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 638
5
Diseases
2
Unique genes
0.433
Avg. similarity score
Immunodeficiency 73a with defective neutrophil chemotaxis and leukocytosis
Most-connected disease (4 links)
Disease
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Immunodeficiency 73a with defective neutrophil chemotaxis and leukocytosis
Immunodeficiency 73b with defective neutrophil chemotaxis and lymphopenia
Immunodeficiency 73c with defective neutrophil chemotaxis and hypogammaglobulinemia
Neutrophil immunodeficiency syndrome
Reticular dysgenesis
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Immunodeficiency 73a with defective neutrophil chemotaxis and leukocytosis | 4 | 4 | 1 |
| Immunodeficiency 73b with defective neutrophil chemotaxis and lymphopenia | 4 | 4 | 1 |
| Immunodeficiency 73c with defective neutrophil chemotaxis and hypogammaglobulinemia | 4 | 4 | 1 |
| Neutrophil immunodeficiency syndrome | 4 | 4 | 1 |
| Reticular dysgenesis | 4 | 4 | 2 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| RAC2 | 5 / 5 | Immunodeficiency 73a with defective neutrophil chemotaxis and leukocytosis, Immunodeficiency 73b with defective neutrophil chemotaxis and lymphopenia, Immunodeficiency 73c with defective neutrophil chemotaxis and hypogammaglobulinemia, Neutrophil immunodeficiency syndrome and 1 more |
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 ⇵ |
|---|---|---|---|---|---|
| Thiamine metabolism | KEGG | 1 / 15 | 400× | 2.50e-3 | 2.23e-2 ✓ sig. |
| PCP/CE pathway | Reactome | 1 / 18 | 334× | 3.00e-3 | 2.54e-2 ✓ sig. |
| RHO GTPases Activate NADPH Oxidases | Reactome | 1 / 24 | 250× | 3.99e-3 | 3.12e-2 ✓ sig. |
| Interconversion of nucleotide di- and triphosphates | Reactome | 1 / 29 | 207× | 4.82e-3 | 3.57e-2 ✓ sig. |
| ROS and RNS production in phagocytes | Reactome | 1 / 34 | 177× | 5.65e-3 | 3.96e-2 ✓ sig. |
| GPVI-mediated activation cascade | Reactome | 1 / 34 | 177× | 5.65e-3 | 3.96e-2 ✓ sig. |
| VEGF signaling pathway | KEGG | 1 / 60 | 100× | 9.97e-3 | 5.67e-2 |
| Fc epsilon RI signaling pathway | KEGG | 1 / 69 | 87.0× | 1.15e-2 | 6.18e-2 |
| Viral myocarditis | KEGG | 1 / 70 | 85.8× | 1.16e-2 | 6.22e-2 |
| Constitutive Signaling by Aberrant PI3K in Cancer | Reactome | 1 / 75 | 80.1× | 1.25e-2 | 6.50e-2 |
| Pancreatic cancer | KEGG | 1 / 77 | 78.0× | 1.28e-2 | 6.58e-2 |
| Nucleotide metabolism | KEGG | 1 / 85 | 70.6× | 1.41e-2 | 7.00e-2 |
| Colorectal cancer | KEGG | 1 / 87 | 69.0× | 1.44e-2 | 7.10e-2 |
| B cell receptor signaling pathway | KEGG | 1 / 91 | 66.0× | 1.51e-2 | 7.28e-2 |
| Adherens junction | KEGG | 1 / 93 | 64.6× | 1.54e-2 | 7.39e-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 ⇵ |
|---|---|---|---|---|---|
| regulation of mast cell chemotaxis | GO:0060753 | 1 / 1 | 9,344× | 1.07e-4 | 3.25e-3 ✓ sig. |
| lymphocyte aggregation | GO:0071593 | 1 / 3 | 3,115× | 3.21e-4 | 7.04e-3 ✓ sig. |
| regulation of respiratory burst | GO:0060263 | 1 / 4 | 2,336× | 4.28e-4 | 8.53e-3 ✓ sig. |
| regulation of neutrophil migration | GO:1902622 | 1 / 4 | 2,336× | 4.28e-4 | 8.53e-3 ✓ sig. |
| mast cell proliferation | GO:0070662 | 1 / 5 | 1,869× | 5.35e-4 | 9.88e-3 ✓ sig. |
| erythrocyte enucleation | GO:0043131 | 1 / 5 | 1,869× | 5.35e-4 | 9.88e-3 ✓ sig. |
| ADP biosynthetic process | GO:0006172 | 1 / 5 | 1,869× | 5.35e-4 | 9.88e-3 ✓ sig. |
| positive regulation of mast cell proliferation | GO:0070668 | 1 / 5 | 1,869× | 5.35e-4 | 9.88e-3 ✓ sig. |
| regulation of hydrogen peroxide metabolic process | GO:0010310 | 1 / 6 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| nucleoside monophosphate metabolic process | GO:0009123 | 1 / 6 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| AMP metabolic process | GO:0046033 | 1 / 7 | 1,335× | 7.49e-4 | 1.23e-2 ✓ sig. |
| regulation of cell-substrate adhesion | GO:0010810 | 1 / 8 | 1,168× | 8.56e-4 | 1.33e-2 ✓ sig. |
| nucleobase-containing small molecule interconversion | GO:0015949 | 1 / 8 | 1,168× | 8.56e-4 | 1.33e-2 ✓ sig. |
| regulation of mast cell degranulation | GO:0043304 | 1 / 8 | 1,168× | 8.56e-4 | 1.33e-2 ✓ sig. |
| cortical cytoskeleton organization | GO:0030865 | 1 / 10 | 934× | 1.07e-3 | 1.51e-2 ✓ sig. |