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 304
6
Diseases
7
Unique genes
0.306
Avg. similarity score
Anaplastic oligoastrocytoma
Most-connected disease (4 links)
Disease
Searched: Anaplastic astrocytoma
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Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Anaplastic astrocytoma
Anaplastic oligoastrocytoma
Anaplastic oligodendroglioma
Gemistocytic astrocytoma
Chordoma
Congenital chromosomal disease
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Anaplastic oligoastrocytoma | 4 | 4 | 1 |
| Anaplastic oligodendroglioma | 4 | 4 | 2 |
| Gemistocytic astrocytoma | 4 | 4 | 1 |
| Anaplastic astrocytoma | 3 | 3 | 2 |
| Chordoma | 2 | 2 | 5 |
| Congenital chromosomal disease | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| IDH2 | 5 / 6 | Anaplastic astrocytoma, Anaplastic oligoastrocytoma, Anaplastic oligodendroglioma, Chordoma and 1 more |
| POT1 | 2 / 6 | Anaplastic oligodendroglioma, Congenital chromosomal disease |
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 ⇵ |
|---|---|---|---|---|---|
| Homologous DNA Pairing and Strand Exchange | Reactome | 2 / 25 | 137× | 8.68e-5 | 2.07e-3 ✓ sig. |
| Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) | Reactome | 2 / 26 | 132× | 9.40e-5 | 2.21e-3 ✓ sig. |
| Citrate cycle (TCA cycle) | KEGG | 2 / 30 | 114× | 1.26e-4 | 2.78e-3 ✓ sig. |
| 2-Oxocarboxylic acid metabolism | KEGG | 2 / 33 | 104× | 1.52e-4 | 3.23e-3 ✓ sig. |
| Resolution of D-loop Structures through Holliday Junction Intermediates | Reactome | 2 / 33 | 104× | 1.52e-4 | 3.23e-3 ✓ sig. |
| Homologous recombination | KEGG | 2 / 41 | 83.7× | 2.36e-4 | 4.56e-3 ✓ sig. |
| HDR through Homologous Recombination (HRR) | Reactome | 2 / 48 | 71.5× | 3.24e-4 | 5.89e-3 ✓ sig. |
| Fanconi anemia pathway | KEGG | 2 / 54 | 63.5× | 4.11e-4 | 7.11e-3 ✓ sig. |
| Glutathione metabolism | KEGG | 2 / 59 | 58.2× | 4.90e-4 | 8.16e-3 ✓ sig. |
| Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate | Reactome | 1 / 1 | 1,716× | 5.83e-4 | 9.31e-3 ✓ sig. |
| NADPH regeneration | Reactome | 1 / 1 | 1,716× | 5.83e-4 | 9.31e-3 ✓ sig. |
| Central carbon metabolism in cancer | KEGG | 2 / 71 | 48.3× | 7.10e-4 | 1.08e-2 ✓ sig. |
| Biosynthesis of amino acids | KEGG | 2 / 75 | 45.8× | 7.92e-4 | 1.18e-2 ✓ sig. |
| Pancreatic cancer | KEGG | 2 / 77 | 44.6× | 8.34e-4 | 1.22e-2 ✓ sig. |
| Peroxisome | KEGG | 2 / 83 | 41.3× | 9.69e-4 | 1.37e-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 ⇵ |
|---|---|---|---|---|---|
| glyoxylate cycle | GO:0006097 | 2 / 2 | 2,670× | 1.20e-7 | 1.44e-5 ✓ sig. |
| isocitrate metabolic process | GO:0006102 | 2 / 5 | 1,068× | 1.20e-6 | 9.86e-5 ✓ sig. |
| establishment of protein localization to telomere | GO:0070200 | 2 / 7 | 763× | 2.52e-6 | 1.80e-4 ✓ sig. |
| NADP+ metabolic process | GO:0006739 | 2 / 14 | 381× | 1.09e-5 | 5.79e-4 ✓ sig. |
| inner cell mass cell proliferation | GO:0001833 | 2 / 15 | 356× | 1.26e-5 | 6.46e-4 ✓ sig. |
| 2-oxoglutarate metabolic process | GO:0006103 | 2 / 18 | 297× | 1.84e-5 | 8.67e-4 ✓ sig. |
| female gonad development | GO:0008585 | 2 / 27 | 198× | 4.20e-5 | 1.63e-3 ✓ sig. |
| tricarboxylic acid cycle | GO:0006099 | 2 / 33 | 162× | 6.32e-5 | 2.21e-3 ✓ sig. |
| mesoderm development | GO:0007498 | 2 / 41 | 130× | 9.79e-5 | 3.09e-3 ✓ sig. |
| somitogenesis | GO:0001756 | 2 / 50 | 107× | 1.46e-4 | 4.14e-3 ✓ sig. |
| regulation of phospholipid catabolic process | GO:0060696 | 1 / 1 | 2,670× | 3.75e-4 | 8.08e-3 ✓ sig. |
| positive regulation of DNA strand elongation | GO:0060383 | 1 / 1 | 2,670× | 3.75e-4 | 8.08e-3 ✓ sig. |
| positive regulation of telomeric D-loop disassembly | GO:1905840 | 1 / 1 | 2,670× | 3.75e-4 | 8.08e-3 ✓ sig. |
| DNA recombination | GO:0006310 | 2 / 110 | 48.5× | 7.07e-4 | 1.25e-2 ✓ sig. |
| regulation of phospholipid biosynthetic process | GO:0071071 | 1 / 2 | 1,335× | 7.49e-4 | 1.30e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Anaplastic oligoastrocytoma | Gemistocytic astrocytoma | 0.500 | 1 | 6.49e-5 | 2.33e-4 ✓ sig. |
| Anaplastic astrocytoma | Anaplastic oligoastrocytoma | 0.333 | 1 | 1.30e-4 | 3.93e-4 ✓ sig. |
| Anaplastic astrocytoma | Gemistocytic astrocytoma | 0.333 | 1 | 1.30e-4 | 3.93e-4 ✓ sig. |
| Anaplastic oligoastrocytoma | Anaplastic oligodendroglioma | 0.333 | 1 | 1.30e-4 | 3.93e-4 ✓ sig. |
| Anaplastic oligodendroglioma | Gemistocytic astrocytoma | 0.333 | 1 | 1.30e-4 | 3.93e-4 ✓ sig. |
| Anaplastic oligodendroglioma | Congenital chromosomal disease | 0.333 | 1 | 1.30e-4 | 3.93e-4 ✓ sig. |
| Anaplastic astrocytoma | Anaplastic oligodendroglioma | 0.250 | 1 | 2.60e-4 | 6.51e-4 ✓ sig. |
| Anaplastic oligoastrocytoma | Chordoma | 0.167 | 1 | 3.25e-4 | 7.71e-4 ✓ sig. |
| Chordoma | Gemistocytic astrocytoma | 0.167 | 1 | 3.25e-4 | 7.71e-4 ✓ sig. |