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 507

6 diseases · 9 shared-gene connections
6 Diseases
5 Unique genes
0.337 Avg. similarity score
Urogenital neoplasms 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 ⇵
Urogenital neoplasms 5 5 5
Fuhrmann syndrome 3 3 1
Limb/pelvis-hypoplasia/aplasia syndrome 3 3 1
Skeletal malformations syndrome 3 3 1
Hypogonadotropic hypogonadism 14 with or without anosmia 2 2 1
Uinary system neoplasms 2 2 2

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

Gene ⇵ Member diseases ⇵ Linked diseases
WNT7A 4 / 6 Fuhrmann syndrome, Limb/pelvis-hypoplasia/aplasia syndrome, Skeletal malformations syndrome, Urogenital neoplasms
WDR11 3 / 6 Hypogonadotropic hypogonadism 14 with or without anosmia, Uinary system neoplasms, Urogenital neoplasms
SLC2A13 2 / 6 Uinary system neoplasms, Urogenital neoplasms
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 ⇵
Stabilization of p53
CDKN2A, TP53
 Reactome 2 / 11 437× 7.62e-6 2.33e-4 ✓ sig.
SUMOylation of transcription factors
CDKN2A, TP53
 Reactome 2 / 18 267× 2.12e-5 5.46e-4 ✓ sig.
Hepatocellular carcinoma
CDKN2A, TP53, WNT7A
 KEGG 3 / 170 42.4× 2.73e-5 6.73e-4 ✓ sig.
Oncogene Induced Senescence
CDKN2A, TP53
 Reactome 2 / 33 146× 7.28e-5 1.47e-3 ✓ sig.
Regulation of TP53 Degradation
CDKN2A, TP53
 Reactome 2 / 36 133× 8.69e-5 1.70e-3 ✓ sig.
Transcriptional Regulation by VENTX
CDKN2A, TP53
 Reactome 2 / 38 126× 9.69e-5 1.85e-3 ✓ sig.
Bladder cancer
CDKN2A, TP53
 KEGG 2 / 41 117× 1.13e-4 2.09e-3 ✓ sig.
Basal cell carcinoma
TP53, WNT7A
 KEGG 2 / 63 76.3× 2.68e-4 4.13e-3 ✓ sig.
Melanoma
CDKN2A, TP53
 KEGG 2 / 73 65.8× 3.60e-4 5.18e-3 ✓ sig.
Non-small cell lung cancer
CDKN2A, TP53
 KEGG 2 / 73 65.8× 3.60e-4 5.18e-3 ✓ sig.
Platinum drug resistance
CDKN2A, TP53
 KEGG 2 / 75 64.1× 3.80e-4 5.40e-3 ✓ sig.
p53 signaling pathway
CDKN2A, TP53
 KEGG 2 / 75 64.1× 3.80e-4 5.40e-3 ✓ sig.
Glioma
CDKN2A, TP53
 KEGG 2 / 76 63.2× 3.90e-4 5.52e-3 ✓ sig.
Pancreatic cancer
CDKN2A, TP53
 KEGG 2 / 77 62.4× 4.01e-4 5.63e-3 ✓ sig.
Chronic myeloid leukemia
CDKN2A, TP53
 KEGG 2 / 77 62.4× 4.01e-4 5.63e-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 ⇵
somatic stem cell division
CDKN2A, WNT7A
 GO:0048103 2 / 10 747× 2.58e-6 1.86e-4 ✓ sig.
rRNA transcription
CDKN2A, TP53
 GO:0009303 2 / 15 498× 6.01e-6 3.67e-4 ✓ sig.
replicative senescence
CDKN2A, TP53
 GO:0090399 2 / 16 467× 6.86e-6 4.06e-4 ✓ sig.
cellular senescence
CDKN2A, TP53
 GO:0090398 2 / 57 131× 9.09e-5 2.88e-3 ✓ sig.
somatic stem cell population maintenance
CDKN2A, WNT7A
 GO:0035019 2 / 64 117× 1.15e-4 3.42e-3 ✓ sig.
Ras protein signal transduction
CDKN2A, TP53
 GO:0007265 2 / 79 94.6× 1.75e-4 4.62e-3 ✓ sig.
positive regulation of gene expression
CDKN2A, TP53, WNT7A
 GO:0010628 3 / 504 22.2× 1.87e-4 4.86e-3 ✓ sig.
apoptotic signaling pathway
CDKN2A, TP53
 GO:0097190 2 / 84 89.0× 1.98e-4 5.04e-3 ✓ sig.
negative regulation of helicase activity
TP53
 GO:0051097 1 / 1 3,737× 2.68e-4 6.25e-3 ✓ sig.
regulation of intrinsic apoptotic signaling pathway by p53 class mediator
TP53
 GO:1902253 1 / 1 3,737× 2.68e-4 6.25e-3 ✓ sig.
negative regulation of G1 to G0 transition
TP53
 GO:1903451 1 / 1 3,737× 2.68e-4 6.25e-3 ✓ sig.
asymmetric protein localization involved in cell fate determination
WNT7A
 GO:0045167 1 / 1 3,737× 2.68e-4 6.25e-3 ✓ sig.
multicellular organism growth
WDR11, TP53
 GO:0035264 2 / 115 65.0× 3.71e-4 7.80e-3 ✓ sig.
negative regulation of cell growth
CDKN2A, TP53
 GO:0030308 2 / 115 65.0× 3.71e-4 7.80e-3 ✓ sig.
regulation of thymocyte apoptotic process
TP53
 GO:0070243 1 / 2 1,869× 5.35e-4 9.88e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Uinary system neoplasms Urogenital neoplasms 0.400 2 5.00e-8 3.63e-7 ✓ sig.
Fuhrmann syndrome Skeletal malformations syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Fuhrmann syndrome Limb/pelvis-hypoplasia/aplasia syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Limb/pelvis-hypoplasia/aplasia syndrome Skeletal malformations syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hypogonadotropic hypogonadism 14 with or without anosmia Uinary system neoplasms 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Fuhrmann syndrome Urogenital neoplasms 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Hypogonadotropic hypogonadism 14 with or without anosmia Urogenital neoplasms 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Limb/pelvis-hypoplasia/aplasia syndrome Urogenital neoplasms 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Skeletal malformations syndrome Urogenital neoplasms 0.200 1 2.58e-4 5.38e-4 ✓ sig.