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 563

5 diseases · 6 shared-gene connections
5 Diseases
19 Unique genes
0.212 Avg. similarity score
Undifferentiated high grade pleomorphic sarcoma of bone Most-connected disease (4 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 ⇵
Undifferentiated high grade pleomorphic sarcoma of bone 4 4 7
Diffuse hemispheric glioma, h3 g34-mutant 3 3 6
Mixed neuronal-glial tumor 2 2 11
Testicular granulosa cell tumor 2 2 4
Childhood cancer retinoblastoma 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
H3-3A 4 / 5 Diffuse hemispheric glioma, h3 g34-mutant, Mixed neuronal-glial tumor, Testicular granulosa cell tumor, Undifferentiated high grade pleomorphic sarcoma of bone
CDKN2A 3 / 5 Diffuse hemispheric glioma, h3 g34-mutant, Testicular granulosa cell tumor, Undifferentiated high grade pleomorphic sarcoma of bone
TP53 3 / 5 Diffuse hemispheric glioma, h3 g34-mutant, Mixed neuronal-glial tumor, Undifferentiated high grade pleomorphic sarcoma of bone
ATRX 2 / 5 Diffuse hemispheric glioma, h3 g34-mutant, Mixed neuronal-glial tumor
FGFR1 2 / 5 Mixed neuronal-glial tumor, Undifferentiated high grade pleomorphic sarcoma of bone
RB1 2 / 5 Childhood cancer retinoblastoma, Undifferentiated high grade pleomorphic sarcoma of bone
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 ⇵
Melanoma
TP53, CDKN2A, PDGFRA, KRAS, BRAF, FGFR1, PIK3CA, RB1
 KEGG 8 / 73 69.3× 9.00e-14 2.14e-11 ✓ sig.
Chronic myeloid leukemia
TP53, CDKN2A, KRAS, STAT5B, PTPN11, BRAF, PIK3CA, RB1
 KEGG 8 / 77 65.7× 1.40e-13 3.16e-11 ✓ sig.
Prostate cancer
TP53, PDGFRA, CTNNB1, KRAS, BRAF, FGFR1, PIK3CA, RB1
 KEGG 8 / 98 51.6× 1.03e-12 1.96e-10 ✓ sig.
Pathways in cancer
TP53, CDKN2A, PDGFRA, CTNNB1, KRAS, STAT5B, SUFU, BRAF, FGFR1, PIK3CA, MLH1, RB1
 KEGG 12 / 533 14.2× 1.96e-12 3.48e-10 ✓ sig.
Non-small cell lung cancer
TP53, CDKN2A, KRAS, STAT5B, BRAF, PIK3CA, RB1
 KEGG 7 / 73 60.6× 1.09e-11 1.64e-9 ✓ sig.
Glioma
TP53, CDKN2A, PDGFRA, KRAS, BRAF, PIK3CA, RB1
 KEGG 7 / 76 58.2× 1.45e-11 2.11e-9 ✓ sig.
Endometrial cancer
TP53, CTNNB1, KRAS, BRAF, PIK3CA, MLH1
 KEGG 6 / 59 64.3× 2.80e-10 2.95e-8 ✓ sig.
Downstream signal transduction
PDGFRA, KRAS, STAT5B, PTPN11, PIK3CA
 Reactome 5 / 29 109× 6.48e-10 6.33e-8 ✓ sig.
Pancreatic cancer
TP53, CDKN2A, KRAS, BRAF, PIK3CA, RB1
 KEGG 6 / 77 49.3× 1.45e-9 1.30e-7 ✓ sig.
Breast cancer
TP53, CTNNB1, KRAS, BRAF, FGFR1, PIK3CA, RB1
 KEGG 7 / 148 29.9× 1.67e-9 1.47e-7 ✓ sig.
Gastric cancer
TP53, CTNNB1, KRAS, BRAF, PIK3CA, MLH1, RB1
 KEGG 7 / 150 29.5× 1.83e-9 1.60e-7 ✓ sig.
Colorectal cancer
TP53, CTNNB1, KRAS, BRAF, PIK3CA, MLH1
 KEGG 6 / 87 43.6× 3.05e-9 2.56e-7 ✓ sig.
Bladder cancer
TP53, CDKN2A, KRAS, BRAF, RB1
 KEGG 5 / 41 77.1× 4.04e-9 3.30e-7 ✓ sig.
Hepatocellular carcinoma
TP53, CDKN2A, CTNNB1, KRAS, BRAF, PIK3CA, RB1
 KEGG 7 / 170 26.0× 4.39e-9 3.55e-7 ✓ sig.
Endocrine resistance
TP53, CDKN2A, KRAS, BRAF, PIK3CA, RB1
 KEGG 6 / 99 38.3× 6.70e-9 5.18e-7 ✓ 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 ⇵
cell population proliferation
TP53, H3-3A, CTNNB1, KRAS, STAT5B, FGFR1, RB1
 GO:0008283 7 / 263 26.2× 4.40e-9 8.55e-7 ✓ sig.
T cell differentiation in thymus
TP53, CTNNB1, STAT5B, BRAF
 GO:0033077 4 / 41 96.0× 7.55e-8 1.00e-5 ✓ sig.
subtelomeric heterochromatin formation
ATRX, EZH2, H3-3A
 GO:0031509 3 / 11 268× 1.46e-7 1.76e-5 ✓ sig.
negative regulation of transcription by RNA polymerase II
DNMT3A, TP53, EZH2, CDKN2A, CTNNB1, FOXL2, SUFU, FGFR1, RB1
 GO:0000122 9 / 1,002 8.8× 2.01e-7 2.27e-5 ✓ sig.
epidermal growth factor receptor signaling pathway
CTNNB1, PTPN11, BRAF, PIK3CA
 GO:0007173 4 / 64 61.5× 4.67e-7 4.60e-5 ✓ sig.
glial cell proliferation
TP53, KRAS, RB1
 GO:0014009 3 / 18 164× 7.20e-7 6.58e-5 ✓ sig.
negative regulation of gene expression
TP53, EZH2, CTNNB1, FGFR1, PIK3CA, RB1
 GO:0010629 6 / 339 17.4× 7.58e-7 6.84e-5 ✓ sig.
Ras protein signal transduction
TP53, CDKN2A, KRAS, RB1
 GO:0007265 4 / 79 49.8× 1.09e-6 9.24e-5 ✓ sig.
response to estradiol
DNMT3A, EZH2, CTNNB1, STAT5B
 GO:0032355 4 / 84 46.8× 1.40e-6 1.13e-4 ✓ sig.
regulation of cell population proliferation
TP53, EZH2, CTNNB1, STAT5B, BRAF
 GO:0042127 5 / 201 24.5× 1.41e-6 1.14e-4 ✓ sig.
negative regulation of DNA-templated transcription
DNMT3A, TP53, EZH2, CDKN2A, CTNNB1, FOXL2, RB1
 GO:0045892 7 / 631 10.9× 1.71e-6 1.34e-4 ✓ sig.
regulation of gene expression
DNMT3A, EZH2, CDKN2A, CTNNB1, FGFR1, PIK3CA
 GO:0010468 6 / 402 14.7× 2.04e-6 1.54e-4 ✓ sig.
regulation of centromere complex assembly
H3-3A, RB1
 GO:0090230 2 / 3 656× 2.94e-6 2.06e-4 ✓ sig.
multicellular organism growth
ATRX, TP53, H3-3A, PTPN11
 GO:0035264 4 / 115 34.2× 4.91e-6 3.13e-4 ✓ sig.
MAPK cascade
CTNNB1, KRAS, BRAF, FGFR1
 GO:0000165 4 / 147 26.8× 1.30e-5 6.67e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Diffuse hemispheric glioma, h3 g34-mutant Testicular granulosa cell tumor 0.286 2 3.00e-7 1.96e-6 ✓ sig.
Diffuse hemispheric glioma, h3 g34-mutant Undifferentiated high grade pleomorphic sarcoma of bone 0.250 2 5.00e-7 3.18e-6 ✓ sig.
Testicular granulosa cell tumor Undifferentiated high grade pleomorphic sarcoma of bone 0.250 2 5.00e-7 3.18e-6 ✓ sig.
Diffuse hemispheric glioma, h3 g34-mutant Mixed neuronal-glial tumor 0.167 2 1.80e-6 1.06e-5 ✓ sig.
Mixed neuronal-glial tumor Undifferentiated high grade pleomorphic sarcoma of bone 0.154 2 3.00e-6 1.72e-5 ✓ sig.
Childhood cancer retinoblastoma Undifferentiated high grade pleomorphic sarcoma of bone 0.167 1 3.23e-4 6.41e-4 ✓ sig.