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 120

10 diseases · 20 shared-gene connections
10 Diseases
33 Unique genes
0.177 Avg. similarity score
Rhabdoid tumor predisposition syndrome Most-connected disease (7 links)
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Disease Searched: Carotid atherosclerosis 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 ⇵
Rhabdoid tumor predisposition syndrome 7 7 2
Small cell ovary carcinoma 5 5 1
Atypical teratoid rhabdoid tumor 4 4 1
Carotid atherosclerosis 4 4 6
Coffin-siris syndrome 4 4 17
Rhabdoid tumor 4 4 2
Thoracic neoplasms 4 4 2
hereditary nonpolyposis colon cancer 4 4 8
Schwannomatosis 3 3 3
thrombocytopenia 10 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
SMARCA4 6 / 10 Carotid atherosclerosis, Coffin-siris syndrome, hereditary nonpolyposis colon cancer, Rhabdoid tumor predisposition syndrome and 2 more
SMARCB1 5 / 10 Atypical teratoid rhabdoid tumor, Coffin-siris syndrome, Rhabdoid tumor, Rhabdoid tumor predisposition syndrome and 1 more
PTPRJ 2 / 10 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
SMARCB1, SMARCA4, ARID1A, ARID1B, ARID2, SMARCA2, SMARCC2, SMARCD1, SMARCE1
 Reactome 9 / 38 86.2× 4.18e-16 1.65e-13 ✓ sig.
ATP-dependent chromatin remodeling
SMARCB1, SMARCA4, ARID1A, ARID1B, ARID2, BICRA, DPF2, SMARCA2, SMARCC2, SMARCD1, SMARCE1
 KEGG 11 / 117 34.2× 7.51e-15 2.37e-12 ✓ sig.
RMTs methylate histone arginines
SMARCB1, SMARCA4, ARID1A, ARID1B, ARID2, SMARCA2, SMARCC2, SMARCD1, SMARCE1
 Reactome 9 / 79 41.5× 4.90e-13 1.11e-10 ✓ sig.
Hepatocellular carcinoma
SMARCB1, SMARCA4, ARID1A, ARID1B, ARID2, SMARCA2, SMARCC2, SMARCD1, SMARCE1
 KEGG 9 / 170 19.3× 5.32e-10 6.66e-8 ✓ sig.
Thermogenesis
SMARCB1, SMARCA4, RPS6KA3, ARID1A, ARID1B, SMARCA2, SMARCC2, SMARCD1, SMARCE1
 KEGG 9 / 234 14.0× 8.91e-9 8.26e-7 ✓ sig.
Deactivation of the beta-catenin transactivating complex
SOX4, SOX2
 Reactome 2 / 42 17.3× 5.89e-3 5.06e-2
POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation
SOX2
 Reactome 1 / 3 121× 8.22e-3 6.26e-2
RSK activation
RPS6KA3
 Reactome 1 / 4 91.0× 1.09e-2 7.50e-2
CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling
RPS6KA3
 Reactome 1 / 5 72.8× 1.37e-2 8.55e-2
PTK6 Regulates Cell Cycle
CDKN1B
 Reactome 1 / 6 60.7× 1.64e-2 9.53e-2
p53-Dependent G1 DNA Damage Response
CDKN1B
 Reactome 1 / 7 52.0× 1.91e-2 1.04e-1
2-LTR circle formation
XRCC4
 Reactome 1 / 7 52.0× 1.91e-2 1.04e-1
CREB phosphorylation
RPS6KA3
 Reactome 1 / 7 52.0× 1.91e-2 1.04e-1
Gastrin-CREB signalling pathway via PKC and MAPK
RPS6KA3
 Reactome 1 / 9 40.4× 2.45e-2 1.20e-1
AKT phosphorylates targets in the cytosol
CDKN1B
 Reactome 1 / 11 33.1× 2.98e-2 1.33e-1

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
regulation of G0 to G1 transition
SMARCB1, SMARCA4, ARID1A, ARID1B, ARID2, DPF2, SMARCA2, SMARCC2, SMARCD1, SMARCE1
 GO:0070316 10 / 25 227× 2.08e-22 4.69e-19 ✓ sig.
regulation of nucleotide-excision repair
SMARCB1, SMARCA4, ARID1A, ARID1B, ARID2, DPF2, SMARCA2, SMARCC2, SMARCD1, SMARCE1
 GO:2000819 10 / 28 202× 8.34e-22 1.71e-18 ✓ sig.
positive regulation of double-strand break repair
SMARCB1, FMN2, SMARCA4, ARID1A, ARID1B, ARID2, DPF2, SMARCA2, SMARCC2, SMARCD1, SMARCE1
 GO:2000781 11 / 47 133× 1.34e-21 2.69e-18 ✓ sig.
regulation of mitotic metaphase/anaphase transition
SMARCB1, SMARCA4, ARID1A, ARID1B, ARID2, DPF2, SMARCA2, SMARCC2, SMARCD1, SMARCE1
 GO:0030071 10 / 34 167× 8.28e-21 1.45e-17 ✓ sig.
positive regulation of cell differentiation
SMARCB1, SMARCA4, RPS6KA3, ARID1A, ARID1B, ARID2, SMARCA2, SMARCC2, SMARCD1, SMARCE1, NF2, SOX2
 GO:0045597 12 / 83 81.9× 8.46e-21 1.47e-17 ✓ sig.
regulation of G1/S transition of mitotic cell cycle
SMARCB1, SMARCA4, ARID1A, ARID1B, ARID2, DPF2, SMARCA2, SMARCC2, SMARCD1, SMARCE1, CDKN1B
 GO:2000045 11 / 57 109× 1.40e-20 2.42e-17 ✓ sig.
positive regulation of myoblast differentiation
SMARCB1, SMARCA4, ARID1A, ARID1B, ARID2, SMARCA2, SMARCC2, SMARCD1, SMARCE1, SOX4
 GO:0045663 10 / 47 120× 3.22e-19 4.36e-16 ✓ sig.
positive regulation of T cell differentiation
SMARCB1, SMARCA4, ARID1A, ARID1B, ARID2, SMARCA2, SMARCC2, SMARCD1, SMARCE1
 GO:0045582 9 / 40 127× 1.33e-17 1.47e-14 ✓ sig.
chromatin remodeling
SMARCB1, CFDP1, SMARCA4, ARID1A, ARID1B, ARID2, BICRA, DPF2, KDM8, SMARCA2, SMARCC2, SMARCD1
 GO:0006338 14 / 320 24.8× 8.58e-17 8.20e-14 ✓ sig.
nucleosome disassembly
SMARCB1, SMARCA4, ARID1A, ARID2, SMARCC2, SMARCD1, SMARCE1
 GO:0006337 7 / 21 189× 3.10e-15 2.26e-12 ✓ sig.
positive regulation of stem cell population maintenance
SMARCB1, SMARCA4, ARID1A, BICRA, DPF2, SMARCA2, SMARCD1, SMARCE1
 GO:1902459 8 / 47 96.4× 1.13e-14 7.44e-12 ✓ sig.
chromatin organization
SMARCB1, SMARCA4, ARID1A, ARID1B, ARID2, DPF2, KDM8, SMARCC2, SMARCD1, SMARCE1, SOX2, NFKBIZ
 GO:0006325 12 / 449 15.1× 7.19e-12 2.74e-9 ✓ sig.
positive regulation of DNA-templated transcription
SMARCA4, ARID1A, ARID1B, BICRA, KDM8, SMARCA2, SMARCC2, SMARCD1, SMARCE1, SOX11, SOX4, SOX2
 GO:0045893 13 / 778 9.5× 2.71e-10 7.08e-8 ✓ sig.
nervous system development
SMARCB1, SMARCA4, ARID1A, ARID1B, DPF2, SMARCA2, SMARCC2, SMARCD1, SMARCE1, SOX11, SOX4
 GO:0007399 11 / 631 9.9× 5.87e-9 1.07e-6 ✓ sig.
transcription initiation-coupled chromatin remodeling
SMARCB1, SMARCA4, ARID1A, ARID1B, SMARCD1
 GO:0045815 5 / 41 69.1× 8.96e-9 1.54e-6 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Coffin-siris syndrome Rhabdoid tumor predisposition syndrome 0.111 2 1.15e-6 6.66e-6 ✓ sig.
Atypical teratoid rhabdoid tumor Rhabdoid tumor predisposition syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Small cell ovary carcinoma Thoracic neoplasms 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Rhabdoid tumor predisposition syndrome Small cell ovary carcinoma 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Atypical teratoid rhabdoid tumor Rhabdoid tumor 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Atypical teratoid rhabdoid tumor Schwannomatosis 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Rhabdoid tumor predisposition syndrome Thoracic neoplasms 0.250 1 2.60e-4 6.51e-4 ✓ sig.
Rhabdoid tumor Rhabdoid tumor predisposition syndrome 0.250 1 2.60e-4 6.51e-4 ✓ sig.
Rhabdoid tumor predisposition syndrome Schwannomatosis 0.200 1 3.90e-4 8.67e-4 ✓ sig.
Rhabdoid tumor Schwannomatosis 0.200 1 3.90e-4 8.67e-4 ✓ sig.
Carotid atherosclerosis Small cell ovary carcinoma 0.143 1 3.90e-4 8.67e-4 ✓ sig.
hereditary nonpolyposis colon cancer Small cell ovary carcinoma 0.111 1 5.20e-4 1.06e-3 ✓ sig.
hereditary nonpolyposis colon cancer thrombocytopenia 10 0.111 1 5.20e-4 1.06e-3 ✓ sig.
Carotid atherosclerosis Thoracic neoplasms 0.125 1 7.79e-4 1.41e-3 ✓ sig.
Carotid atherosclerosis Rhabdoid tumor predisposition syndrome 0.125 1 7.79e-4 1.41e-3 ✓ sig.
hereditary nonpolyposis colon cancer Thoracic neoplasms 0.100 1 1.04e-3 1.74e-3 ✓ sig.
Coffin-siris syndrome Small cell ovary carcinoma 0.056 1 1.10e-3 1.83e-3 ✓ sig.
Atypical teratoid rhabdoid tumor Coffin-siris syndrome 0.056 1 1.10e-3 1.83e-3 ✓ sig.
Coffin-siris syndrome Rhabdoid tumor 0.053 1 2.21e-3 3.11e-3 ✓ sig.
Carotid atherosclerosis hereditary nonpolyposis colon cancer 0.071 1 3.11e-3 4.10e-3 ✓ sig.