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 479
6
Diseases
11
Unique genes
0.240
Avg. similarity score
Congenital dyserythropoietic anemia
Most-connected disease (5 links)
Disease
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Congenital dyserythropoietic anemia
Glutaric aciduria 1
Glutaricacidemia
Glutaryl-CoA dehydrogenase deficiency
Cda iii
Irak4 deficiency
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Congenital dyserythropoietic anemia | 5 | 5 | 11 |
| Glutaric aciduria 1 | 3 | 3 | 1 |
| Glutaricacidemia | 3 | 3 | 1 |
| Glutaryl-CoA dehydrogenase deficiency | 3 | 3 | 1 |
| Cda iii | 1 | 1 | 1 |
| Irak4 deficiency | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| GCDH | 4 / 6 | Congenital dyserythropoietic anemia, Glutaric aciduria 1, Glutaricacidemia, Glutaryl-CoA dehydrogenase deficiency |
| IRAK4 | 2 / 6 | Congenital dyserythropoietic anemia, Irak4 deficiency |
| KIF23 | 2 / 6 | Cda iii, Congenital dyserythropoietic anemia |
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 ⇵ |
|---|---|---|---|---|---|
| Kinesins | Reactome | 2 / 59 | 37.0× | 1.27e-3 | 1.36e-2 ✓ sig. |
| Mitotic Telophase/Cytokinesis | Reactome | 1 / 3 | 364× | 2.75e-3 | 2.39e-2 ✓ sig. |
| COPI-dependent Golgi-to-ER retrograde traffic | Reactome | 2 / 99 | 22.1× | 3.52e-3 | 2.85e-2 ✓ sig. |
| IRAK4 deficiency (TLR5) | Reactome | 1 / 4 | 273× | 3.66e-3 | 2.93e-2 ✓ sig. |
| MHC class II antigen presentation | Reactome | 2 / 123 | 17.8× | 5.39e-3 | 3.83e-2 ✓ sig. |
| Alcoholic liver disease | KEGG | 2 / 144 | 15.2× | 7.31e-3 | 4.67e-2 ✓ sig. |
| MyD88 dependent cascade initiated on endosome | Reactome | 1 / 8 | 136× | 7.31e-3 | 4.67e-2 ✓ sig. |
| MyD88 cascade initiated on plasma membrane | Reactome | 1 / 9 | 121× | 8.22e-3 | 5.04e-2 |
| TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation | Reactome | 1 / 10 | 109× | 9.12e-3 | 5.37e-2 |
| IRAK4 deficiency (TLR2/4) | Reactome | 1 / 11 | 99.3× | 1.00e-2 | 5.69e-2 |
| Lysine catabolism | Reactome | 1 / 12 | 91.0× | 1.09e-2 | 6.01e-2 |
| Synthesis of PE | Reactome | 1 / 12 | 91.0× | 1.09e-2 | 6.01e-2 |
| Triglyceride biosynthesis | Reactome | 1 / 13 | 84.0× | 1.18e-2 | 6.31e-2 |
| Depolymerisation of the Nuclear Lamina | Reactome | 1 / 15 | 72.8× | 1.37e-2 | 6.87e-2 |
| TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling | Reactome | 1 / 15 | 72.8× | 1.37e-2 | 6.87e-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 ⇵ |
|---|---|---|---|---|---|
| erythrocyte differentiation | GO:0030218 | 3 / 65 | 78.4× | 6.50e-6 | 3.90e-4 ✓ sig. |
| mitotic spindle midzone assembly | GO:0051256 | 2 / 11 | 309× | 1.73e-5 | 8.27e-4 ✓ sig. |
| positive regulation of cytokinesis | GO:0032467 | 2 / 41 | 82.9× | 2.55e-4 | 6.04e-3 ✓ sig. |
| daunorubicin transport | GO:0043215 | 1 / 1 | 1,699× | 5.89e-4 | 1.06e-2 ✓ sig. |
| terpenoid transport | GO:0046865 | 1 / 1 | 1,699× | 5.89e-4 | 1.06e-2 ✓ sig. |
| cellular response to nonylphenol | GO:1904148 | 1 / 1 | 1,699× | 5.89e-4 | 1.06e-2 ✓ sig. |
| positive regulation of establishment of Sertoli cell barrier | GO:1904446 | 1 / 1 | 1,699× | 5.89e-4 | 1.06e-2 ✓ sig. |
| cellular response to borneol | GO:1905231 | 1 / 1 | 1,699× | 5.89e-4 | 1.06e-2 ✓ sig. |
| response to codeine | GO:1905233 | 1 / 1 | 1,699× | 5.89e-4 | 1.06e-2 ✓ sig. |
| response to quercetin | GO:1905235 | 1 / 1 | 1,699× | 5.89e-4 | 1.06e-2 ✓ sig. |
| positive regulation of response to drug | GO:2001025 | 1 / 1 | 1,699× | 5.89e-4 | 1.06e-2 ✓ sig. |
| mitotic cytokinesis | GO:0000281 | 2 / 68 | 50.0× | 7.03e-4 | 1.19e-2 ✓ sig. |
| response to antineoplastic agent | GO:0097327 | 1 / 2 | 849× | 1.18e-3 | 1.59e-2 ✓ sig. |
| hormone transport | GO:0009914 | 1 / 2 | 849× | 1.18e-3 | 1.59e-2 ✓ sig. |
| cellular response to mycotoxin | GO:0036146 | 1 / 2 | 849× | 1.18e-3 | 1.59e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Glutaric aciduria 1 | Glutaryl-CoA dehydrogenase deficiency | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Glutaric aciduria 1 | Glutaricacidemia | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Glutaricacidemia | Glutaryl-CoA dehydrogenase deficiency | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Cda iii | Congenital dyserythropoietic anemia | 0.083 | 1 | 7.10e-4 | 1.17e-3 ✓ sig. |
| Congenital dyserythropoietic anemia | Irak4 deficiency | 0.083 | 1 | 7.10e-4 | 1.17e-3 ✓ sig. |
| Congenital dyserythropoietic anemia | Glutaric aciduria 1 | 0.083 | 1 | 7.10e-4 | 1.17e-3 ✓ sig. |
| Congenital dyserythropoietic anemia | Glutaricacidemia | 0.083 | 1 | 7.10e-4 | 1.17e-3 ✓ sig. |
| Congenital dyserythropoietic anemia | Glutaryl-CoA dehydrogenase deficiency | 0.083 | 1 | 7.10e-4 | 1.17e-3 ✓ sig. |