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 428
5
Diseases
15
Unique genes
0.204
Avg. similarity score
Pancytopenia
Most-connected disease (4 links)
Disease
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Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Pancytopenia
Congenital folate absorption defect
Hereditary folate malabsorption
Malabsorption syndrome
MECOM-associated syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Pancytopenia | 4 | 4 | 14 |
| Congenital folate absorption defect | 3 | 3 | 1 |
| Hereditary folate malabsorption | 3 | 3 | 2 |
| Malabsorption syndrome | 3 | 3 | 1 |
| MECOM-associated syndrome | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| SLC46A1 | 4 / 5 | Congenital folate absorption defect, Hereditary folate malabsorption, Malabsorption syndrome, Pancytopenia |
| MECOM | 2 / 5 | MECOM-associated syndrome, Pancytopenia |
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 ⇵ |
|---|---|---|---|---|---|
| Metabolism of folate and pterines | Reactome | 2 / 17 | 94.2× | 1.96e-4 | 3.85e-3 ✓ sig. |
| Vitamin digestion and absorption | KEGG | 2 / 26 | 61.6× | 4.65e-4 | 7.54e-3 ✓ sig. |
| Folate biosynthesis | KEGG | 2 / 28 | 57.2× | 5.40e-4 | 8.45e-3 ✓ sig. |
| Antifolate resistance | KEGG | 2 / 30 | 53.4× | 6.21e-4 | 9.45e-3 ✓ sig. |
| Folate transport and metabolism | KEGG | 2 / 31 | 51.7× | 6.63e-4 | 9.93e-3 ✓ sig. |
| Defective TCN2 causes hereditary megaloblastic anemia | Reactome | 1 / 1 | 801× | 1.25e-3 | 1.60e-2 ✓ sig. |
| Defective CD320 causes methylmalonic aciduria | Reactome | 1 / 2 | 400× | 2.50e-3 | 2.69e-2 ✓ sig. |
| Coronavirus disease - COVID-19 | KEGG | 3 / 238 | 10.1× | 2.93e-3 | 3.02e-2 ✓ sig. |
| Toll Like Receptor 3 (TLR3) Cascade | Reactome | 1 / 3 | 267× | 3.74e-3 | 3.59e-2 ✓ sig. |
| Chronic myeloid leukemia | KEGG | 2 / 77 | 20.8× | 4.04e-3 | 3.79e-2 ✓ sig. |
| RUNX2 regulates genes involved in differentiation of myeloid cells | Reactome | 1 / 4 | 200× | 4.99e-3 | 4.37e-2 ✓ sig. |
| Viral mRNA Translation | Reactome | 2 / 89 | 18.0× | 5.36e-3 | 4.58e-2 ✓ sig. |
| SRP-dependent cotranslational protein targeting to membrane | Reactome | 2 / 93 | 17.2× | 5.83e-3 | 4.85e-2 ✓ sig. |
| Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) | Reactome | 2 / 95 | 16.9× | 6.08e-3 | 4.98e-2 ✓ sig. |
| RUNX1 regulates expression of components of tight junctions | Reactome | 1 / 5 | 160× | 6.23e-3 | 5.06e-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 ⇵ |
|---|---|---|---|---|---|
| tetrahydrofolate biosynthetic process | GO:0046654 | 2 / 7 | 356× | 1.26e-5 | 6.25e-4 ✓ sig. |
| folic acid metabolic process | GO:0046655 | 2 / 15 | 166× | 6.28e-5 | 2.13e-3 ✓ sig. |
| hematopoietic stem cell proliferation | GO:0071425 | 2 / 25 | 99.7× | 1.79e-4 | 4.67e-3 ✓ sig. |
| response to axon injury | GO:0048678 | 2 / 37 | 67.3× | 3.94e-4 | 8.11e-3 ✓ sig. |
| interstrand cross-link repair | GO:0036297 | 2 / 39 | 63.9× | 4.38e-4 | 8.72e-3 ✓ sig. |
| negative regulation of erythrocyte apoptotic process | GO:1902251 | 1 / 1 | 1,246× | 8.03e-4 | 1.30e-2 ✓ sig. |
| negative regulation of MyD88-independent toll-like receptor signaling pathway | GO:0034128 | 1 / 1 | 1,246× | 8.03e-4 | 1.30e-2 ✓ sig. |
| molybdopterin cofactor metabolic process | GO:0043545 | 1 / 1 | 1,246× | 8.03e-4 | 1.30e-2 ✓ sig. |
| erythrocyte differentiation | GO:0030218 | 2 / 65 | 38.3× | 1.21e-3 | 1.70e-2 ✓ sig. |
| response to methotrexate | GO:0031427 | 1 / 2 | 623× | 1.60e-3 | 1.98e-2 ✓ sig. |
| methotrexate transport | GO:0051958 | 1 / 2 | 623× | 1.60e-3 | 1.98e-2 ✓ sig. |
| intestinal folate absorption | GO:0098829 | 1 / 2 | 623× | 1.60e-3 | 1.98e-2 ✓ sig. |
| NAD+ catabolic process | GO:0019677 | 1 / 3 | 415× | 2.41e-3 | 2.50e-2 ✓ sig. |
| regulation of plasminogen activation | GO:0010755 | 1 / 3 | 415× | 2.41e-3 | 2.50e-2 ✓ sig. |
| regulation of connective tissue replacement | GO:1905203 | 1 / 3 | 415× | 2.41e-3 | 2.50e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Congenital folate absorption defect | Malabsorption syndrome | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Congenital folate absorption defect | Hereditary folate malabsorption | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Hereditary folate malabsorption | Malabsorption syndrome | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Congenital folate absorption defect | Pancytopenia | 0.067 | 1 | 9.09e-4 | 1.56e-3 ✓ sig. |
| Malabsorption syndrome | Pancytopenia | 0.067 | 1 | 9.09e-4 | 1.56e-3 ✓ sig. |
| MECOM-associated syndrome | Pancytopenia | 0.067 | 1 | 9.09e-4 | 1.56e-3 ✓ sig. |
| Hereditary folate malabsorption | Pancytopenia | 0.063 | 1 | 1.82e-3 | 2.66e-3 ✓ sig. |