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 427
5
Diseases
12
Unique genes
0.077
Avg. similarity score
Glycosylphosphatidylinositol biosynthesis defect
Most-connected disease (4 links)
Disease
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Glycosylphosphatidylinositol biosynthesis defect
glycosylphosphatidylinositol biosynthesis defect 15
glycosylphosphatidylinositol biosynthesis defect 17
glycosylphosphatidylinositol biosynthesis defect 18
glycosylphosphatidylinositol biosynthesis defect 21
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Glycosylphosphatidylinositol biosynthesis defect | 4 | 4 | 12 |
| glycosylphosphatidylinositol biosynthesis defect 15 | 1 | 1 | 1 |
| glycosylphosphatidylinositol biosynthesis defect 17 | 1 | 1 | 1 |
| glycosylphosphatidylinositol biosynthesis defect 18 | 1 | 1 | 1 |
| glycosylphosphatidylinositol biosynthesis defect 21 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| GPAA1 | 2 / 5 | Glycosylphosphatidylinositol biosynthesis defect, glycosylphosphatidylinositol biosynthesis defect 15 |
| PIGH | 2 / 5 | Glycosylphosphatidylinositol biosynthesis defect, glycosylphosphatidylinositol biosynthesis defect 17 |
| PIGS | 2 / 5 | Glycosylphosphatidylinositol biosynthesis defect, glycosylphosphatidylinositol biosynthesis defect 18 |
| PIGU | 2 / 5 | Glycosylphosphatidylinositol biosynthesis defect, glycosylphosphatidylinositol biosynthesis defect 21 |
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 ⇵ |
|---|---|---|---|---|---|
| Glycosylphosphatidylinositol (GPI)-anchor biosynthesis | KEGG | 7 / 30 | 234× | 2.24e-16 | 9.74e-14 ✓ sig. |
| Synthesis of glycosylphosphatidylinositol (GPI) | Reactome | 4 / 17 | 235× | 1.35e-9 | 1.45e-7 ✓ sig. |
| Attachment of GPI anchor to uPAR | Reactome | 3 / 7 | 429× | 2.66e-8 | 2.07e-6 ✓ sig. |
| Metabolic pathways | KEGG | 8 / 1,563 | 5.1× | 2.46e-5 | 7.08e-4 ✓ sig. |
| Molybdenum cofactor biosynthesis | Reactome | 1 / 6 | 167× | 5.98e-3 | 4.92e-2 ✓ sig. |
| Folate biosynthesis | KEGG | 1 / 28 | 35.7× | 2.76e-2 | 1.23e-1 |
| GABAergic synapse | KEGG | 1 / 89 | 11.2× | 8.54e-2 | 2.27e-1 |
| Biosynthesis of cofactors | KEGG | 1 / 154 | 6.5× | 1.44e-1 | 3.02e-1 |
| Motor proteins | KEGG | 1 / 194 | 5.2× | 1.78e-1 | 3.41e-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 ⇵ |
|---|---|---|---|---|---|
| GPI anchor biosynthetic process | GO:0006506 | 7 / 31 | 352× | 1.31e-17 | 1.50e-14 ✓ sig. |
| GPI anchored protein biosynthesis | GO:0180046 | 3 / 5 | 934× | 2.02e-9 | 4.17e-7 ✓ sig. |
| attachment of GPI anchor to protein | GO:0016255 | 3 / 6 | 779× | 4.04e-9 | 7.71e-7 ✓ sig. |
| glycine receptor clustering | GO:0072579 | 1 / 1 | 1,557× | 6.42e-4 | 1.13e-2 ✓ sig. |
| mitochondrion migration along actin filament | GO:0034642 | 1 / 1 | 1,557× | 6.42e-4 | 1.13e-2 ✓ sig. |
| establishment of synaptic specificity at neuromuscular junction | GO:0007529 | 1 / 2 | 779× | 1.28e-3 | 1.75e-2 ✓ sig. |
| GPI anchor metabolic process | GO:0006505 | 1 / 2 | 779× | 1.28e-3 | 1.75e-2 ✓ sig. |
| establishment of mitochondrion localization | GO:0051654 | 1 / 4 | 389× | 2.57e-3 | 2.58e-2 ✓ sig. |
| molybdopterin cofactor biosynthetic process | GO:0032324 | 1 / 4 | 389× | 2.57e-3 | 2.58e-2 ✓ sig. |
| gamma-aminobutyric acid receptor clustering | GO:0097112 | 1 / 6 | 260× | 3.85e-3 | 3.22e-2 ✓ sig. |
| Mo-molybdopterin cofactor biosynthetic process | GO:0006777 | 1 / 6 | 260× | 3.85e-3 | 3.22e-2 ✓ sig. |
| mitocytosis | GO:0160040 | 1 / 6 | 260× | 3.85e-3 | 3.22e-2 ✓ sig. |
| protein retention in ER lumen | GO:0006621 | 1 / 7 | 222× | 4.49e-3 | 3.47e-2 ✓ sig. |
| regulation of mitochondrial fission | GO:0090140 | 1 / 8 | 195× | 5.13e-3 | 3.71e-2 ✓ sig. |
| regulation of receptor signaling pathway via JAK-STAT | GO:0046425 | 1 / 16 | 97.3× | 1.02e-2 | 5.19e-2 |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Glycosylphosphatidylinositol biosynthesis defect | glycosylphosphatidylinositol biosynthesis defect 21 | 0.077 | 1 | 7.79e-4 | 1.39e-3 ✓ sig. |
| Glycosylphosphatidylinositol biosynthesis defect | glycosylphosphatidylinositol biosynthesis defect 17 | 0.077 | 1 | 7.79e-4 | 1.39e-3 ✓ sig. |
| Glycosylphosphatidylinositol biosynthesis defect | glycosylphosphatidylinositol biosynthesis defect 18 | 0.077 | 1 | 7.79e-4 | 1.39e-3 ✓ sig. |
| Glycosylphosphatidylinositol biosynthesis defect | glycosylphosphatidylinositol biosynthesis defect 15 | 0.077 | 1 | 7.79e-4 | 1.39e-3 ✓ sig. |