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 556

5 diseases · 9 shared-gene connections
5 Diseases
16 Unique genes
0.251 Avg. similarity score
Hyperparathyroidism 2 with jaw tumors Most-connected disease (4 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 ⇵
Hyperparathyroidism 2 with jaw tumors 4 4 1
Hyperparathyroidism, familial primary 4 4 1
Parathyroid neoplasm 4 4 1
Apocrine adenocarcinoma 3 3 10
Cervical adenosarcoma 3 3 7

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

Gene ⇵ Member diseases ⇵ Linked diseases
CDC73 5 / 5 Apocrine adenocarcinoma, Cervical adenosarcoma, Hyperparathyroidism 2 with jaw tumors, Hyperparathyroidism, familial primary and 1 more
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 ⇵
Prostate cancer
KRAS, PIK3CA, PTEN, CTNNB1, HRAS, TP53, PDGFRA, AR
 KEGG 8 / 98 61.3× 1.79e-13 3.94e-11 ✓ sig.
Endometrial cancer
KRAS, PIK3CA, PTEN, CTNNB1, HRAS, TP53
 KEGG 6 / 59 76.3× 8.35e-11 9.99e-9 ✓ sig.
Pathways in cancer
KRAS, PIK3CA, PTEN, CTNNB1, ESR1, JAK2, HRAS, TP53, PDGFRA, AR
 KEGG 10 / 533 14.1× 1.72e-10 1.89e-8 ✓ sig.
Central carbon metabolism in cancer
KRAS, PIK3CA, PTEN, HRAS, TP53, PDGFRA
 KEGG 6 / 71 63.4× 2.63e-10 2.80e-8 ✓ sig.
Melanoma
KRAS, PIK3CA, PTEN, HRAS, TP53, PDGFRA
 KEGG 6 / 73 61.7× 3.12e-10 3.26e-8 ✓ sig.
Breast cancer
KRAS, PIK3CA, PTEN, CTNNB1, ESR1, HRAS, TP53
 KEGG 7 / 148 35.5× 3.90e-10 3.99e-8 ✓ sig.
Glioma
KRAS, PIK3CA, PTEN, HRAS, TP53, PDGFRA
 KEGG 6 / 76 59.3× 4.00e-10 4.08e-8 ✓ sig.
EGFR tyrosine kinase inhibitor resistance
KRAS, PIK3CA, PTEN, JAK2, HRAS, PDGFRA
 KEGG 6 / 80 56.3× 5.48e-10 5.44e-8 ✓ sig.
Hepatocellular carcinoma
KRAS, PIK3CA, PTEN, CTNNB1, HRAS, ARID1A, TP53
 KEGG 7 / 170 30.9× 1.03e-9 9.59e-8 ✓ sig.
Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants
KRAS, PIK3CA, HRAS, PDGFRA
 Reactome 4 / 12 250× 1.03e-9 9.59e-8 ✓ sig.
Signaling by PDGFRA extracellular domain mutants
KRAS, PIK3CA, HRAS, PDGFRA
 Reactome 4 / 12 250× 1.03e-9 9.59e-8 ✓ sig.
MicroRNAs in cancer
KRAS, PIK3CA, PTEN, ATM, HRAS, TP53, PDGFRA, DICER1
 KEGG 8 / 311 19.3× 1.99e-9 1.72e-7 ✓ sig.
Thyroid hormone signaling pathway
KRAS, PIK3CA, CTNNB1, ESR1, HRAS, TP53
 KEGG 6 / 122 36.9× 7.16e-9 5.47e-7 ✓ sig.
Prolactin signaling pathway
KRAS, PIK3CA, ESR1, JAK2, HRAS
 KEGG 5 / 71 52.9× 2.60e-8 1.72e-6 ✓ sig.
Cellular senescence
KRAS, PIK3CA, PTEN, ATM, HRAS, TP53
 KEGG 6 / 157 28.7× 3.26e-8 2.11e-6 ✓ 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 ⇵
positive regulation of transcription by RNA polymerase II
CDC73, PTEN, CTNNB1, KMT2C, ESR1, ATM, JAK2, HRAS, TP53, AR
 GO:0045944 10 / 1,208 9.7× 6.87e-9 1.27e-6 ✓ sig.
