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 392

6 diseases · 12 shared-gene connections
6 Diseases
22 Unique genes
0.254 Avg. similarity score
Intellectual developmental disorder growth microcephaly Most-connected disease (5 links)
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Disease Searched: Gastric tubular adenocarcinoma 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 ⇵
Intellectual developmental disorder growth microcephaly 5 5 1
Intellectual developmental disorder, autosomal dominant 21 5 5 1
Mental retardation, autosomal dominant 21 5 5 1
Gastric tubular adenocarcinoma 3 3 14
Hidradenocarcinoma 3 3 10
Intellectual developmental disorder dysmorphic microcephaly 3 3 2

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

Gene ⇵ Member diseases ⇵ Linked diseases
CTCF 6 / 6 Gastric tubular adenocarcinoma, Hidradenocarcinoma, Intellectual developmental disorder dysmorphic microcephaly, Intellectual developmental disorder growth microcephaly and 2 more
ARID1A 2 / 6 Gastric tubular adenocarcinoma, Hidradenocarcinoma
TP53 2 / 6 Gastric tubular adenocarcinoma, Hidradenocarcinoma
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 ⇵
Pathways in cancer
TP53, PML, PIK3CA, IL6ST, AR, GNAS, PTCH1, AKT1, CDH1
 KEGG 9 / 533 9.2× 1.85e-7 9.58e-6 ✓ sig.
Endometrial cancer
TP53, PIK3CA, AKT1, CDH1
 KEGG 4 / 59 37.0× 3.60e-6 1.25e-4 ✓ sig.
Melanoma
TP53, PIK3CA, AKT1, CDH1
 KEGG 4 / 73 29.9× 8.46e-6 2.54e-4 ✓ sig.
Regulation of TP53 Activity through Acetylation
TP53, PML, AKT1
 Reactome 3 / 23 71.2× 9.23e-6 2.73e-4 ✓ sig.
Herpes simplex virus 1 infection
TP53, DAXX, PML, PIK3CA, AKT1
 KEGG 5 / 182 15.0× 1.62e-5 4.36e-4 ✓ sig.
B cell receptor signaling pathway
MALT1, PIK3CA, CARD11, AKT1
 KEGG 4 / 91 24.0× 2.03e-5 5.28e-4 ✓ sig.
Prostate cancer
TP53, PIK3CA, AR, AKT1
 KEGG 4 / 98 22.3× 2.72e-5 6.71e-4 ✓ sig.
Endocrine resistance
TP53, PIK3CA, GNAS, AKT1
 KEGG 4 / 99 22.1× 2.84e-5 6.92e-4 ✓ sig.
Chemical carcinogenesis - receptor activation
PIK3CA, AR, GNAS, BCL6, AKT1
 KEGG 5 / 215 12.7× 3.61e-5 8.42e-4 ✓ sig.
Regulation of TP53 Degradation
TP53, DAXX, AKT1
 Reactome 3 / 36 45.5× 3.66e-5 8.52e-4 ✓ sig.
Neurotrophin signaling pathway
TP53, PIK3CA, MAP3K1, AKT1
 KEGG 4 / 120 18.2× 6.03e-5 1.27e-3 ✓ sig.
T cell receptor signaling pathway
MALT1, PIK3CA, CARD11, AKT1
 KEGG 4 / 122 17.9× 6.44e-5 1.33e-3 ✓ sig.
Growth hormone synthesis, secretion and action
PIK3CA, MAP3K1, GNAS, AKT1
 KEGG 4 / 122 17.9× 6.44e-5 1.33e-3 ✓ sig.
Apoptosis
TP53, DAXX, PIK3CA, AKT1
 KEGG 4 / 137 15.9× 1.01e-4 1.91e-3 ✓ sig.
Gastric cancer
TP53, PIK3CA, AKT1, CDH1
 KEGG 4 / 150 14.6× 1.44e-4 2.53e-3 ✓ 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 ⇵
in utero embryonic development
CTCF, TP53, NBN, BAP1, AR, PTCH1
 GO:0001701 6 / 252 20.2× 3.53e-7 3.64e-5 ✓ sig.
regulation of apoptotic process
TP53, DAXX, MALT1, CARD11, BCL6, AKT1
 GO:0042981 6 / 254 20.1× 3.70e-7 3.77e-5 ✓ sig.
positive regulation of DNA-templated transcription
CTCF, TP53, DAXX, ARID1A, PML, AR, PTCH1, CDH1
 GO:0045893 8 / 778 8.7× 1.66e-6 1.30e-4 ✓ sig.
