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 383
5
Diseases
5
Unique genes
0.292
Avg. similarity score
Glucocorticoid deficiency with achalasia
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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Glucocorticoid deficiency with achalasia
Triple a syndrome
Intellectual disability with strabismus syndrome
alacrima, achalasia, and intellectual disability syndrome
Intellectual developmental disorder movement cerebellar
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Glucocorticoid deficiency with achalasia | 4 | 4 | 3 |
| Triple a syndrome | 4 | 4 | 3 |
| Intellectual disability with strabismus syndrome | 3 | 3 | 3 |
| alacrima, achalasia, and intellectual disability syndrome | 3 | 3 | 1 |
| Intellectual developmental disorder movement cerebellar | 2 | 2 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| GMPPA | 4 / 5 | alacrima, achalasia, and intellectual disability syndrome, Glucocorticoid deficiency with achalasia, Intellectual disability with strabismus syndrome, Triple a syndrome |
| TRAPPC11 | 3 / 5 | Glucocorticoid deficiency with achalasia, Intellectual developmental disorder movement cerebellar, Triple a syndrome |
| AAAS | 2 / 5 | Glucocorticoid deficiency with achalasia, Triple a syndrome |
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)
None of these pathways reaches significance (all FDR q ≥ 0.05). They’re the best candidates found, but treat them as weak evidence for why this cluster groups together.
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 phosphate metabolic process | GO:0045936 | 1 / 1 | 3,737× | 2.68e-4 | 6.20e-3 ✓ sig. |
| negative regulation of nucleobase-containing compound metabolic process | GO:0045934 | 1 / 2 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| negative regulation of small molecule metabolic process | GO:0062014 | 1 / 2 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| negative regulation of biosynthetic process | GO:0009890 | 1 / 3 | 1,246× | 8.03e-4 | 1.30e-2 ✓ sig. |
| GDP-mannose biosynthetic process | GO:0009298 | 1 / 6 | 623× | 1.60e-3 | 1.98e-2 ✓ sig. |
| GDP-mannose metabolic process | GO:0019673 | 1 / 6 | 623× | 1.60e-3 | 1.98e-2 ✓ sig. |
| constitutive secretory pathway | GO:0045054 | 1 / 6 | 623× | 1.60e-3 | 1.98e-2 ✓ sig. |
| regulation of nucleocytoplasmic transport | GO:0046822 | 1 / 9 | 415× | 2.41e-3 | 2.50e-2 ✓ sig. |
| muscle organ morphogenesis | GO:0048644 | 1 / 10 | 374× | 2.67e-3 | 2.65e-2 ✓ sig. |
| skeletal muscle organ development | GO:0060538 | 1 / 11 | 340× | 2.94e-3 | 2.79e-2 ✓ sig. |
| regulation of protein complex stability | GO:0061635 | 1 / 16 | 234× | 4.27e-3 | 3.38e-2 ✓ sig. |
| vesicle tethering | GO:0099022 | 1 / 16 | 234× | 4.27e-3 | 3.38e-2 ✓ sig. |
| glycoprotein metabolic process | GO:0009100 | 1 / 22 | 170× | 5.87e-3 | 3.98e-2 ✓ sig. |
| COPII vesicle coating | GO:0048208 | 1 / 23 | 162× | 6.14e-3 | 4.07e-2 ✓ sig. |
| telencephalon development | GO:0021537 | 1 / 29 | 129× | 7.74e-3 | 4.54e-2 ✓ sig. |