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 168

10 diseases · 26 shared-gene connections
10 Diseases
20 Unique genes
0.311 Avg. similarity score
Hemangioma Most-connected disease (7 links)
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Disease Searched: High grade surface osteosarcoma 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 ⇵
Hemangioma 7 7 3
Ollier disease 7 7 2
Spindle cell hemangioma 7 7 3
D-2-hydroxyglutaric aciduria 6 6 5
Chondroma 5 5 8
Gemistocytic astrocytoma 5 5 1
High grade surface osteosarcoma 5 5 2
Combined d-2- and l-2-hydroxyglutaric aciduria 4 4 4
Maffucci syndrome 4 4 9
L2-hydroxyglutaric aciduria 2 2 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
IDH2 9 / 10 Chondroma, Combined d-2- and l-2-hydroxyglutaric aciduria, D-2-hydroxyglutaric aciduria, Gemistocytic astrocytoma and 5 more
IDH1 6 / 10 Chondroma, D-2-hydroxyglutaric aciduria, Hemangioma, Maffucci syndrome and 2 more
D2HGDH 3 / 10 Combined d-2- and l-2-hydroxyglutaric aciduria, D-2-hydroxyglutaric aciduria, L2-hydroxyglutaric aciduria
COL2A1 2 / 10 Chondroma, Maffucci syndrome
L2HGDH 2 / 10 Combined d-2- and l-2-hydroxyglutaric aciduria, D-2-hydroxyglutaric aciduria
SLC25A1 2 / 10 Combined d-2- and l-2-hydroxyglutaric aciduria, D-2-hydroxyglutaric aciduria
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 ⇵
Central carbon metabolism in cancer
IDH2, HIF1A, IDH1, MET, TP53, KRAS, PIK3CA, FGFR3
 KEGG 8 / 71 67.7× 1.18e-13 2.74e-11 ✓ sig.
Renal cell carcinoma
HIF1A, PTPN11, VHL, MET, KRAS, PIK3CA
 KEGG 6 / 70 51.5× 1.15e-9 1.05e-7 ✓ sig.
MicroRNAs in cancer
CDKN2A, MET, TP53, KRAS, PIK3CA, ATM, APC, FGFR3
 KEGG 8 / 311 15.4× 1.78e-8 1.23e-6 ✓ sig.
Pathways in cancer
CDKN2A, HIF1A, VHL, MET, TP53, KRAS, PIK3CA, APC, FGFR3
 KEGG 9 / 533 10.1× 6.77e-8 3.97e-6 ✓ sig.
Melanoma
CDKN2A, MET, TP53, KRAS, PIK3CA
 KEGG 5 / 73 41.1× 1.04e-7 5.80e-6 ✓ sig.
Non-small cell lung cancer
CDKN2A, MET, TP53, KRAS, PIK3CA
 KEGG 5 / 73 41.1× 1.04e-7 5.80e-6 ✓ sig.
Chronic myeloid leukemia
CDKN2A, PTPN11, TP53, KRAS, PIK3CA
 KEGG 5 / 77 39.0× 1.37e-7 7.35e-6 ✓ sig.
Hepatocellular carcinoma
CDKN2A, MET, TP53, KRAS, PIK3CA, APC
 KEGG 6 / 170 21.2× 2.42e-7 1.22e-5 ✓ sig.
Signaling by FGFR3 fusions in cancer
KRAS, PIK3CA, FGFR3
 Reactome 3 / 10 180× 4.70e-7 2.17e-5 ✓ sig.
Bladder cancer
CDKN2A, TP53, KRAS, FGFR3
 KEGG 4 / 41 58.6× 5.44e-7 2.46e-5 ✓ sig.
Stabilization of p53
CDKN2A, TP53, ATM
 Reactome 3 / 11 164× 6.46e-7 2.86e-5 ✓ sig.
Proteoglycans in cancer
HIF1A, PTPN11, MET, TP53, KRAS, PIK3CA
 KEGG 6 / 204 17.7× 7.09e-7 3.10e-5 ✓ sig.
Endometrial cancer
TP53, KRAS, PIK3CA, APC
 KEGG 4 / 59 40.7× 2.40e-6 8.80e-5 ✓ sig.
PI-3K cascade:FGFR3
PTPN11, PIK3CA, FGFR3
 Reactome 3 / 18 100× 3.17e-6 1.12e-4 ✓ sig.
Tie2 Signaling
PTPN11, KRAS, PIK3CA
 Reactome 3 / 18 100× 3.17e-6 1.12e-4 ✓ 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 ⇵
2-oxoglutarate metabolic process
D2HGDH, IDH2, L2HGDH, IDH1
 GO:0006103 4 / 18 208× 2.89e-9 5.89e-7 ✓ sig.
regulation of gene expression
CDKN2A, COL2A1, HIF1A, KDM4C, VHL, MET, PIK3CA, ATM
 GO:0010468 8 / 402 18.6× 4.30e-9 8.37e-7 ✓ sig.
replicative senescence
CDKN2A, TP53, ATM
 GO:0090399 3 / 16 175× 5.82e-7 5.53e-5 ✓ sig.
regulation of thymocyte apoptotic process
HIF1A, TP53
 GO:0070243 2 / 2 934× 1.09e-6 9.21e-5 ✓ sig.
glyoxylate cycle
IDH2, IDH1
 GO:0006097 2 / 2 934× 1.09e-6 9.21e-5 ✓ sig.
neuron apoptotic process
HIF1A, TP53, KRAS, ATM
 GO:0051402 4 / 98 38.1× 3.23e-6 2.22e-4 ✓ sig.
isocitrate metabolic process
IDH2, IDH1
 GO:0006102 2 / 5 374× 1.09e-5 5.80e-4 ✓ sig.
cellular senescence
CDKN2A, TP53, ATM
 GO:0090398 3 / 57 49.2× 2.96e-5 1.24e-3 ✓ sig.
chondrocyte differentiation
COL2A1, HIF1A, FGFR3
 GO:0002062 3 / 61 46.0× 3.63e-5 1.45e-3 ✓ sig.
negative regulation of cyclin-dependent protein serine/threonine kinase activity
CDKN2A, APC
 GO:0045736 2 / 9 208× 3.90e-5 1.53e-3 ✓ sig.
lactate metabolic process
D2HGDH, HIF1A
 GO:0006089 2 / 10 187× 4.87e-5 1.81e-3 ✓ sig.
negative regulation of glial cell proliferation
IDH2, TP53
 GO:0060253 2 / 11 170× 5.95e-5 2.10e-3 ✓ sig.
regulation of protein export from nucleus
CDKN2A, PTPN11
 GO:0046825 2 / 11 170× 5.95e-5 2.10e-3 ✓ sig.
Ras protein signal transduction
CDKN2A, TP53, KRAS
 GO:0007265 3 / 79 35.5× 7.87e-5 2.59e-3 ✓ sig.
NADP+ metabolic process
IDH2, IDH1
 GO:0006739 2 / 14 133× 9.83e-5 3.05e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Combined d-2- and l-2-hydroxyglutaric aciduria D-2-hydroxyglutaric aciduria 0.667 4 2.09e-15 2.56e-14 ✓ sig.
Chondroma Maffucci syndrome 0.214 3 4.74e-9 3.89e-8 ✓ sig.
Ollier disease Spindle cell hemangioma 0.667 2 8.34e-9 6.60e-8 ✓ sig.
Hemangioma Ollier disease 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Hemangioma Spindle cell hemangioma 0.500 2 2.50e-8 1.87e-7 ✓ sig.
D-2-hydroxyglutaric aciduria Ollier disease 0.333 2 8.34e-8 5.85e-7 ✓ sig.
D-2-hydroxyglutaric aciduria Spindle cell hemangioma 0.333 2 8.34e-8 5.85e-7 ✓ sig.
Chondroma Ollier disease 0.250 2 1.75e-7 1.18e-6 ✓ sig.
Chondroma Spindle cell hemangioma 0.250 2 1.75e-7 1.18e-6 ✓ sig.
D-2-hydroxyglutaric aciduria Hemangioma 0.286 2 2.50e-7 1.65e-6 ✓ sig.
Maffucci syndrome Ollier disease 0.200 2 3.00e-7 1.96e-6 ✓ sig.
Maffucci syndrome Spindle cell hemangioma 0.200 2 3.00e-7 1.96e-6 ✓ sig.
Chondroma Hemangioma 0.222 2 5.25e-7 3.32e-6 ✓ sig.
Hemangioma Maffucci syndrome 0.182 2 9.00e-7 5.50e-6 ✓ sig.
Chondroma D-2-hydroxyglutaric aciduria 0.182 2 1.75e-6 1.03e-5 ✓ sig.
Gemistocytic astrocytoma High grade surface osteosarcoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Gemistocytic astrocytoma Spindle cell hemangioma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Gemistocytic astrocytoma Ollier disease 0.333 1 1.29e-4 3.27e-4 ✓ sig.
High grade surface osteosarcoma Spindle cell hemangioma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
High grade surface osteosarcoma Ollier disease 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Gemistocytic astrocytoma Hemangioma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Hemangioma High grade surface osteosarcoma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Combined d-2- and l-2-hydroxyglutaric aciduria High grade surface osteosarcoma 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Combined d-2- and l-2-hydroxyglutaric aciduria L2-hydroxyglutaric aciduria 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Combined d-2- and l-2-hydroxyglutaric aciduria Gemistocytic astrocytoma 0.200 1 2.58e-4 5.38e-4 ✓ sig.
D-2-hydroxyglutaric aciduria L2-hydroxyglutaric aciduria 0.167 1 3.23e-4 6.41e-4 ✓ sig.