negative regulation of gene expression
CTCF, TP53, DAXX, PML, PIK3CA, AKT1
 GO:0010629 6 / 339 15.0× 1.99e-6 1.51e-4 ✓ sig.
negative regulation of DNA-templated transcription
CTCF, TP53, DAXX, PML, BAP1, BCL6, PTCH1
 GO:0045892 7 / 631 9.4× 5.30e-6 3.32e-4 ✓ sig.
regulation of gene expression
DAXX, PIK3CA, BAP1, SETD2, AR, CDH1
 GO:0010468 6 / 402 12.7× 5.32e-6 3.32e-4 ✓ sig.
insulin-like growth factor receptor signaling pathway
PIK3CA, AR, AKT1
 GO:0048009 3 / 33 77.2× 7.55e-6 4.39e-4 ✓ sig.
negative regulation of cell population proliferation
CTCF, TP53, PML, BAP1, AR, PTCH1
 GO:0008285 6 / 444 11.5× 9.39e-6 5.18e-4 ✓ sig.
cell population proliferation
TP53, BIRC6, BAP1, BCL6, AKT1
 GO:0008283 5 / 263 16.1× 1.15e-5 6.07e-4 ✓ sig.
DNA damage response, signal transduction by p53 class mediator
TP53, PML, NBN
 GO:0030330 3 / 48 53.1× 2.37e-5 1.05e-3 ✓ sig.
negative regulation of apoptotic process
TP53, BIRC6, MALT1, IL6ST, BCL6, AKT1
 GO:0043066 6 / 524 9.7× 2.40e-5 1.06e-3 ✓ sig.
vascular endothelial cell response to laminar fluid shear stress
GNAS, AKT1
 GO:0097700 2 / 9 189× 4.74e-5 1.78e-3 ✓ sig.
response to alkaloid
SETD2, PTCH1
 GO:0043279 2 / 11 154× 7.23e-5 2.43e-3 ✓ sig.
regulation of cell population proliferation
TP53, BIRC6, BCL6, PTCH1
 GO:0042127 4 / 201 16.9× 8.16e-5 2.66e-3 ✓ sig.
anoikis
PIK3CA, AKT1
 GO:0043276 2 / 12 142× 8.67e-5 2.78e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Intellectual developmental disorder growth microcephaly Mental retardation, autosomal dominant 21 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Intellectual developmental disorder growth microcephaly Intellectual developmental disorder, autosomal dominant 21 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Intellectual developmental disorder, autosomal dominant 21 Mental retardation, autosomal dominant 21 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Intellectual developmental disorder dysmorphic microcephaly Intellectual developmental disorder growth microcephaly 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Intellectual developmental disorder dysmorphic microcephaly Mental retardation, autosomal dominant 21 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Intellectual developmental disorder dysmorphic microcephaly Intellectual developmental disorder, autosomal dominant 21 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Hidradenocarcinoma Intellectual developmental disorder growth microcephaly 0.111 1 5.17e-4 9.13e-4 ✓ sig.
Hidradenocarcinoma Mental retardation, autosomal dominant 21 0.111 1 5.17e-4 9.13e-4 ✓ sig.
Hidradenocarcinoma Intellectual developmental disorder, autosomal dominant 21 0.111 1 5.17e-4 9.13e-4 ✓ sig.
Gastric tubular adenocarcinoma Intellectual developmental disorder growth microcephaly 0.071 1 8.39e-4 1.34e-3 ✓ sig.
Gastric tubular adenocarcinoma Intellectual developmental disorder, autosomal dominant 21 0.071 1 8.39e-4 1.34e-3 ✓ sig.
Gastric tubular adenocarcinoma Mental retardation, autosomal dominant 21 0.071 1 8.39e-4 1.34e-3 ✓ sig.