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 436
6
Diseases
5
Unique genes
0.222
Avg. similarity score
Isolated igg subclass deficiency
Most-connected disease (5 links)
Disease
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Isolated igg subclass deficiency
Antibody deficiency
Immunodeficiency, common variable, 3
Combined immunodeficiency with recurrent sinopulmonary infections and recalcitrant warts
Immunodeficiency, common variable, 4
Immunodeficiency, common variable, 6
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Isolated igg subclass deficiency | 5 | 5 | 5 |
| Antibody deficiency | 2 | 2 | 1 |
| Immunodeficiency, common variable, 3 | 2 | 2 | 1 |
| Combined immunodeficiency with recurrent sinopulmonary infections and recalcitrant warts | 1 | 1 | 1 |
| Immunodeficiency, common variable, 4 | 1 | 1 | 1 |
| Immunodeficiency, common variable, 6 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| CD19 | 3 / 6 | Antibody deficiency, Immunodeficiency, common variable, 3, Isolated igg subclass deficiency |
| CD81 | 2 / 6 | Immunodeficiency, common variable, 6, Isolated igg subclass deficiency |
| ICOS | 2 / 6 | Combined immunodeficiency with recurrent sinopulmonary infections and recalcitrant warts, Isolated igg subclass deficiency |
| TNFRSF13C | 2 / 6 | Immunodeficiency, common variable, 4, Isolated igg subclass deficiency |
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 ⇵ |
|---|---|---|---|---|---|
| Primary immunodeficiency | KEGG | 3 / 38 | 190× | 2.91e-7 | 1.42e-5 ✓ sig. |
| Regulation of Complement cascade | Reactome | 3 / 47 | 153× | 5.59e-7 | 2.51e-5 ✓ sig. |
| B cell receptor signaling pathway | KEGG | 3 / 91 | 79.2× | 4.16e-6 | 1.41e-4 ✓ sig. |
| Intestinal immune network for IgA production | KEGG | 2 / 50 | 96.1× | 1.69e-4 | 2.87e-3 ✓ sig. |
| Constitutive Signaling by Aberrant PI3K in Cancer | Reactome | 2 / 75 | 64.1× | 3.80e-4 | 5.40e-3 ✓ sig. |
| PIP3 activates AKT signaling | Reactome | 2 / 93 | 51.7× | 5.84e-4 | 7.53e-3 ✓ sig. |
| Hematopoietic cell lineage | KEGG | 2 / 100 | 48.0× | 6.75e-4 | 8.40e-3 ✓ sig. |
| PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling | Reactome | 2 / 103 | 46.6× | 7.16e-4 | 8.80e-3 ✓ sig. |
| Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | Reactome | 2 / 130 | 37.0× | 1.14e-3 | 1.25e-2 ✓ sig. |
| Epstein-Barr virus infection | KEGG | 2 / 204 | 23.5× | 2.78e-3 | 2.41e-2 ✓ sig. |
| Costimulation by the CD28 family | Reactome | 1 / 11 | 218× | 4.57e-3 | 3.44e-2 ✓ sig. |
| TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway | Reactome | 1 / 18 | 133× | 7.47e-3 | 4.73e-2 ✓ sig. |
| Antigen activates B Cell Receptor (BCR) leading to generation of second messengers | Reactome | 1 / 23 | 104× | 9.54e-3 | 5.53e-2 |
| Virion - Hepatitis viruses | KEGG | 1 / 48 | 50.0× | 1.98e-2 | 8.52e-2 |
| Malaria | KEGG | 1 / 50 | 48.0× | 2.06e-2 | 8.75e-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 ⇵ |
|---|---|---|---|---|---|
| immune system process | GO:0002376 | 4 / 943 | 15.9× | 3.09e-5 | 1.28e-3 ✓ sig. |
| B cell proliferation | GO:0042100 | 2 / 38 | 197× | 4.01e-5 | 1.56e-3 ✓ sig. |
| T cell costimulation | GO:0031295 | 2 / 45 | 166× | 5.64e-5 | 2.02e-3 ✓ sig. |
| positive regulation of B cell proliferation | GO:0030890 | 2 / 47 | 159× | 6.16e-5 | 2.16e-3 ✓ sig. |
| adaptive immune response | GO:0002250 | 3 / 507 | 22.1× | 1.91e-4 | 4.92e-3 ✓ sig. |
| macrophage fusion | GO:0034238 | 1 / 1 | 3,737× | 2.68e-4 | 6.25e-3 ✓ sig. |
| CD4-positive, alpha-beta T cell costimulation | GO:0035783 | 1 / 1 | 3,737× | 2.68e-4 | 6.25e-3 ✓ sig. |
| positive regulation of adaptive immune memory response | GO:1905676 | 1 / 1 | 3,737× | 2.68e-4 | 6.25e-3 ✓ sig. |
| symbiont entry into host cell | GO:0046718 | 2 / 112 | 66.7× | 3.52e-4 | 7.52e-3 ✓ sig. |
| T cell tolerance induction | GO:0002517 | 1 / 2 | 1,869× | 5.35e-4 | 9.88e-3 ✓ sig. |
| B-1 B cell differentiation | GO:0001923 | 1 / 2 | 1,869× | 5.35e-4 | 9.88e-3 ✓ sig. |
| positive regulation of receptor clustering | GO:1903911 | 1 / 2 | 1,869× | 5.35e-4 | 9.88e-3 ✓ sig. |
| positive regulation of protein catabolic process in the vacuole | GO:1904352 | 1 / 2 | 1,869× | 5.35e-4 | 9.88e-3 ✓ sig. |
| positive regulation of inflammatory response to antigenic stimulus | GO:0002863 | 1 / 3 | 1,246× | 8.03e-4 | 1.28e-2 ✓ sig. |
| B cell costimulation | GO:0031296 | 1 / 3 | 1,246× | 8.03e-4 | 1.28e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Antibody deficiency | Immunodeficiency, common variable, 3 | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Antibody deficiency | Isolated igg subclass deficiency | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |
| Combined immunodeficiency with recurrent sinopulmonary infections and recalcitrant warts | Isolated igg subclass deficiency | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |
| Immunodeficiency, common variable, 3 | Isolated igg subclass deficiency | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |
| Immunodeficiency, common variable, 4 | Isolated igg subclass deficiency | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |
| Immunodeficiency, common variable, 6 | Isolated igg subclass deficiency | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |