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 406
5
Diseases
2
Unique genes
0.433
Avg. similarity score
Bruton type agammaglobulinemia
Most-connected disease (4 links)
Disease
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Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Bruton type agammaglobulinemia
Bruton-type agammaglobulinemia
X-linked agammaglobulinemia
X-linked agammaglobulinemia with growth hormone deficiency
X-linked hypogammaglobulinemia
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Bruton type agammaglobulinemia | 4 | 4 | 1 |
| Bruton-type agammaglobulinemia | 4 | 4 | 1 |
| X-linked agammaglobulinemia | 4 | 4 | 1 |
| X-linked agammaglobulinemia with growth hormone deficiency | 4 | 4 | 2 |
| X-linked hypogammaglobulinemia | 4 | 4 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| BTK | 5 / 5 | Bruton type agammaglobulinemia, Bruton-type agammaglobulinemia, X-linked agammaglobulinemia, X-linked agammaglobulinemia with growth hormone deficiency 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 ⇵ |
|---|---|---|---|---|---|
| MyD88 deficiency (TLR2/4) | Reactome | 1 / 10 | 601× | 1.66e-3 | 2.00e-2 ✓ sig. |
| IRAK4 deficiency (TLR2/4) | Reactome | 1 / 11 | 546× | 1.83e-3 | 2.14e-2 ✓ sig. |
| G beta:gamma signalling through BTK | Reactome | 1 / 18 | 334× | 3.00e-3 | 3.07e-2 ✓ sig. |
| MyD88:MAL(TIRAP) cascade initiated on plasma membrane | Reactome | 1 / 19 | 316× | 3.16e-3 | 3.20e-2 ✓ sig. |
| Antigen activates B Cell Receptor (BCR) leading to generation of second messengers | Reactome | 1 / 23 | 261× | 3.83e-3 | 3.65e-2 ✓ sig. |
| FCERI mediated Ca+2 mobilization | Reactome | 1 / 29 | 207× | 4.82e-3 | 4.28e-2 ✓ sig. |
| DAP12 signaling | Reactome | 1 / 30 | 200× | 4.99e-3 | 4.37e-2 ✓ sig. |
| ER-Phagosome pathway | Reactome | 1 / 30 | 200× | 4.99e-3 | 4.37e-2 ✓ sig. |
| RHO GTPases Activate WASPs and WAVEs | Reactome | 1 / 36 | 167× | 5.99e-3 | 4.93e-2 ✓ sig. |
| Primary immunodeficiency | KEGG | 1 / 38 | 158× | 6.32e-3 | 5.11e-2 |
| FCGR3A-mediated phagocytosis | Reactome | 1 / 59 | 102× | 9.80e-3 | 6.78e-2 |
| Regulation of actin dynamics for phagocytic cup formation | Reactome | 1 / 60 | 100× | 9.97e-3 | 6.82e-2 |
| Fc epsilon RI signaling pathway | KEGG | 1 / 69 | 87.0× | 1.15e-2 | 7.45e-2 |
| G alpha (12/13) signalling events | Reactome | 1 / 80 | 75.1× | 1.33e-2 | 8.08e-2 |
| B cell receptor signaling pathway | KEGG | 1 / 91 | 66.0× | 1.51e-2 | 8.72e-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 B cell cytokine production | GO:0002721 | 1 / 1 | 9,344× | 1.07e-4 | 3.18e-3 ✓ sig. |
| monocyte proliferation | GO:0061516 | 1 / 1 | 9,344× | 1.07e-4 | 3.18e-3 ✓ sig. |
| positive regulation of interleukin-17A production | GO:0150153 | 1 / 1 | 9,344× | 1.07e-4 | 3.18e-3 ✓ sig. |
| positive regulation of type I hypersensitivity | GO:0001812 | 1 / 2 | 4,672× | 2.14e-4 | 5.28e-3 ✓ sig. |
| B cell affinity maturation | GO:0002344 | 1 / 2 | 4,672× | 2.14e-4 | 5.28e-3 ✓ sig. |
| regulation of B cell apoptotic process | GO:0002902 | 1 / 2 | 4,672× | 2.14e-4 | 5.28e-3 ✓ sig. |
| proteoglycan catabolic process | GO:0030167 | 1 / 3 | 3,115× | 3.21e-4 | 7.03e-3 ✓ sig. |
| positive regulation of type III hypersensitivity | GO:0001805 | 1 / 3 | 3,115× | 3.21e-4 | 7.03e-3 ✓ sig. |
| NK T cell proliferation | GO:0001866 | 1 / 3 | 3,115× | 3.21e-4 | 7.03e-3 ✓ sig. |
| negative regulation of leukocyte proliferation | GO:0070664 | 1 / 3 | 3,115× | 3.21e-4 | 7.03e-3 ✓ sig. |
| eosinophil homeostasis | GO:1990959 | 1 / 3 | 3,115× | 3.21e-4 | 7.03e-3 ✓ sig. |
| cellular response to molecule of fungal origin | GO:0071226 | 1 / 4 | 2,336× | 4.28e-4 | 8.59e-3 ✓ sig. |
| positive regulation of synoviocyte proliferation | GO:1901647 | 1 / 4 | 2,336× | 4.28e-4 | 8.59e-3 ✓ sig. |
| natural killer cell proliferation | GO:0001787 | 1 / 5 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| histamine secretion by mast cell | GO:0002553 | 1 / 5 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |