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 261

7 diseases · 14 shared-gene connections
7 Diseases
15 Unique genes
0.218 Avg. similarity score
Small cell ovary carcinoma 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 ⇵
Small cell ovary carcinoma 5 5 1
Thoracic neoplasms 5 5 2
rhabdoid tumor predisposition syndrome 2 5 5 1
Carotid atherosclerosis 4 4 6
Rhabdoid tumor predisposition syndrome 4 4 2
hereditary nonpolyposis colon cancer 4 4 8
thrombocytopenia 10 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
SMARCA4 6 / 7 Carotid atherosclerosis, hereditary nonpolyposis colon cancer, Rhabdoid tumor predisposition syndrome, rhabdoid tumor predisposition syndrome 2 and 2 more
PTPRJ 2 / 7 hereditary nonpolyposis colon cancer, thrombocytopenia 10
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 ⇵
RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known
SMARCA4, SMARCB1
 Reactome 2 / 38 42.1× 9.97e-4 1.35e-2 ✓ sig.
POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation
SOX2
 Reactome 1 / 3 267× 3.74e-3 3.59e-2 ✓ sig.
RMTs methylate histone arginines
SMARCA4, SMARCB1
 Reactome 2 / 79 20.3× 4.24e-3 3.93e-2 ✓ sig.
PTK6 Regulates Cell Cycle
CDKN1B
 Reactome 1 / 6 133× 7.47e-3 5.69e-2
p53-Dependent G1 DNA Damage Response
CDKN1B
 Reactome 1 / 7 114× 8.71e-3 6.31e-2
2-LTR circle formation
XRCC4
 Reactome 1 / 7 114× 8.71e-3 6.31e-2
ATP-dependent chromatin remodeling
SMARCA4, SMARCB1
 KEGG 2 / 117 13.7× 9.09e-3 6.49e-2
AKT phosphorylates targets in the cytosol
CDKN1B
 Reactome 1 / 11 72.8× 1.37e-2 8.23e-2
Stabilization of p53
CHEK2
 Reactome 1 / 11 72.8× 1.37e-2 8.23e-2
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex
CHEK2
 Reactome 1 / 12 66.7× 1.49e-2 8.66e-2
Non-homologous end-joining
XRCC4
 KEGG 1 / 13 61.6× 1.61e-2 9.11e-2
POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation
SOX2
 Reactome 1 / 13 61.6× 1.61e-2 9.11e-2
Cell cycle
CDKN1B, CHEK2
 KEGG 2 / 158 10.1× 1.61e-2 9.11e-2
TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest
CDKN1B
 Reactome 1 / 14 57.2× 1.74e-2 9.50e-2
Hepatocellular carcinoma
SMARCA4, SMARCB1
 KEGG 2 / 170 9.4× 1.85e-2 9.85e-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 ⇵
positive regulation of glucose mediated signaling pathway
SMARCA4, SMARCB1
 GO:1902661 2 / 3 831× 1.80e-6 1.33e-4 ✓ sig.
positive regulation of double-strand break repair
FMN2, SMARCA4, SMARCB1
 GO:2000781 3 / 47 79.5× 6.64e-6 3.76e-4 ✓ sig.
regulation of G1/S transition of mitotic cell cycle
SMARCA4, SMARCB1, CDKN1B
 GO:2000045 3 / 57 65.6× 1.19e-5 5.98e-4 ✓ sig.
positive regulation of transcription of nucleolar large rRNA by RNA polymerase I
SMARCA4, SMARCB1
 GO:1901838 2 / 10 249× 2.70e-5 1.13e-3 ✓ sig.
RNA polymerase I preinitiation complex assembly
SMARCA4, SMARCB1
 GO:0001188 2 / 11 227× 3.29e-5 1.31e-3 ✓ sig.
positive regulation of cell differentiation
SMARCA4, SMARCB1, SOX2
 GO:0045597 3 / 83 45.0× 3.70e-5 1.43e-3 ✓ sig.
cellular response to lithium ion
CDKN1B, XRCC4
 GO:0071285 2 / 15 166× 6.28e-5 2.13e-3 ✓ sig.
host-mediated activation of viral transcription
SMARCA4, SMARCB1
 GO:0043923 2 / 18 138× 9.13e-5 2.83e-3 ✓ sig.
negative regulation of cell growth
SMARCA4, PTPRJ, CDKN1B
 GO:0030308 3 / 115 32.5× 9.79e-5 2.97e-3 ✓ sig.
chromatin remodeling
CFDP1, SMARCA4, SMARCB1, NFKBIZ
 GO:0006338 4 / 320 15.6× 9.92e-5 3.00e-3 ✓ sig.
epithelial cell apoptotic process
CDKN1B, NFKBIZ
 GO:1904019 2 / 20 125× 1.13e-4 3.32e-3 ✓ sig.
nucleosome disassembly
SMARCA4, SMARCB1
 GO:0006337 2 / 21 119× 1.25e-4 3.58e-3 ✓ sig.
regulation of G0 to G1 transition
SMARCA4, SMARCB1
 GO:0070316 2 / 25 99.7× 1.79e-4 4.67e-3 ✓ sig.
regulation of nucleotide-excision repair
SMARCA4, SMARCB1
 GO:2000819 2 / 28 89.0× 2.25e-4 5.47e-3 ✓ sig.
regulation of mitotic metaphase/anaphase transition
SMARCA4, SMARCB1
 GO:0030071 2 / 34 73.3× 3.32e-4 7.20e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
rhabdoid tumor predisposition syndrome 2 Small cell ovary carcinoma 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Rhabdoid tumor predisposition syndrome Small cell ovary carcinoma 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Rhabdoid tumor predisposition syndrome rhabdoid tumor predisposition syndrome 2 0.333 1 1.30e-4 3.90e-4 ✓ sig.
rhabdoid tumor predisposition syndrome 2 Thoracic neoplasms 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Small cell ovary carcinoma Thoracic neoplasms 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Rhabdoid tumor predisposition syndrome Thoracic neoplasms 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Carotid atherosclerosis Small cell ovary carcinoma 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Carotid atherosclerosis rhabdoid tumor predisposition syndrome 2 0.143 1 3.90e-4 8.52e-4 ✓ sig.
hereditary nonpolyposis colon cancer Small cell ovary carcinoma 0.111 1 5.20e-4 1.04e-3 ✓ sig.
hereditary nonpolyposis colon cancer rhabdoid tumor predisposition syndrome 2 0.111 1 5.20e-4 1.04e-3 ✓ sig.
hereditary nonpolyposis colon cancer thrombocytopenia 10 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Carotid atherosclerosis Rhabdoid tumor predisposition syndrome 0.125 1 7.79e-4 1.39e-3 ✓ sig.
Carotid atherosclerosis Thoracic neoplasms 0.125 1 7.79e-4 1.39e-3 ✓ sig.
hereditary nonpolyposis colon cancer Thoracic neoplasms 0.100 1 1.04e-3 1.72e-3 ✓ sig.