 / 6 | arhinia, choanal atresia, and microphthalmia, Arhinia-choanal atresia-microphthalmia syndrome, Bosma arhinia microphthalmia syndrome, Chediak-higashi syndrome and 1 more |
| DNMT3B | 2 / 6 | Facioscapulohumeral muscular dystrophy, immunodeficiency-centromeric instability-facial anomalies syndrome 1 |
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 ⇵ |
|---|---|---|---|---|---|
| SUMOylation of DNA methylation proteins | Reactome | 1 / 4 | 500× | 2.00e-3 | 2.28e-2 ✓ sig. |
| Cysteine and methionine metabolism | KEGG | 1 / 52 | 38.5× | 2.57e-2 | 1.18e-1 |
| PRC2 methylates histones and DNA | Reactome | 1 / 73 | 27.4× | 3.59e-2 | 1.43e-1 |
| MicroRNAs in cancer | KEGG | 1 / 311 | 6.4× | 1.46e-1 | 3.04e-1 |
| Metabolic pathways | KEGG | 1 / 1,563 | 1.3× | 5.67e-1 | 6.99e-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 ⇵ |
|---|---|---|---|---|---|
| dosage compensation by inactivation of X chromosome | GO:0009048 | 2 / 10 | 623× | 3.86e-6 | 2.44e-4 ✓ sig. |
| lymphocyte mediated immunity | GO:0002449 | 1 / 1 | 3,115× | 3.21e-4 | 7.03e-3 ✓ sig. |
| mast cell secretory granule organization | GO:0033364 | 1 / 2 | 1,557× | 6.42e-4 | 1.13e-2 ✓ sig. |
| endosome to lysosome transport via multivesicular body sorting pathway | GO:0032510 | 1 / 6 | 519× | 1.93e-3 | 2.20e-2 ✓ sig. |
| nose development | GO:0043584 | 1 / 8 | 389× | 2.57e-3 | 2.58e-2 ✓ sig. |
| negative regulation of G0 to G1 transition | GO:0070317 | 1 / 9 | 346× | 2.89e-3 | 2.76e-2 ✓ sig. |
| leukocyte chemotaxis | GO:0030595 | 1 / 16 | 195× | 5.13e-3 | 3.71e-2 ✓ sig. |
| positive regulation of double-strand break repair via nonhomologous end joining | GO:2001034 | 1 / 17 | 183× | 5.45e-3 | 3.84e-2 ✓ sig. |
| defense response to other organism | GO:0098542 | 1 / 19 | 164× | 6.09e-3 | 4.05e-2 ✓ sig. |
| melanosome organization | GO:0032438 | 1 / 25 | 125× | 8.00e-3 | 4.60e-2 ✓ sig. |
| defense response to protozoan | GO:0042832 | 1 / 30 | 104× | 9.60e-3 | 5.01e-2 |
| negative regulation of double-strand break repair via homologous recombination | GO:2000042 | 1 / 30 | 104× | 9.60e-3 | 5.01e-2 |
| pigmentation | GO:0043473 | 1 / 39 | 79.9× | 1.25e-2 | 5.72e-2 |
| natural killer cell mediated cytotoxicity | GO:0042267 | 1 / 41 | 76.0× | 1.31e-2 | 5.85e-2 |
| positive regulation of DNA repair | GO:0045739 | 1 / 46 | 67.7× | 1.47e-2 | 6.16e-2 |