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 450

6 diseases · 15 shared-gene connections
6 Diseases
6 Unique genes
0.400 Avg. similarity score
Autosomal recessive nonsyndromic deafness 97 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 ⇵
Autosomal recessive nonsyndromic deafness 97 5 5 1
Deafness, autosomal recessive 97 5 5 1
Dysplasia of larynx 5 5 5
Malignant bladder paraganglioma 5 5 1
Mixed cell type cancer 5 5 3
Osteofibrous dysplasia 5 5 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
MET 6 / 6 Autosomal recessive nonsyndromic deafness 97, Deafness, autosomal recessive 97, Dysplasia of larynx, Malignant bladder paraganglioma and 2 more
TP53 2 / 6 Dysplasia of larynx, Mixed cell type cancer
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 ⇵
Non-small cell lung cancer
MET, TP53, PIK3CA, JAK3
 KEGG 4 / 73 110× 1.87e-8 1.28e-6 ✓ sig.
Gastric cancer
MET, TP53, PIK3CA, TGFBR2
 KEGG 4 / 150 53.4× 3.44e-7 1.65e-5 ✓ sig.
Hepatitis B
TP53, PIK3CA, TGFBR2, JAK3
 KEGG 4 / 163 49.1× 4.80e-7 2.21e-5 ✓ sig.
Hepatocellular carcinoma
MET, TP53, PIK3CA, TGFBR2
 KEGG 4 / 170 47.1× 5.69e-7 2.55e-5 ✓ sig.
Pathways in cancer
MET, TP53, PIK3CA, TGFBR2, JAK3
 KEGG 5 / 533 18.8× 9.77e-7 4.09e-5 ✓ sig.
Human T-cell leukemia virus 1 infection
TP53, PIK3CA, TGFBR2, JAK3
 KEGG 4 / 224 35.7× 1.72e-6 6.66e-5 ✓ sig.
MET activates PI3K/AKT signaling
MET, PIK3CA
 Reactome 2 / 6 667× 3.12e-6 1.10e-4 ✓ sig.
Central carbon metabolism in cancer
MET, TP53, PIK3CA
 KEGG 3 / 71 84.6× 3.91e-6 1.34e-4 ✓ sig.
Melanoma
MET, TP53, PIK3CA
 KEGG 3 / 73 82.3× 4.25e-6 1.44e-4 ✓ sig.
Pancreatic cancer
TP53, PIK3CA, TGFBR2
 KEGG 3 / 77 78.0× 5.00e-6 1.64e-4 ✓ sig.
Chronic myeloid leukemia
TP53, PIK3CA, TGFBR2
 KEGG 3 / 77 78.0× 5.00e-6 1.64e-4 ✓ sig.
Colorectal cancer
TP53, PIK3CA, TGFBR2
 KEGG 3 / 87 69.0× 7.23e-6 2.23e-4 ✓ sig.
PI3K-Akt signaling pathway
MET, TP53, PIK3CA, JAK3
 KEGG 4 / 361 22.2× 1.15e-5 3.26e-4 ✓ sig.
Measles
TP53, PIK3CA, JAK3
 KEGG 3 / 139 43.2× 2.96e-5 7.16e-4 ✓ sig.
Cellular senescence
TP53, PIK3CA, TGFBR2
 KEGG 3 / 157 38.2× 4.26e-5 9.64e-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 ⇵
vasculature development
FBXW7, PIK3CA
 GO:0001944 2 / 33 189× 4.52e-5 1.71e-3 ✓ sig.
positive regulation of reactive oxygen species metabolic process
TP53, TGFBR2
 GO:2000379 2 / 34 183× 4.80e-5 1.79e-3 ✓ sig.
gastrulation
TP53, TGFBR2
 GO:0007369 2 / 38 164× 6.01e-5 2.12e-3 ✓ sig.
negative regulation of gene expression
TP53, FBXW7, PIK3CA
 GO:0010629 3 / 339 27.6× 1.14e-4 3.39e-3 ✓ sig.
cellular response to UV
TP53, FBXW7
 GO:0034644 2 / 55 113× 1.27e-4 3.66e-3 ✓ sig.
regulation of gene expression
MET, PIK3CA, TGFBR2
 GO:0010468 3 / 402 23.2× 1.88e-4 4.88e-3 ✓ sig.
regulation of mitotic cell cycle
TP53, FBXW7
 GO:0007346 2 / 77 80.9× 2.49e-4 5.92e-3 ✓ sig.
liver development
MET, PIK3CA
 GO:0001889 2 / 87 71.6× 3.18e-4 7.04e-3 ✓ sig.
negative regulation of helicase activity
TP53
 GO:0051097 1 / 1 3,115× 3.21e-4 7.04e-3 ✓ sig.
regulation of intrinsic apoptotic signaling pathway by p53 class mediator
TP53
 GO:1902253 1 / 1 3,115× 3.21e-4 7.04e-3 ✓ sig.
negative regulation of G1 to G0 transition
TP53
 GO:1903451 1 / 1 3,115× 3.21e-4 7.04e-3 ✓ sig.
negative regulation of dendritic cell cytokine production
JAK3
 GO:0002731 1 / 1 3,115× 3.21e-4 7.04e-3 ✓ sig.
positive regulation of tolerance induction to self antigen
TGFBR2
 GO:0002651 1 / 1 3,115× 3.21e-4 7.04e-3 ✓ sig.
positive regulation of B cell tolerance induction
TGFBR2
 GO:0002663 1 / 1 3,115× 3.21e-4 7.04e-3 ✓ sig.
cell proliferation involved in endocardial cushion morphogenesis
TGFBR2
 GO:1905315 1 / 1 3,115× 3.21e-4 7.04e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Autosomal recessive nonsyndromic deafness 97 Osteofibrous dysplasia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Autosomal recessive nonsyndromic deafness 97 Mixed cell type cancer 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Autosomal recessive nonsyndromic deafness 97 Malignant bladder paraganglioma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Autosomal recessive nonsyndromic deafness 97 Deafness, autosomal recessive 97 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Deafness, autosomal recessive 97 Osteofibrous dysplasia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Deafness, autosomal recessive 97 Mixed cell type cancer 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Deafness, autosomal recessive 97 Malignant bladder paraganglioma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Malignant bladder paraganglioma Osteofibrous dysplasia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Malignant bladder paraganglioma Mixed cell type cancer 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Mixed cell type cancer Osteofibrous dysplasia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Autosomal recessive nonsyndromic deafness 97 Dysplasia of larynx 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Deafness, autosomal recessive 97 Dysplasia of larynx 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Dysplasia of larynx Malignant bladder paraganglioma 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Dysplasia of larynx Mixed cell type cancer 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Dysplasia of larynx Osteofibrous dysplasia 0.200 1 2.58e-4 5.38e-4 ✓ sig.