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 372
7
Diseases
79
Unique genes
0.054
Avg. similarity score
Nonimmune hydrops fetalis
Most-connected disease (6 links)
Disease
Searched: Sulfite oxidase deficiency due to molybdenum cofactor deficiency type B2
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Sulfite oxidase deficiency due to molybdenum cofactor deficiency type B2
Nonimmune hydrops fetalis
Hydrops fetalis
Lymphatic malformation
Mucopolysaccharidosis type 7
Congenital malrotation of intestine
Desmosterolosis
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Nonimmune hydrops fetalis | 6 | 6 | 48 |
| Hydrops fetalis | 3 | 3 | 33 |
| Lymphatic malformation | 2 | 2 | 13 |
| Mucopolysaccharidosis type 7 | 2 | 2 | 1 |
| Congenital malrotation of intestine | 1 | 1 | 1 |
| Desmosterolosis | 1 | 1 | 1 |
| Sulfite oxidase deficiency due to molybdenum cofactor deficiency type B2 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| CALCRL | 3 / 7 | Hydrops fetalis, Lymphatic malformation, Nonimmune hydrops fetalis |
| EPHB4 | 3 / 7 | Hydrops fetalis, Lymphatic malformation, Nonimmune hydrops fetalis |
| GUSB | 3 / 7 | Hydrops fetalis, Mucopolysaccharidosis type 7, Nonimmune hydrops fetalis |
| PIEZO1 | 3 / 7 | Hydrops fetalis, Lymphatic malformation, Nonimmune hydrops fetalis |
| ANGPT2 | 2 / 7 | Lymphatic malformation, Nonimmune hydrops fetalis |
| ASAH1 | 2 / 7 | Hydrops fetalis, Nonimmune hydrops fetalis |
| CELSR1 | 2 / 7 | Hydrops fetalis, Lymphatic malformation |
| CHRNA1 | 2 / 7 | Hydrops fetalis, Nonimmune hydrops fetalis |
| DHCR24 | 2 / 7 | Desmosterolosis, Nonimmune hydrops fetalis |
| FLT4 | 2 / 7 | Lymphatic malformation, Nonimmune hydrops fetalis |
| GALNT14 | 2 / 7 | Congenital malrotation of intestine, Nonimmune hydrops fetalis |
| MDFIC | 2 / 7 | Hydrops fetalis, Lymphatic malformation |
| MOCS3 | 2 / 7 | Nonimmune hydrops fetalis, Sulfite oxidase deficiency due to molybdenum cofactor deficiency type B2 |
| SERPINA11 | 2 / 7 | Hydrops fetalis, Nonimmune hydrops fetalis |
| THSD1 | 2 / 7 | Lymphatic malformation, Nonimmune hydrops fetalis |
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 ⇵ |
|---|---|---|---|---|---|
| Tie2 Signaling | Reactome | 4 / 18 | 33.8× | 4.95e-6 | 1.63e-4 ✓ sig. |
| EPHB-mediated forward signaling | Reactome | 5 / 39 | 19.5× | 5.24e-6 | 1.71e-4 ✓ sig. |
| Ras signaling pathway | KEGG | 9 / 237 | 5.8× | 2.41e-5 | 6.09e-4 ✓ sig. |
| Axon guidance | KEGG | 8 / 183 | 6.6× | 2.59e-5 | 6.44e-4 ✓ sig. |
| Downstream signal transduction | Reactome | 4 / 29 | 21.0× | 3.63e-5 | 8.47e-4 ✓ sig. |
| PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases | Reactome | 3 / 14 | 32.6× | 9.46e-5 | 1.82e-3 ✓ sig. |
| VEGFR2 mediated cell proliferation | Reactome | 3 / 14 | 32.6× | 9.46e-5 | 1.82e-3 ✓ sig. |
| Defective NEU1 causes sialidosis | Reactome | 2 / 3 | 101× | 1.28e-4 | 2.30e-3 ✓ sig. |
| RAS GTPase cycle mutants | Reactome | 2 / 3 | 101× | 1.28e-4 | 2.30e-3 ✓ sig. |
| FRS-mediated FGFR3 signaling | Reactome | 3 / 20 | 22.8× | 2.88e-4 | 4.37e-3 ✓ sig. |
| NCAM signaling for neurite out-growth | Reactome | 3 / 20 | 22.8× | 2.88e-4 | 4.37e-3 ✓ sig. |
| FRS-mediated FGFR4 signaling | Reactome | 3 / 22 | 20.7× | 3.86e-4 | 5.46e-3 ✓ sig. |
| Activation of RAS in B cells | Reactome | 2 / 5 | 60.8× | 4.22e-4 | 5.86e-3 ✓ sig. |
| FRS-mediated FGFR1 signaling | Reactome | 3 / 23 | 19.8× | 4.41e-4 | 6.06e-3 ✓ sig. |
| FRS-mediated FGFR2 signaling | Reactome | 3 / 25 | 18.2× | 5.68e-4 | 7.37e-3 ✓ sig. |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| lymphangiogenesis | GO:0001946 | 3 / 14 | 50.7× | 2.56e-5 | 1.11e-3 ✓ sig. |
| angiogenesis | GO:0001525 | 8 / 284 | 6.7× | 2.64e-5 | 1.14e-3 ✓ sig. |
| lymph vessel development | GO:0001945 | 3 / 15 | 47.3× | 3.19e-5 | 1.31e-3 ✓ sig. |
| establishment of body hair planar orientation | GO:0048105 | 2 / 4 | 118× | 1.05e-4 | 3.22e-3 ✓ sig. |
| positive regulation of lymphangiogenesis | GO:1901492 | 2 / 4 | 118× | 1.05e-4 | 3.22e-3 ✓ sig. |
| vascular endothelial growth factor receptor signaling pathway | GO:0048010 | 3 / 31 | 22.9× | 3.00e-4 | 6.79e-3 ✓ sig. |
| Ras protein signal transduction | GO:0007265 | 4 / 79 | 12.0× | 3.49e-4 | 7.48e-3 ✓ sig. |
| Wnt signaling pathway, planar cell polarity pathway | GO:0060071 | 3 / 34 | 20.9× | 3.96e-4 | 8.12e-3 ✓ sig. |
| blood vessel morphogenesis | GO:0048514 | 3 / 34 | 20.9× | 3.96e-4 | 8.12e-3 ✓ sig. |
| host-mediated perturbation of viral process | GO:0044788 | 2 / 8 | 59.1× | 4.86e-4 | 9.30e-3 ✓ sig. |
| sprouting angiogenesis | GO:0002040 | 3 / 37 | 19.2× | 5.09e-4 | 9.61e-3 ✓ sig. |
| release of sequestered calcium ion into cytosol by sarcoplasmic reticulum | GO:0014808 | 2 / 9 | 52.6× | 6.23e-4 | 1.11e-2 ✓ sig. |
| cellular response to caffeine | GO:0071313 | 2 / 11 | 43.0× | 9.47e-4 | 1.42e-2 ✓ sig. |
| regulation of actin cytoskeleton organization | GO:0032956 | 4 / 104 | 9.1× | 9.88e-4 | 1.45e-2 ✓ sig. |
| positive regulation of protein secretion | GO:0050714 | 3 / 49 | 14.5× | 1.16e-3 | 1.59e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Lymphatic malformation | Nonimmune hydrops fetalis | 0.109 | 6 | 9.47e-13 | 1.02e-11 ✓ sig. |
| Hydrops fetalis | Nonimmune hydrops fetalis | 0.095 | 7 | 5.98e-12 | 6.13e-11 ✓ sig. |
| Hydrops fetalis | Lymphatic malformation | 0.119 | 5 | 4.07e-11 | 3.94e-10 ✓ sig. |
| Hydrops fetalis | Mucopolysaccharidosis type 7 | 0.029 | 1 | 2.13e-3 | 2.85e-3 ✓ sig. |
| Congenital malrotation of intestine | Nonimmune hydrops fetalis | 0.021 | 1 | 3.03e-3 | 3.86e-3 ✓ sig. |
| Desmosterolosis | Nonimmune hydrops fetalis | 0.021 | 1 | 3.03e-3 | 3.86e-3 ✓ sig. |
| Mucopolysaccharidosis type 7 | Nonimmune hydrops fetalis | 0.021 | 1 | 3.03e-3 | 3.86e-3 ✓ sig. |
| Nonimmune hydrops fetalis | Sulfite oxidase deficiency due to molybdenum cofactor deficiency type B2 | 0.021 | 1 | 3.03e-3 | 3.86e-3 ✓ sig. |