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 416
5
Diseases
13
Unique genes
0.275
Avg. similarity score
Neonatal diabetes mellitus with congenital hypothyroidism
Most-connected disease (4 links)
Disease
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Neonatal diabetes mellitus with congenital hypothyroidism
Interleukin 2 receptor deficiency
Neonatal diabetes-congenital hypothyroidism-congenital glaucoma-hepatic fibrosis-polycystic kidney syndrome
Periprosthetic osteolysis
immunodeficiency due to CD25 deficiency
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Neonatal diabetes mellitus with congenital hypothyroidism | 4 | 4 | 2 |
| Interleukin 2 receptor deficiency | 2 | 2 | 1 |
| Neonatal diabetes-congenital hypothyroidism-congenital glaucoma-hepatic fibrosis-polycystic kidney syndrome | 2 | 2 | 1 |
| Periprosthetic osteolysis | 2 | 2 | 12 |
| immunodeficiency due to CD25 deficiency | 2 | 2 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| GLIS3 | 3 / 5 | Neonatal diabetes mellitus with congenital hypothyroidism, Neonatal diabetes-congenital hypothyroidism-congenital glaucoma-hepatic fibrosis-polycystic kidney syndrome, Periprosthetic osteolysis |
| IL2RA | 3 / 5 | immunodeficiency due to CD25 deficiency, Interleukin 2 receptor deficiency, Neonatal diabetes mellitus with congenital hypothyroidism |
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 ⇵ |
|---|---|---|---|---|---|
| Hyaluronan biosynthesis and export | Reactome | 1 / 5 | 185× | 5.40e-3 | 4.60e-2 ✓ sig. |
| RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) | Reactome | 1 / 10 | 92.4× | 1.08e-2 | 7.19e-2 |
| Activation of Ca-permeable Kainate Receptor | Reactome | 1 / 12 | 77.0× | 1.29e-2 | 7.95e-2 |
| Interleukin-2 signaling | Reactome | 1 / 12 | 77.0× | 1.29e-2 | 7.95e-2 |
| Synthesis of IP2, IP, and Ins in the cytosol | Reactome | 1 / 12 | 77.0× | 1.29e-2 | 7.95e-2 |
| Myogenesis | Reactome | 1 / 27 | 34.2× | 2.88e-2 | 1.26e-1 |
| Interleukin receptor SHC signaling | Reactome | 1 / 27 | 34.2× | 2.88e-2 | 1.26e-1 |
| Ovarian tumor domain proteases | Reactome | 1 / 38 | 24.3× | 4.04e-2 | 1.53e-1 |
| ECM proteoglycans | Reactome | 1 / 51 | 18.1× | 5.38e-2 | 1.79e-1 |
| Endometrial cancer | KEGG | 1 / 59 | 15.7× | 6.20e-2 | 1.92e-1 |
| Inositol phosphate metabolism | KEGG | 1 / 73 | 12.7× | 7.62e-2 | 2.14e-1 |
| Bacterial invasion of epithelial cells | KEGG | 1 / 78 | 11.8× | 8.13e-2 | 2.22e-1 |
| Polycomb repressive complex | KEGG | 1 / 83 | 11.1× | 8.63e-2 | 2.29e-1 |
| Arrhythmogenic right ventricular cardiomyopathy | KEGG | 1 / 86 | 10.7× | 8.92e-2 | 2.33e-1 |
| Adherens junction | KEGG | 1 / 93 | 9.9× | 9.62e-2 | 2.43e-1 |
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 T cell tolerance induction | GO:0002664 | 1 / 1 | 1,437× | 6.96e-4 | 1.19e-2 ✓ sig. |
| growth plate cartilage chondrocyte morphogenesis | GO:0003429 | 1 / 1 | 1,437× | 6.96e-4 | 1.19e-2 ✓ sig. |
| mesoderm morphogenesis | GO:0048332 | 1 / 1 | 1,437× | 6.96e-4 | 1.19e-2 ✓ sig. |
| negative regulation of cell proliferation involved in heart morphogenesis | GO:2000137 | 1 / 1 | 1,437× | 6.96e-4 | 1.19e-2 ✓ sig. |
| limbic system development | GO:0021761 | 1 / 2 | 719× | 1.39e-3 | 1.84e-2 ✓ sig. |
| hepatoblast differentiation | GO:0061017 | 1 / 2 | 719× | 1.39e-3 | 1.84e-2 ✓ sig. |
| negative regulation of phospholipase C-activating G protein-coupled receptor signaling pathway | GO:1900737 | 1 / 2 | 719× | 1.39e-3 | 1.84e-2 ✓ sig. |
| regulation of CD4-positive, alpha-beta T cell proliferation | GO:2000561 | 1 / 2 | 719× | 1.39e-3 | 1.84e-2 ✓ sig. |
| follicle-stimulating hormone secretion | GO:0046884 | 1 / 2 | 719× | 1.39e-3 | 1.84e-2 ✓ sig. |
| ureteric peristalsis | GO:0072105 | 1 / 2 | 719× | 1.39e-3 | 1.84e-2 ✓ sig. |
| radial glia guided migration of Purkinje cell | GO:0021942 | 1 / 3 | 479× | 2.09e-3 | 2.31e-2 ✓ sig. |
| negative regulation of protein tyrosine kinase activity | GO:0061099 | 1 / 3 | 479× | 2.09e-3 | 2.31e-2 ✓ sig. |
| atrioventricular bundle cell differentiation | GO:0003167 | 1 / 3 | 479× | 2.09e-3 | 2.31e-2 ✓ sig. |
| specification of animal organ position | GO:0010159 | 1 / 3 | 479× | 2.09e-3 | 2.31e-2 ✓ sig. |
| regulation of T cell homeostatic proliferation | GO:0046013 | 1 / 3 | 479× | 2.09e-3 | 2.31e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| immunodeficiency due to CD25 deficiency | Interleukin 2 receptor deficiency | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| immunodeficiency due to CD25 deficiency | Neonatal diabetes mellitus with congenital hypothyroidism | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Interleukin 2 receptor deficiency | Neonatal diabetes mellitus with congenital hypothyroidism | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Neonatal diabetes mellitus with congenital hypothyroidism | Neonatal diabetes-congenital hypothyroidism-congenital glaucoma-hepatic fibrosis-polycystic kidney syndrome | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Neonatal diabetes-congenital hypothyroidism-congenital glaucoma-hepatic fibrosis-polycystic kidney syndrome | Periprosthetic osteolysis | 0.077 | 1 | 7.79e-4 | 1.39e-3 ✓ sig. |
| Neonatal diabetes mellitus with congenital hypothyroidism | Periprosthetic osteolysis | 0.071 | 1 | 1.56e-3 | 2.36e-3 ✓ sig. |