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 346
6
Diseases
4
Unique genes
0.313
Avg. similarity score
Galactosemia
Most-connected disease (5 links)
Disease
Searched: Galactosemia
Pinned (dragged)
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Galactosemia
Erythrocyte udp-galactose-4-epimerase deficiency
Udp-glucose 4-epimerase deficiency
galactose epimerase deficiency
Galactose mutarotase deficiency
Udp-glucose-hexose-1-phosphate uridylyltransferase
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Galactosemia | 5 | 5 | 4 |
| Erythrocyte udp-galactose-4-epimerase deficiency | 3 | 3 | 1 |
| Udp-glucose 4-epimerase deficiency | 3 | 3 | 1 |
| galactose epimerase deficiency | 3 | 3 | 1 |
| Galactose mutarotase deficiency | 1 | 1 | 1 |
| Udp-glucose-hexose-1-phosphate uridylyltransferase | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| GALE | 4 / 6 | Erythrocyte udp-galactose-4-epimerase deficiency, galactose epimerase deficiency, Galactosemia, Udp-glucose 4-epimerase deficiency |
| GALM | 2 / 6 | Galactose mutarotase deficiency, Galactosemia |
| GALT | 2 / 6 | Galactosemia, Udp-glucose-hexose-1-phosphate uridylyltransferase |
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 ⇵ |
|---|---|---|---|---|---|
| Galactose metabolism | KEGG | 4 / 32 | 375× | 4.15e-11 | 6.08e-9 ✓ sig. |
| Galactose catabolism | Reactome | 3 / 5 | 1,802× | 1.39e-10 | 1.83e-8 ✓ sig. |
| Biosynthesis of nucleotide sugars | KEGG | 3 / 37 | 243× | 1.07e-7 | 6.74e-6 ✓ sig. |
| Amino sugar and nucleotide sugar metabolism | KEGG | 3 / 38 | 237× | 1.17e-7 | 7.23e-6 ✓ sig. |
| Metabolic pathways | KEGG | 4 / 1,563 | 7.7× | 2.86e-4 | 5.05e-3 ✓ sig. |
| Defective GALE can cause Epimerase-deficiency galactosemia (EDG) | Reactome | 1 / 1 | 3,003× | 3.33e-4 | 5.72e-3 ✓ sig. |
| Defective GALK1 can cause Galactosemia II (GALCT2) | Reactome | 1 / 1 | 3,003× | 3.33e-4 | 5.72e-3 ✓ sig. |
| Defective GALT can cause Galactosemia | Reactome | 1 / 1 | 3,003× | 3.33e-4 | 5.72e-3 ✓ sig. |
| Glycolysis / Gluconeogenesis | KEGG | 1 / 67 | 44.8× | 2.21e-2 | 1.11e-1 |
| Prolactin signaling pathway | KEGG | 1 / 71 | 42.3× | 2.34e-2 | 1.15e-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 ⇵ |
|---|---|---|---|---|---|
| galactose catabolic process via UDP-galactose, Leloir pathway | GO:0033499 | 4 / 5 | 3,737× | 9.84e-16 | 7.66e-13 ✓ sig. |
| galactose metabolic process | GO:0006012 | 4 / 8 | 2,336× | 1.38e-14 | 8.82e-12 ✓ sig. |
| galactitol metabolic process | GO:0019402 | 1 / 1 | 4,672× | 2.14e-4 | 5.29e-3 ✓ sig. |
| glycolytic process from galactose | GO:0061623 | 1 / 1 | 4,672× | 2.14e-4 | 5.29e-3 ✓ sig. |
| UDP-alpha-D-glucose metabolic process | GO:0006011 | 1 / 3 | 1,557× | 6.42e-4 | 1.14e-2 ✓ sig. |
| galactose catabolic process | GO:0019388 | 1 / 5 | 934× | 1.07e-3 | 1.58e-2 ✓ sig. |
| hexose metabolic process | GO:0019318 | 1 / 6 | 779× | 1.28e-3 | 1.76e-2 ✓ sig. |
| organophosphate metabolic process | GO:0019637 | 1 / 8 | 584× | 1.71e-3 | 2.10e-2 ✓ sig. |
| carbohydrate derivative metabolic process | GO:1901135 | 1 / 18 | 260× | 3.85e-3 | 3.26e-2 ✓ sig. |
| carbohydrate phosphorylation | GO:0046835 | 1 / 24 | 195× | 5.13e-3 | 3.78e-2 ✓ sig. |
| phosphate-containing compound metabolic process | GO:0006796 | 1 / 25 | 187× | 5.34e-3 | 3.86e-2 ✓ sig. |
| glucose metabolic process | GO:0006006 | 1 / 66 | 70.8× | 1.41e-2 | 6.12e-2 |
| carbohydrate metabolic process | GO:0005975 | 1 / 175 | 26.7× | 3.69e-2 | 1.00e-1 |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Erythrocyte udp-galactose-4-epimerase deficiency | Udp-glucose 4-epimerase deficiency | 0.500 | 1 | 6.49e-5 | 2.33e-4 ✓ sig. |
| Erythrocyte udp-galactose-4-epimerase deficiency | galactose epimerase deficiency | 0.500 | 1 | 6.49e-5 | 2.33e-4 ✓ sig. |
| galactose epimerase deficiency | Udp-glucose 4-epimerase deficiency | 0.500 | 1 | 6.49e-5 | 2.33e-4 ✓ sig. |
| Erythrocyte udp-galactose-4-epimerase deficiency | Galactosemia | 0.200 | 1 | 2.60e-4 | 6.51e-4 ✓ sig. |
| galactose epimerase deficiency | Galactosemia | 0.200 | 1 | 2.60e-4 | 6.51e-4 ✓ sig. |
| Galactose mutarotase deficiency | Galactosemia | 0.200 | 1 | 2.60e-4 | 6.51e-4 ✓ sig. |
| Galactosemia | Udp-glucose-hexose-1-phosphate uridylyltransferase | 0.200 | 1 | 2.60e-4 | 6.51e-4 ✓ sig. |
| Galactosemia | Udp-glucose 4-epimerase deficiency | 0.200 | 1 | 2.60e-4 | 6.51e-4 ✓ sig. |