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 383
5
Diseases
32
Unique genes
0.143
Avg. similarity score
Middle ear cholesteatoma
Most-connected disease (3 links)
Disease
Searched: IL21-related infantile inflammatory bowel disease
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IL21-related infantile inflammatory bowel disease
Middle ear cholesteatoma
Cholesteatoma
Progressive supranuclear palsy
Vaginal neoplasms
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Middle ear cholesteatoma | 3 | 3 | 1 |
| Cholesteatoma | 2 | 2 | 5 |
| Progressive supranuclear palsy | 2 | 2 | 27 |
| Vaginal neoplasms | 2 | 2 | 2 |
| IL21-related infantile inflammatory bowel disease | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| IL2 | 4 / 5 | Cholesteatoma, Middle ear cholesteatoma, Progressive supranuclear palsy, Vaginal neoplasms |
| IL21 | 2 / 5 | IL21-related infantile inflammatory bowel disease, Progressive supranuclear palsy |
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 ⇵ |
|---|---|---|---|---|---|
| Defective HK1 causes hexokinase deficiency (HK deficiency) | Reactome | 1 / 1 | 375× | 2.66e-3 | 2.82e-2 ✓ sig. |
| Th17 cell differentiation | KEGG | 3 / 109 | 10.3× | 2.98e-3 | 3.05e-2 ✓ sig. |
| Acetylation | Reactome | 1 / 2 | 188× | 5.32e-3 | 4.56e-2 ✓ sig. |
| Inositol transporters | Reactome | 1 / 2 | 188× | 5.32e-3 | 4.56e-2 ✓ sig. |
| Activation of gene expression by SREBF (SREBP) | Reactome | 2 / 42 | 17.9× | 5.54e-3 | 4.69e-2 ✓ sig. |
| Yersinia infection | KEGG | 3 / 138 | 8.2× | 5.77e-3 | 4.82e-2 ✓ sig. |
| Measles | KEGG | 3 / 139 | 8.1× | 5.89e-3 | 4.89e-2 ✓ sig. |
| Alcoholic liver disease | KEGG | 3 / 144 | 7.8× | 6.49e-3 | 5.22e-2 |
| RUNX2 regulates osteoblast differentiation | Reactome | 1 / 3 | 125× | 7.97e-3 | 5.98e-2 |
| Autoimmune thyroid disease | KEGG | 2 / 54 | 13.9× | 9.03e-3 | 6.49e-2 |
| JAK-STAT signaling pathway | KEGG | 3 / 168 | 6.7× | 9.90e-3 | 6.89e-2 |
| RUNX2 regulates genes involved in differentiation of myeloid cells | Reactome | 1 / 4 | 93.8× | 1.06e-2 | 7.20e-2 |
| Herpes simplex virus 1 infection | KEGG | 3 / 182 | 6.2× | 1.23e-2 | 7.89e-2 |
| Neomycin, kanamycin and gentamicin biosynthesis | KEGG | 1 / 5 | 75.1× | 1.33e-2 | 8.23e-2 |
| PERK regulates gene expression | Reactome | 1 / 5 | 75.1× | 1.33e-2 | 8.23e-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 ⇵ |
|---|---|---|---|---|---|
| positive regulation of tissue remodeling | GO:0034105 | 2 / 6 | 195× | 4.24e-5 | 1.60e-3 ✓ sig. |
| positive regulation of amyloid-beta formation | GO:1902004 | 2 / 21 | 55.6× | 5.85e-4 | 1.07e-2 ✓ sig. |
| chondrocyte development | GO:0002063 | 2 / 21 | 55.6× | 5.85e-4 | 1.07e-2 ✓ sig. |
| positive regulation of interleukin-17 production | GO:0032740 | 2 / 27 | 43.3× | 9.71e-4 | 1.49e-2 ✓ sig. |
| positive regulation of immunoglobulin production | GO:0002639 | 2 / 33 | 35.4× | 1.45e-3 | 1.90e-2 ✓ sig. |
| plus-end-directed organelle transport along microtubule | GO:0072386 | 1 / 1 | 584× | 1.71e-3 | 2.10e-2 ✓ sig. |
| ligamentous ossification | GO:0036076 | 1 / 1 | 584× | 1.71e-3 | 2.10e-2 ✓ sig. |
| positive regulation of cell fate determination | GO:1905935 | 1 / 1 | 584× | 1.71e-3 | 2.10e-2 ✓ sig. |
| cellular response to wortmannin | GO:1904568 | 1 / 1 | 584× | 1.71e-3 | 2.10e-2 ✓ sig. |
| positive regulation of hydrogen sulfide biosynthetic process | GO:1904828 | 1 / 1 | 584× | 1.71e-3 | 2.10e-2 ✓ sig. |
| cell maturation | GO:0048469 | 2 / 37 | 31.6× | 1.82e-3 | 2.18e-2 ✓ sig. |
| positive regulation of cell population proliferation | GO:0008284 | 5 / 532 | 5.5× | 1.96e-3 | 2.26e-2 ✓ sig. |
| positive regulation of interleukin-10 production | GO:0032733 | 2 / 43 | 27.2× | 2.46e-3 | 2.58e-2 ✓ sig. |
| positive regulation of B cell proliferation | GO:0030890 | 2 / 47 | 24.8× | 2.93e-3 | 2.84e-2 ✓ sig. |
| neurofibrillary tangle assembly | GO:1902988 | 1 / 2 | 292× | 3.42e-3 | 3.08e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Middle ear cholesteatoma | Vaginal neoplasms | 0.333 | 1 | 1.30e-4 | 3.93e-4 ✓ sig. |
| Cholesteatoma | Middle ear cholesteatoma | 0.167 | 1 | 3.25e-4 | 7.70e-4 ✓ sig. |
| Cholesteatoma | Vaginal neoplasms | 0.143 | 1 | 6.49e-4 | 1.24e-3 ✓ sig. |
| IL21-related infantile inflammatory bowel disease | Progressive supranuclear palsy | 0.036 | 1 | 1.75e-3 | 2.61e-3 ✓ sig. |
| Middle ear cholesteatoma | Progressive supranuclear palsy | 0.036 | 1 | 1.75e-3 | 2.61e-3 ✓ sig. |