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 424
6
Diseases
6
Unique genes
0.321
Avg. similarity score
Amegakaryocytic thrombocytopenia
Most-connected disease (5 links)
Disease
Searched: Myelofibrosis with myeloid metaplasia
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Myelofibrosis with myeloid metaplasia
Amegakaryocytic thrombocytopenia
Congenital amegakaryocytic thrombocytopenia
Thrombocythemia
Thrombocythemia with distal limb defects
Thrombocytopenia and thrombocythemia 1
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Amegakaryocytic thrombocytopenia | 5 | 5 | 2 |
| Congenital amegakaryocytic thrombocytopenia | 5 | 5 | 2 |
| Thrombocythemia | 5 | 5 | 6 |
| Thrombocythemia with distal limb defects | 4 | 4 | 1 |
| Thrombocytopenia and thrombocythemia 1 | 4 | 4 | 1 |
| Myelofibrosis with myeloid metaplasia | 3 | 3 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| THPO | 5 / 6 | Amegakaryocytic thrombocytopenia, Congenital amegakaryocytic thrombocytopenia, Thrombocythemia, Thrombocythemia with distal limb defects and 1 more |
| MPL | 4 / 6 | Amegakaryocytic thrombocytopenia, Congenital amegakaryocytic thrombocytopenia, Myelofibrosis with myeloid metaplasia, Thrombocythemia |
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 ⇵ |
|---|---|---|---|---|---|
| JAK-STAT signaling pathway | KEGG | 3 / 168 | 35.7× | 5.21e-5 | 1.13e-3 ✓ sig. |
| Hormone signaling | KEGG | 3 / 219 | 27.4× | 1.15e-4 | 2.12e-3 ✓ sig. |
| Factors involved in megakaryocyte development and platelet production | Reactome | 2 / 99 | 40.4× | 9.87e-4 | 1.12e-2 ✓ sig. |
| Assembly of Viral Components at the Budding Site | Reactome | 1 / 2 | 1,001× | 9.99e-4 | 1.13e-2 ✓ sig. |
| Efferocytosis | KEGG | 2 / 157 | 25.5× | 2.46e-3 | 2.22e-2 ✓ sig. |
| Calnexin/calreticulin cycle | Reactome | 1 / 5 | 400× | 2.50e-3 | 2.23e-2 ✓ sig. |
| Scavenging by Class F Receptors | Reactome | 1 / 6 | 334× | 2.99e-3 | 2.54e-2 ✓ sig. |
| Herpes simplex virus 1 infection | KEGG | 2 / 182 | 22.0× | 3.29e-3 | 2.72e-2 ✓ sig. |
| Interleukin-23 signaling | Reactome | 1 / 9 | 222× | 4.49e-3 | 3.39e-2 ✓ sig. |
| ATF6 (ATF6-alpha) activates chaperone genes | Reactome | 1 / 9 | 222× | 4.49e-3 | 3.39e-2 ✓ sig. |
| MAPK1 (ERK2) activation | Reactome | 1 / 9 | 222× | 4.49e-3 | 3.39e-2 ✓ sig. |
| Erythropoietin activates RAS | Reactome | 1 / 10 | 200× | 4.99e-3 | 3.64e-2 ✓ sig. |
| MAPK3 (ERK1) activation | Reactome | 1 / 10 | 200× | 4.99e-3 | 3.64e-2 ✓ sig. |
| Interleukin-12 signaling | Reactome | 1 / 10 | 200× | 4.99e-3 | 3.64e-2 ✓ sig. |
| Interleukin-27 signaling | Reactome | 1 / 11 | 182× | 5.48e-3 | 3.87e-2 ✓ sig. |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| thrombopoietin-mediated signaling pathway | GO:0038163 | 4 / 7 | 1,780× | 1.03e-13 | 5.92e-11 ✓ sig. |
| monocyte homeostasis | GO:0035702 | 2 / 3 | 2,076× | 2.58e-7 | 2.79e-5 ✓ sig. |
| cellular response to interleukin-3 | GO:0036016 | 2 / 7 | 890× | 1.80e-6 | 1.39e-4 ✓ sig. |
| neutrophil homeostasis | GO:0001780 | 2 / 11 | 566× | 4.72e-6 | 3.03e-4 ✓ sig. |
| megakaryocyte development | GO:0035855 | 2 / 23 | 271× | 2.17e-5 | 9.82e-4 ✓ sig. |
| nuclear receptor-mediated mineralocorticoid signaling pathway | GO:0031959 | 1 / 1 | 3,115× | 3.21e-4 | 7.04e-3 ✓ sig. |
| symbiont-induced defense-related programmed cell death | GO:0034050 | 1 / 1 | 3,115× | 3.21e-4 | 7.04e-3 ✓ sig. |
| interleukin-35-mediated signaling pathway | GO:0070757 | 1 / 1 | 3,115× | 3.21e-4 | 7.04e-3 ✓ sig. |
| basophil homeostasis | GO:1990960 | 1 / 1 | 3,115× | 3.21e-4 | 7.04e-3 ✓ sig. |
| cellular response to virus | GO:0098586 | 2 / 89 | 70.0× | 3.32e-4 | 7.21e-3 ✓ sig. |
| positive regulation of cell population proliferation | GO:0008284 | 3 / 532 | 17.6× | 4.30e-4 | 8.57e-3 ✓ sig. |
| negative regulation of Kit signaling pathway | GO:1900235 | 1 / 2 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| response to interleukin-12 | GO:0070671 | 1 / 2 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| positive regulation of growth factor dependent skeletal muscle satellite cell proliferation | GO:1902728 | 1 / 2 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| regulation of postsynapse to nucleus signaling pathway | GO:1905539 | 1 / 2 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |