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 200

8 diseases · 12 shared-gene connections
8 Diseases
8 Unique genes
0.306 Avg. similarity score
Anaplastic astrocytoma Most-connected disease (5 links)
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Disease Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details · click a node to select it and show its pairs below (double-click or Ctrl/⌘-click opens the disease page) · drag a node to pin it in place · scroll/pinch to zoom.

Member diseases (most connected first ‐ the cluster's core)

Disease ⇵ Connections in cluster ⇵ Significant partners ⇵ Curated genes ⇵
Anaplastic astrocytoma 5 5 2
Anaplastic oligoastrocytoma 4 4 1
Gemistocytic astrocytoma 4 4 1
Anaplastic oligodendroglioma 3 3 2
Tethered cord syndrome 3 3 2
Chordoma 2 2 5
Hairy cell leukemia 2 2 1
Craniofaciocardiohepatic syndrome 1 1 1

Top shared genes (genes linked to 2+ member diseases)

Gene ⇵ Member diseases ⇵ Linked diseases
IDH2 5 / 8 Anaplastic astrocytoma, Anaplastic oligoastrocytoma, Anaplastic oligodendroglioma, Chordoma and 1 more
BRAF 3 / 8 Anaplastic astrocytoma, Hairy cell leukemia, Tethered cord syndrome
AMOTL1 2 / 8 Craniofaciocardiohepatic syndrome, Tethered cord syndrome
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
BRCA2, PALB2
 Reactome 2 / 25 120× 1.16e-4 2.52e-3 ✓ sig.
Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA)
BRCA2, PALB2
 Reactome 2 / 26 115× 1.25e-4 2.69e-3 ✓ sig.
Citrate cycle (TCA cycle)
IDH2, IDH1
 KEGG 2 / 30 100× 1.67e-4 3.40e-3 ✓ sig.
2-Oxocarboxylic acid metabolism
IDH2, IDH1
 KEGG 2 / 33 91.0× 2.03e-4 3.95e-3 ✓ sig.
Resolution of D-loop Structures through Holliday Junction Intermediates
BRCA2, PALB2
 Reactome 2 / 33 91.0× 2.03e-4 3.95e-3 ✓ sig.
Homologous recombination
BRCA2, PALB2
 KEGG 2 / 41 73.2× 3.14e-4 5.56e-3 ✓ sig.
HDR through Homologous Recombination (HRR)
BRCA2, PALB2
 Reactome 2 / 48 62.6× 4.31e-4 7.10e-3 ✓ sig.
Fanconi anemia pathway
BRCA2, PALB2
 KEGG 2 / 54 55.6× 5.46e-4 8.52e-3 ✓ sig.
Glutathione metabolism
IDH2, IDH1
 KEGG 2 / 59 50.9× 6.52e-4 9.79e-3 ✓ sig.
Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate
IDH1
 Reactome 1 / 1 1,501× 6.66e-4 9.96e-3 ✓ sig.
NADPH regeneration
IDH1
 Reactome 1 / 1 1,501× 6.66e-4 9.96e-3 ✓ sig.
Central carbon metabolism in cancer
IDH2, IDH1
 KEGG 2 / 71 42.3× 9.43e-4 1.30e-2 ✓ sig.
Biosynthesis of amino acids
IDH2, IDH1
 KEGG 2 / 75 40.0× 1.05e-3 1.41e-2 ✓ sig.
Pancreatic cancer
BRAF, BRCA2
 KEGG 2 / 77 39.0× 1.11e-3 1.46e-2 ✓ sig.
Peroxisome
IDH2, IDH1
 KEGG 2 / 83 36.2× 1.29e-3 1.64e-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
IDH2, IDH1
 GO:0006097 2 / 2 2,336× 1.60e-7 1.80e-5 ✓ sig.
isocitrate metabolic process
IDH2, IDH1
 GO:0006102 2 / 5 934× 1.60e-6 1.21e-4 ✓ sig.
establishment of protein localization to telomere
POT1, BRCA2
 GO:0070200 2 / 7 667× 3.36e-6 2.19e-4 ✓ sig.
NADP+ metabolic process
IDH2, IDH1
 GO:0006739 2 / 14 334× 1.46e-5 7.00e-4 ✓ sig.
inner cell mass cell proliferation
BRCA2, PALB2
 GO:0001833 2 / 15 311× 1.68e-5 7.83e-4 ✓ sig.
2-oxoglutarate metabolic process
IDH2, IDH1
 GO:0006103 2 / 18 260× 2.45e-5 1.05e-3 ✓ sig.
female gonad development
IDH1, BRCA2
 GO:0008585 2 / 27 173× 5.60e-5 1.96e-3 ✓ sig.
tricarboxylic acid cycle
IDH2, IDH1
 GO:0006099 2 / 33 142× 8.41e-5 2.66e-3 ✓ sig.
mesoderm development
PALB2, TBXT
 GO:0007498 2 / 41 114× 1.30e-4 3.70e-3 ✓ sig.
somitogenesis
PALB2, TBXT
 GO:0001756 2 / 50 93.4× 1.94e-4 4.95e-3 ✓ sig.
regulation of phospholipid catabolic process
IDH1
 GO:0060696 1 / 1 2,336× 4.28e-4 8.59e-3 ✓ sig.
positive regulation of DNA strand elongation
POT1
 GO:0060383 1 / 1 2,336× 4.28e-4 8.59e-3 ✓ sig.
positive regulation of telomeric D-loop disassembly
POT1
 GO:1905840 1 / 1 2,336× 4.28e-4 8.59e-3 ✓ sig.
regulation of phospholipid biosynthetic process
IDH1
 GO:0071071 1 / 2 1,168× 8.56e-4 1.36e-2 ✓ sig.
negative regulation of glial cell migration
IDH2
 GO:1903976 1 / 2 1,168× 8.56e-4 1.36e-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 2.34e-4 ✓ sig.
Anaplastic astrocytoma Hairy cell leukemia 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Anaplastic astrocytoma Anaplastic oligoastrocytoma 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Anaplastic astrocytoma Gemistocytic astrocytoma 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Anaplastic oligoastrocytoma Anaplastic oligodendroglioma 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Anaplastic oligodendroglioma Gemistocytic astrocytoma 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Craniofaciocardiohepatic syndrome Tethered cord syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Hairy cell leukemia Tethered cord syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Anaplastic astrocytoma Anaplastic oligodendroglioma 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Anaplastic astrocytoma Tethered cord syndrome 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Anaplastic oligoastrocytoma Chordoma 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Chordoma Gemistocytic astrocytoma 0.167 1 3.25e-4 7.58e-4 ✓ sig.