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 255
7
Diseases
8
Unique genes
0.187
Avg. similarity score
Immune system disorder
Most-connected disease (6 links)
Disease
Searched: macrothrombocytopenia, isolated
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macrothrombocytopenia, isolated
Immune system disorder
Colonic polyps
Parkinson-dementia complex of guam
Anterior cruciate ligament injury
Arginase deficiency
pulmonary veno-occlusive disease and/or pulmonary capillary haemangiomatosis
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Immune system disorder | 6 | 6 | 5 |
| Colonic polyps | 3 | 3 | 2 |
| Parkinson-dementia complex of guam | 3 | 3 | 2 |
| macrothrombocytopenia, isolated | 3 | 3 | 2 |
| Anterior cruciate ligament injury | 1 | 1 | 1 |
| Arginase deficiency | 1 | 1 | 1 |
| pulmonary veno-occlusive disease and/or pulmonary capillary haemangiomatosis | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| TRPM7 | 4 / 7 | Colonic polyps, Immune system disorder, macrothrombocytopenia, isolated, Parkinson-dementia complex of guam |
| ARG1 | 2 / 7 | Arginase deficiency, Immune system disorder |
| CNR2 | 2 / 7 | Anterior cruciate ligament injury, Immune system disorder |
| EIF2AK4 | 2 / 7 | Immune system disorder, pulmonary veno-occlusive disease and/or pulmonary capillary haemangiomatosis |
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 GNE causes sialuria, Nonaka myopathy and inclusion body myopathy 2 | Reactome | 1 / 1 | 1,501× | 6.66e-4 | 1.03e-2 ✓ sig. |
| Defective ACTH causes Obesity and Pro-opiomelanocortinin deficiency (POMCD) | Reactome | 1 / 2 | 751× | 1.33e-3 | 1.75e-2 ✓ sig. |
| Peptide hormone biosynthesis | Reactome | 1 / 2 | 751× | 1.33e-3 | 1.75e-2 ✓ sig. |
| Opioid Signalling | Reactome | 1 / 3 | 500× | 2.00e-3 | 2.36e-2 ✓ sig. |
| Localization of the PINCH-ILK-PARVIN complex to focal adhesions | Reactome | 1 / 4 | 375× | 2.66e-3 | 2.91e-2 ✓ sig. |
| Urea cycle | Reactome | 1 / 10 | 150× | 6.64e-3 | 5.47e-2 |
| Glucocorticoid biosynthesis | Reactome | 1 / 10 | 150× | 6.64e-3 | 5.47e-2 |
| Androgen biosynthesis | Reactome | 1 / 11 | 136× | 7.31e-3 | 5.81e-2 |
| Cell-extracellular matrix interactions | Reactome | 1 / 12 | 125× | 7.97e-3 | 6.13e-2 |
| Biosynthesis of various nucleotide sugars | KEGG | 1 / 15 | 100× | 9.95e-3 | 7.05e-2 |
| G alpha (i) signalling events | Reactome | 2 / 249 | 12.1× | 1.10e-2 | 7.53e-2 |
| Class A/1 (Rhodopsin-like receptors) | Reactome | 1 / 19 | 79.0× | 1.26e-2 | 8.17e-2 |
| Arginine biosynthesis | KEGG | 1 / 23 | 65.3× | 1.52e-2 | 9.13e-2 |
| Endogenous sterols | Reactome | 1 / 25 | 60.1× | 1.65e-2 | 9.59e-2 |
| G-protein activation | Reactome | 1 / 28 | 53.6× | 1.85e-2 | 1.02e-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 ⇵ |
|---|---|---|---|---|---|
| positive regulation of neutrophil mediated killing of fungus | GO:0070965 | 2 / 2 | 2,336× | 1.60e-7 | 1.84e-5 ✓ sig. |
| regulation of translational initiation by eIF2 alpha phosphorylation | GO:0010998 | 1 / 1 | 2,336× | 4.28e-4 | 8.87e-3 ✓ sig. |
| positive regulation of translational initiation in response to starvation | GO:0071264 | 1 / 1 | 2,336× | 4.28e-4 | 8.87e-3 ✓ sig. |
| positive regulation of acute inflammatory response to antigenic stimulus | GO:0002866 | 1 / 1 | 2,336× | 4.28e-4 | 8.87e-3 ✓ sig. |
| regulation of TRAIL production | GO:0032679 | 1 / 1 | 2,336× | 4.28e-4 | 8.87e-3 ✓ sig. |
| cellular response to glyoxal | GO:0036471 | 1 / 1 | 2,336× | 4.28e-4 | 8.87e-3 ✓ sig. |
| glycolate biosynthetic process | GO:0046295 | 1 / 1 | 2,336× | 4.28e-4 | 8.87e-3 ✓ sig. |
| detoxification of mercury ion | GO:0050787 | 1 / 1 | 2,336× | 4.28e-4 | 8.87e-3 ✓ sig. |
| detoxification of hydrogen peroxide | GO:0061691 | 1 / 1 | 2,336× | 4.28e-4 | 8.87e-3 ✓ sig. |
| methylglyoxal catabolic process to lactate | GO:0061727 | 1 / 1 | 2,336× | 4.28e-4 | 8.87e-3 ✓ sig. |
| guanine deglycation | GO:0106044 | 1 / 1 | 2,336× | 4.28e-4 | 8.87e-3 ✓ sig. |
| guanine deglycation, methylglyoxal removal | GO:0106045 | 1 / 1 | 2,336× | 4.28e-4 | 8.87e-3 ✓ sig. |
| guanine deglycation, glyoxal removal | GO:0106046 | 1 / 1 | 2,336× | 4.28e-4 | 8.87e-3 ✓ sig. |
| cellular detoxification of methylglyoxal | GO:0140041 | 1 / 1 | 2,336× | 4.28e-4 | 8.87e-3 ✓ sig. |
| negative regulation of death-inducing signaling complex assembly | GO:1903073 | 1 / 1 | 2,336× | 4.28e-4 | 8.87e-3 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Colonic polyps | Parkinson-dementia complex of guam | 0.250 | 1 | 2.60e-4 | 6.51e-4 ✓ sig. |
| Colonic polyps | macrothrombocytopenia, isolated | 0.250 | 1 | 2.60e-4 | 6.51e-4 ✓ sig. |
| macrothrombocytopenia, isolated | Parkinson-dementia complex of guam | 0.250 | 1 | 2.60e-4 | 6.51e-4 ✓ sig. |
| Anterior cruciate ligament injury | Immune system disorder | 0.167 | 1 | 3.25e-4 | 7.71e-4 ✓ sig. |
| Arginase deficiency | Immune system disorder | 0.167 | 1 | 3.25e-4 | 7.71e-4 ✓ sig. |
| Immune system disorder | pulmonary veno-occlusive disease and/or pulmonary capillary haemangiomatosis | 0.167 | 1 | 3.25e-4 | 7.71e-4 ✓ sig. |
| Colonic polyps | Immune system disorder | 0.143 | 1 | 6.49e-4 | 1.24e-3 ✓ sig. |
| Immune system disorder | macrothrombocytopenia, isolated | 0.143 | 1 | 6.49e-4 | 1.24e-3 ✓ sig. |
| Immune system disorder | Parkinson-dementia complex of guam | 0.143 | 1 | 6.49e-4 | 1.24e-3 ✓ sig. |