negative regulation of cell population proliferation
CDC73, PTEN, CTNNB1, JAK2, HRAS, TP53, AR
 GO:0008285 7 / 444 18.4× 3.88e-8 5.68e-6 ✓ sig.
chromatin remodeling
KMT2C, ESR1, KDM6A, ATM, JAK2, ARID1A
 GO:0006338 6 / 320 21.9× 1.67e-7 1.95e-5 ✓ sig.
negative regulation of neuron apoptotic process
KRAS, PIK3CA, CTNNB1, JAK2, HRAS
 GO:0043524 5 / 160 36.5× 1.75e-7 2.02e-5 ✓ sig.
negative regulation of gene expression
PIK3CA, CTNNB1, ESR1, HRAS, TP53, DICER1
 GO:0010629 6 / 339 20.7× 2.34e-7 2.58e-5 ✓ sig.
positive regulation of cell differentiation
CTNNB1, JAK2, ARID1A, AR
 GO:0045597 4 / 83 56.3× 6.32e-7 5.91e-5 ✓ sig.
neuron apoptotic process
KRAS, ATM, HRAS, TP53
 GO:0051402 4 / 98 47.7× 1.23e-6 1.02e-4 ✓ sig.
cellular response to gamma radiation
ATM, HRAS, TP53
 GO:0071480 3 / 28 125× 1.67e-6 1.31e-4 ✓ sig.
positive regulation of epithelial cell proliferation involved in prostate gland development
CTNNB1, AR
 GO:0060769 2 / 3 779× 2.06e-6 1.55e-4 ✓ sig.
positive regulation of gene expression
KRAS, CTNNB1, ATM, HRAS, TP53, AR
 GO:0010628 6 / 504 13.9× 2.38e-6 1.75e-4 ✓ sig.
heart development
PTEN, CTNNB1, KDM6A, ATM, TP53
 GO:0007507 5 / 273 21.4× 2.46e-6 1.79e-4 ✓ sig.
positive regulation of cell population proliferation
PTEN, CTNNB1, JAK2, HRAS, PDGFRA, AR
 GO:0008284 6 / 532 13.2× 3.25e-6 2.23e-4 ✓ sig.
fibroblast proliferation
ESR1, HRAS, TP53
 GO:0048144 3 / 42 83.4× 5.79e-6 3.56e-4 ✓ sig.
MAPK cascade
KRAS, CTNNB1, HRAS, AR
 GO:0000165 4 / 147 31.8× 6.22e-6 3.77e-4 ✓ sig.
epithelial cell differentiation involved in prostate gland development
CTNNB1, AR
 GO:0060742 2 / 5 467× 6.86e-6 4.06e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Hyperparathyroidism 2 with jaw tumors Parathyroid neoplasm 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hyperparathyroidism 2 with jaw tumors Hyperparathyroidism, familial primary 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hyperparathyroidism, familial primary Parathyroid neoplasm 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cervical adenosarcoma Hyperparathyroidism 2 with jaw tumors 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Cervical adenosarcoma Hyperparathyroidism, familial primary 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Cervical adenosarcoma Parathyroid neoplasm 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Apocrine adenocarcinoma Hyperparathyroidism 2 with jaw tumors 0.111 1 5.17e-4 9.13e-4 ✓ sig.
Apocrine adenocarcinoma Hyperparathyroidism, familial primary 0.111 1 5.17e-4 9.13e-4 ✓ sig.
Apocrine adenocarcinoma Parathyroid neoplasm 0.111 1 5.17e-4 9.13e-4 ✓ sig.