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 432
6
Diseases
12
Unique genes
0.269
Avg. similarity score
Sideroblastic anemia
Most-connected disease (5 links)
Disease
Searched: Pyridoxine refractory sideroblastic anemia 3
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Pyridoxine refractory sideroblastic anemia 3
Sideroblastic anemia
Anemia, sideroblastic, 3, pyridoxine-refractory
Anemia, sideroblastic, pyridoxine-refractory, autosomal recessive
Spasticity with hyperglycinemia
Linear skin defects with multiple congenital anomalies 3
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Sideroblastic anemia | 5 | 5 | 12 |
| Anemia, sideroblastic, 3, pyridoxine-refractory | 4 | 4 | 1 |
| Anemia, sideroblastic, pyridoxine-refractory, autosomal recessive | 4 | 4 | 2 |
| Pyridoxine refractory sideroblastic anemia 3 | 4 | 4 | 1 |
| Spasticity with hyperglycinemia | 4 | 4 | 1 |
| Linear skin defects with multiple congenital anomalies 3 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| GLRX5 | 5 / 6 | Anemia, sideroblastic, 3, pyridoxine-refractory, Anemia, sideroblastic, pyridoxine-refractory, autosomal recessive, Pyridoxine refractory sideroblastic anemia 3, Sideroblastic anemia and 1 more |
| NDUFB11 | 2 / 6 | Linear skin defects with multiple congenital anomalies 3, Sideroblastic anemia |
| SLC25A38 | 2 / 6 | Anemia, sideroblastic, pyridoxine-refractory, autosomal recessive, Sideroblastic anemia |
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 ⇵ |
|---|---|---|---|---|---|
| Mitochondrial iron-sulfur cluster biogenesis | Reactome | 2 / 10 | 200× | 4.10e-5 | 9.33e-4 ✓ sig. |
| Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation | Reactome | 2 / 38 | 52.7× | 6.31e-4 | 7.99e-3 ✓ sig. |
| Assembly of Viral Components at the Budding Site | Reactome | 1 / 2 | 500× | 2.00e-3 | 1.90e-2 ✓ sig. |
| Mitochondrial ABC transporters | Reactome | 1 / 4 | 250× | 3.99e-3 | 3.12e-2 ✓ sig. |
| Calnexin/calreticulin cycle | Reactome | 1 / 5 | 200× | 4.99e-3 | 3.64e-2 ✓ sig. |
| tRNA processing in the mitochondrion | Reactome | 1 / 5 | 200× | 4.99e-3 | 3.64e-2 ✓ sig. |
| Scavenging by Class F Receptors | Reactome | 1 / 6 | 167× | 5.98e-3 | 4.10e-2 ✓ sig. |
| ATF6 (ATF6-alpha) activates chaperone genes | Reactome | 1 / 9 | 111× | 8.96e-3 | 5.31e-2 |
| FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes | Reactome | 1 / 10 | 100× | 9.95e-3 | 5.67e-2 |
| Scavenging by Class A Receptors | Reactome | 1 / 11 | 91.0× | 1.09e-2 | 6.01e-2 |
| The activation of arylsulfatases | Reactome | 1 / 13 | 77.0× | 1.29e-2 | 6.62e-2 |
| Heme biosynthesis | Reactome | 1 / 14 | 71.5× | 1.39e-2 | 6.94e-2 |
| Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models | Reactome | 1 / 16 | 62.6× | 1.59e-2 | 7.50e-2 |
| Mitochondrial protein import | Reactome | 1 / 19 | 52.7× | 1.88e-2 | 8.28e-2 |
| Chemical carcinogenesis - reactive oxygen species | KEGG | 2 / 227 | 8.8× | 2.07e-2 | 8.77e-2 |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| iron-sulfur cluster assembly | GO:0016226 | 4 / 27 | 231× | 1.70e-9 | 3.68e-7 ✓ sig. |
| erythrocyte differentiation | GO:0030218 | 3 / 65 | 71.9× | 8.64e-6 | 4.86e-4 ✓ sig. |
| intracellular iron ion homeostasis | GO:0006879 | 3 / 71 | 65.8× | 1.13e-5 | 5.98e-4 ✓ sig. |
| intracellular oxygen homeostasis | GO:0032364 | 2 / 10 | 311× | 1.70e-5 | 8.17e-4 ✓ sig. |
| [2Fe-2S] cluster assembly | GO:0044571 | 2 / 11 | 283× | 2.07e-5 | 9.51e-4 ✓ sig. |
| heme biosynthetic process | GO:0006783 | 2 / 27 | 115× | 1.32e-4 | 3.76e-3 ✓ sig. |
| protein export from nucleus | GO:0006611 | 2 / 33 | 94.4× | 1.97e-4 | 5.03e-3 ✓ sig. |
| iron-sulfur cluster export from the mitochondrion | GO:0140466 | 1 / 1 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| positive regulation of iron-sulfur cluster assembly | GO:1903331 | 1 / 1 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| glycine import into mitochondrion | GO:1904983 | 1 / 1 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| acetylcholine-mediated vasodilation involved in regulation of systemic arterial blood pressure | GO:0003069 | 1 / 1 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| erythrophore differentiation | GO:0048773 | 1 / 1 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| response to magnetism | GO:0071000 | 1 / 1 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| tRNA surveillance | GO:0106354 | 1 / 1 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| negative regulation of membrane hyperpolarization | GO:1902631 | 1 / 2 | 779× | 1.28e-3 | 1.67e-2 ✓ sig. |