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 405
5
Diseases
51
Unique genes
0.096
Avg. similarity score
Galactokinase deficiency
Most-connected disease (3 links)
Disease
Searched: Ocular hypertension
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Ocular hypertension
Galactokinase deficiency
Glucocorticoid receptor deficiency/resistance
DDOST-congenital disorder of glycosylation
fructose-1,6-bisphosphatase deficiency
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Galactokinase deficiency | 3 | 3 | 4 |
| Ocular hypertension | 3 | 3 | 49 |
| Glucocorticoid receptor deficiency/resistance | 2 | 2 | 1 |
| DDOST-congenital disorder of glycosylation | 1 | 1 | 1 |
| fructose-1,6-bisphosphatase deficiency | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| NR3C1 | 3 / 5 | Galactokinase deficiency, Glucocorticoid receptor deficiency/resistance, Ocular hypertension |
| DDOST | 2 / 5 | DDOST-congenital disorder of glycosylation, Ocular hypertension |
| FBP1 | 2 / 5 | fructose-1,6-bisphosphatase deficiency, Galactokinase deficiency |
| ITGB4 | 2 / 5 | Galactokinase deficiency, Ocular hypertension |
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 GALK1 can cause Galactosemia II (GALCT2) | Reactome | 1 / 1 | 235× | 4.25e-3 | 4.04e-2 ✓ sig. |
| Defective SLC2A9 causes hypouricemia renal 2 (RHUC2) | Reactome | 1 / 1 | 235× | 4.25e-3 | 4.04e-2 ✓ sig. |
| Activation of Na-permeable kainate receptors | Reactome | 1 / 2 | 118× | 8.48e-3 | 6.37e-2 |
| Bladder cancer | KEGG | 2 / 41 | 11.5× | 1.30e-2 | 8.34e-2 |
| Transcriptional activation of cell cycle inhibitor p21 | Reactome | 1 / 4 | 58.9× | 1.69e-2 | 9.71e-2 |
| Assembly of collagen fibrils and other multimeric structures | Reactome | 2 / 51 | 9.2× | 1.97e-2 | 1.06e-1 |
| TFAP2 (AP-2) family regulates transcription of cell cycle factors | Reactome | 1 / 5 | 47.1× | 2.11e-2 | 1.10e-1 |
| PTK6 Expression | Reactome | 1 / 5 | 47.1× | 2.11e-2 | 1.10e-1 |
| Galactose catabolism | Reactome | 1 / 5 | 47.1× | 2.11e-2 | 1.10e-1 |
| p53-Dependent G1 DNA Damage Response | Reactome | 1 / 7 | 33.6× | 2.94e-2 | 1.33e-1 |
| RUNX3 regulates CDKN1A transcription | Reactome | 1 / 7 | 33.6× | 2.94e-2 | 1.33e-1 |
| Transcriptional regulation of white adipocyte differentiation | Reactome | 2 / 67 | 7.0× | 3.28e-2 | 1.41e-1 |
| Interleukin-17 signaling | Reactome | 1 / 8 | 29.4× | 3.35e-2 | 1.42e-1 |
| FOXO-mediated transcription of cell death genes | Reactome | 1 / 9 | 26.2× | 3.76e-2 | 1.51e-1 |
| PPAR signaling pathway | KEGG | 2 / 76 | 6.2× | 4.13e-2 | 1.59e-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 gluconeogenesis | GO:0006111 | 2 / 19 | 38.6× | 1.21e-3 | 1.75e-2 ✓ sig. |
| response to wounding | GO:0009611 | 3 / 81 | 13.6× | 1.41e-3 | 1.91e-2 ✓ sig. |
| myelination in peripheral nervous system | GO:0022011 | 2 / 21 | 34.9× | 1.48e-3 | 1.98e-2 ✓ sig. |
| inner ear receptor cell stereocilium organization | GO:0060122 | 2 / 25 | 29.3× | 2.10e-3 | 2.40e-2 ✓ sig. |
| vibrational conductance of sound to the inner ear | GO:0055127 | 1 / 1 | 366× | 2.73e-3 | 2.78e-2 ✓ sig. |
| intrinsic apoptotic signaling pathway in response to nitrosative stress | GO:1990442 | 1 / 1 | 366× | 2.73e-3 | 2.78e-2 ✓ sig. |
| regulation of glucocorticoid biosynthetic process | GO:0031946 | 1 / 1 | 366× | 2.73e-3 | 2.78e-2 ✓ sig. |
| nuclear receptor-mediated corticosteroid signaling pathway | GO:0031958 | 1 / 1 | 366× | 2.73e-3 | 2.78e-2 ✓ sig. |
| response to ketone | GO:1901654 | 1 / 1 | 366× | 2.73e-3 | 2.78e-2 ✓ sig. |
| negative regulation of exit from mitosis | GO:0001100 | 1 / 1 | 366× | 2.73e-3 | 2.78e-2 ✓ sig. |
| galactitol metabolic process | GO:0019402 | 1 / 1 | 366× | 2.73e-3 | 2.78e-2 ✓ sig. |
| glycolytic process from galactose | GO:0061623 | 1 / 1 | 366× | 2.73e-3 | 2.78e-2 ✓ sig. |
| skeletal muscle hypertrophy | GO:0014734 | 1 / 1 | 366× | 2.73e-3 | 2.78e-2 ✓ sig. |
| intercellular bridge organization | GO:0043063 | 1 / 1 | 366× | 2.73e-3 | 2.78e-2 ✓ sig. |
| cellular response to raffinose | GO:0097403 | 1 / 2 | 183× | 5.45e-3 | 3.93e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Galactokinase deficiency | Ocular hypertension | 0.038 | 2 | 5.93e-5 | 2.33e-4 ✓ sig. |
| fructose-1,6-bisphosphatase deficiency | Galactokinase deficiency | 0.200 | 1 | 2.60e-4 | 6.51e-4 ✓ sig. |
| Galactokinase deficiency | Glucocorticoid receptor deficiency/resistance | 0.200 | 1 | 2.60e-4 | 6.51e-4 ✓ sig. |
| DDOST-congenital disorder of glycosylation | Ocular hypertension | 0.020 | 1 | 3.18e-3 | 4.17e-3 ✓ sig. |
| Glucocorticoid receptor deficiency/resistance | Ocular hypertension | 0.020 | 1 | 3.18e-3 | 4.17e-3 ✓ sig. |