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 264
7
Diseases
6
Unique genes
0.290
Avg. similarity score
Immune dysregulation-inflammatory bowel disease-arthritis-recurrent infection syndrome
Most-connected disease (6 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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Immune dysregulation-inflammatory bowel disease-arthritis-recurrent infection syndrome
Autoinflammation with infantile enterocolitis
Cria syndrome
Immune dysregulation-inflammatory bowel disease-arthritis-recurrent infection-lymphopenia syndrome
immunodeficiency 57
inflammatory bowel disease 25
inflammatory bowel disease 28
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Immune dysregulation-inflammatory bowel disease-arthritis-recurrent infection syndrome | 6 | 6 | 5 |
| Autoinflammation with infantile enterocolitis | 4 | 4 | 2 |
| Cria syndrome | 4 | 4 | 1 |
| Immune dysregulation-inflammatory bowel disease-arthritis-recurrent infection-lymphopenia syndrome | 4 | 4 | 1 |
| immunodeficiency 57 | 4 | 4 | 1 |
| inflammatory bowel disease 25 | 1 | 1 | 1 |
| inflammatory bowel disease 28 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| RIPK1 | 5 / 7 | Autoinflammation with infantile enterocolitis, Cria syndrome, Immune dysregulation-inflammatory bowel disease-arthritis-recurrent infection syndrome, Immune dysregulation-inflammatory bowel disease-arthritis-recurrent infection-lymphopenia syndrome and 1 more |
| IL10RA | 2 / 7 | Immune dysregulation-inflammatory bowel disease-arthritis-recurrent infection syndrome, inflammatory bowel disease 28 |
| IL10RB | 2 / 7 | Immune dysregulation-inflammatory bowel disease-arthritis-recurrent infection syndrome, inflammatory bowel disease 25 |
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 ⇵ |
|---|---|---|---|---|---|
| Toxoplasmosis | KEGG | 4 / 112 | 71.5× | 1.06e-7 | 6.89e-6 ✓ sig. |
| Tuberculosis | KEGG | 4 / 181 | 44.2× | 7.31e-7 | 3.71e-5 ✓ sig. |
| Interleukin-10 signaling | Reactome | 3 / 47 | 128× | 1.11e-6 | 5.37e-5 ✓ sig. |
| Cytokine-cytokine receptor interaction | KEGG | 4 / 298 | 26.9× | 5.36e-6 | 2.01e-4 ✓ sig. |
| Viral protein interaction with cytokine and cytokine receptor | KEGG | 3 / 100 | 60.1× | 1.10e-5 | 3.63e-4 ✓ sig. |
| JAK-STAT signaling pathway | KEGG | 3 / 168 | 35.7× | 5.21e-5 | 1.32e-3 ✓ sig. |
| Human cytomegalovirus infection | KEGG | 3 / 226 | 26.6× | 1.26e-4 | 2.70e-3 ✓ sig. |
| Intestinal immune network for IgA production | KEGG | 2 / 50 | 80.1× | 2.52e-4 | 4.68e-3 ✓ sig. |
| Malaria | KEGG | 2 / 50 | 80.1× | 2.52e-4 | 4.68e-3 ✓ sig. |
| Inflammatory bowel disease | KEGG | 2 / 66 | 60.7× | 4.40e-4 | 7.21e-3 ✓ sig. |
| Leishmaniasis | KEGG | 2 / 78 | 51.3× | 6.14e-4 | 9.37e-3 ✓ sig. |
| Influenza Virus Induced Apoptosis | Reactome | 1 / 2 | 1,001× | 9.99e-4 | 1.35e-2 ✓ sig. |
| The IPAF inflammasome | Reactome | 1 / 2 | 1,001× | 9.99e-4 | 1.35e-2 ✓ sig. |
| TGFBR2 MSI Frameshift Mutants in Cancer | Reactome | 1 / 2 | 1,001× | 9.99e-4 | 1.35e-2 ✓ sig. |
| Chagas disease | KEGG | 2 / 103 | 38.9× | 1.07e-3 | 1.43e-2 ✓ 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 ⇵ |
|---|---|---|---|---|---|
| interleukin-10-mediated signaling pathway | GO:0140105 | 3 / 12 | 779× | 4.04e-9 | 7.71e-7 ✓ sig. |
| positive regulation of receptor signaling pathway via JAK-STAT | GO:0046427 | 3 / 40 | 234× | 1.81e-7 | 1.99e-5 ✓ sig. |
| positive regulation of inflammatory response | GO:0050729 | 3 / 122 | 76.6× | 5.35e-6 | 3.17e-4 ✓ sig. |
| inflammatory response | GO:0006954 | 4 / 467 | 26.7× | 5.55e-6 | 3.26e-4 ✓ sig. |
| liver regeneration | GO:0097421 | 2 / 29 | 215× | 3.47e-5 | 1.37e-3 ✓ sig. |
| regulation of synapse organization | GO:0050807 | 2 / 30 | 208× | 3.72e-5 | 1.44e-3 ✓ sig. |
| positive regulation of apoptotic process | GO:0043065 | 3 / 326 | 28.7× | 1.01e-4 | 3.05e-3 ✓ sig. |
| negative regulation of T cell proliferation | GO:0042130 | 2 / 51 | 122× | 1.09e-4 | 3.22e-3 ✓ sig. |
| positive regulation of miRNA transcription | GO:1902895 | 2 / 56 | 111× | 1.31e-4 | 3.71e-3 ✓ sig. |
| extrinsic apoptotic signaling pathway | GO:0097191 | 2 / 57 | 109× | 1.36e-4 | 3.80e-3 ✓ sig. |
| negative regulation of autophagy | GO:0010507 | 2 / 73 | 85.3× | 2.24e-4 | 5.45e-3 ✓ sig. |
| cellular response to growth factor stimulus | GO:0071363 | 2 / 76 | 82.0× | 2.42e-4 | 5.78e-3 ✓ sig. |
| positive regulation of NF-kappaB transcription factor activity | GO:0051092 | 2 / 80 | 77.9× | 2.68e-4 | 6.21e-3 ✓ sig. |
| negative regulation of chronic inflammatory response to antigenic stimulus | GO:0002875 | 1 / 1 | 3,115× | 3.21e-4 | 7.03e-3 ✓ sig. |
| negative regulation of cytokine activity | GO:0060302 | 1 / 1 | 3,115× | 3.21e-4 | 7.03e-3 ✓ sig. |