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 204
8
Diseases
9
Unique genes
0.301
Avg. similarity score
Cervical dysplasia
Most-connected disease (6 links)
Disease
Searched: homocystinuria due to methylene tetrahydrofolate reductase deficiency
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homocystinuria due to methylene tetrahydrofolate reductase deficiency
Cervical dysplasia
Uterine disease
Microvascular angina
Portal vein thrombosis
Ataxia with intention tremor and hypotonia
Cerebellar dysfunction with variable cognitive and behavioral abnormalities
Congenital plasminogen activator inhibitor deficiency type 1
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Cervical dysplasia | 6 | 6 | 2 |
| Uterine disease | 5 | 5 | 2 |
| Microvascular angina | 4 | 4 | 1 |
| Portal vein thrombosis | 4 | 4 | 3 |
| homocystinuria due to methylene tetrahydrofolate reductase deficiency | 4 | 4 | 1 |
| Ataxia with intention tremor and hypotonia | 3 | 3 | 1 |
| Cerebellar dysfunction with variable cognitive and behavioral abnormalities | 3 | 3 | 6 |
| Congenital plasminogen activator inhibitor deficiency type 1 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| MTHFR | 5 / 8 | Cervical dysplasia, homocystinuria due to methylene tetrahydrofolate reductase deficiency, Microvascular angina, Portal vein thrombosis and 1 more |
| POU4F1 | 4 / 8 | Ataxia with intention tremor and hypotonia, Cerebellar dysfunction with variable cognitive and behavioral abnormalities, Cervical dysplasia, Uterine disease |
| SERPINE1 | 2 / 8 | Congenital plasminogen activator inhibitor deficiency type 1, Portal vein thrombosis |
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 ⇵ |
|---|---|---|---|---|---|
| HIF-1 signaling pathway | KEGG | 2 / 110 | 24.3× | 2.87e-3 | 3.06e-2 ✓ sig. |
| Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) | Reactome | 1 / 4 | 334× | 2.99e-3 | 3.15e-2 ✓ sig. |
| SHC-related events triggered by IGF1R | Reactome | 1 / 6 | 222× | 4.49e-3 | 4.21e-2 ✓ sig. |
| IRS-related events triggered by IGF1R | Reactome | 1 / 6 | 222× | 4.49e-3 | 4.21e-2 ✓ sig. |
| Apelin signaling pathway | KEGG | 2 / 140 | 19.1× | 4.60e-3 | 4.28e-2 ✓ sig. |
| BMAL1:CLOCK,NPAS2 activates circadian gene expression | Reactome | 1 / 7 | 191× | 5.24e-3 | 4.67e-2 ✓ sig. |
| Sodium/Proton exchangers | Reactome | 1 / 9 | 148× | 6.73e-3 | 5.51e-2 |
| Hyaluronan uptake and degradation | Reactome | 1 / 12 | 111× | 8.96e-3 | 6.62e-2 |
| Proteoglycans in cancer | KEGG | 2 / 204 | 13.1× | 9.56e-3 | 6.89e-2 |
| Dissolution of Fibrin Clot | Reactome | 1 / 13 | 103× | 9.70e-3 | 6.96e-2 |
| Regulation of TP53 Activity through Association with Co-factors | Reactome | 1 / 14 | 95.3× | 1.04e-2 | 7.29e-2 |
| Metabolism of folate and pterines | Reactome | 1 / 17 | 78.5× | 1.27e-2 | 8.19e-2 |
| Laminin interactions | Reactome | 1 / 28 | 47.7× | 2.08e-2 | 1.09e-1 |
| Antifolate resistance | KEGG | 1 / 30 | 44.5× | 2.23e-2 | 1.14e-1 |
| Folate transport and metabolism | KEGG | 1 / 31 | 43.0× | 2.30e-2 | 1.16e-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 ⇵ |
|---|---|---|---|---|---|
| heterochromatin organization | GO:0070828 | 2 / 10 | 415× | 9.26e-6 | 5.10e-4 ✓ sig. |
| positive regulation of calcineurin-NFAT signaling cascade | GO:0070886 | 2 / 21 | 198× | 4.31e-5 | 1.66e-3 ✓ sig. |
| positive regulation of transcription by RNA polymerase II | GO:0045944 | 5 / 1,208 | 8.6× | 1.13e-4 | 3.43e-3 ✓ sig. |
| positive regulation of leukotriene production involved in inflammatory response | GO:0035491 | 1 / 1 | 2,076× | 4.82e-4 | 9.61e-3 ✓ sig. |
| peripheral nervous system neuron differentiation | GO:0048934 | 1 / 1 | 2,076× | 4.82e-4 | 9.61e-3 ✓ sig. |
| proprioception involved in equilibrioception | GO:0051355 | 1 / 1 | 2,076× | 4.82e-4 | 9.61e-3 ✓ sig. |
| response to vitamin B2 | GO:0033274 | 1 / 2 | 1,038× | 9.63e-4 | 1.52e-2 ✓ sig. |
| negative regulation of smooth muscle cell-matrix adhesion | GO:2000098 | 1 / 2 | 1,038× | 9.63e-4 | 1.52e-2 ✓ sig. |
| regulation of the force of heart contraction by cardiac conduction | GO:0086092 | 1 / 2 | 1,038× | 9.63e-4 | 1.52e-2 ✓ sig. |
| positive regulation of cold-induced thermogenesis | GO:0120162 | 2 / 102 | 40.7× | 1.04e-3 | 1.60e-2 ✓ sig. |
| positive regulation of mitochondrial membrane permeability | GO:0035794 | 1 / 3 | 692× | 1.44e-3 | 1.94e-2 ✓ sig. |
| habenula development | GO:0021986 | 1 / 3 | 692× | 1.44e-3 | 1.94e-2 ✓ sig. |
| sensory system development | GO:0048880 | 1 / 3 | 692× | 1.44e-3 | 1.94e-2 ✓ sig. |
| cell migration in hindbrain | GO:0021535 | 1 / 3 | 692× | 1.44e-3 | 1.94e-2 ✓ sig. |
| negative regulation of apoptotic process | GO:0043066 | 3 / 524 | 11.9× | 1.62e-3 | 2.07e-2 ✓ sig. |