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 297

6 diseases · 14 shared-gene connections
6 Diseases
25 Unique genes
0.321 Avg. similarity score
Congenital hypothalamic hamartoma syndrome 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 ⇵
Congenital hypothalamic hamartoma syndrome 5 5 1
Curry-jones syndrome 5 5 1
Winter shortland temple syndrome 5 5 1
mosaic SMO syndrome 5 5 1
Ameloblastoma 4 4 2
Meningioma 4 4 24

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

Gene ⇵ Member diseases ⇵ Linked diseases
SMO 6 / 6 Ameloblastoma, Congenital hypothalamic hamartoma syndrome, Curry-jones syndrome, Meningioma and 2 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 ⇵
Hepatocellular carcinoma
BRAF, PTEN, SMARCE1, SMARCB1, AKT1, PIK3CA, TERT
 KEGG 7 / 170 19.8× 3.90e-8 2.86e-6 ✓ sig.
Melanoma
BRAF, PDGFB, PTEN, AKT1, PIK3CA
 KEGG 5 / 73 32.9× 3.49e-7 1.96e-5 ✓ sig.
Glioma
BRAF, PDGFB, PTEN, AKT1, PIK3CA
 KEGG 5 / 76 31.6× 4.27e-7 2.34e-5 ✓ sig.
Breast cancer
BRAF, PTEN, AKT1, HES1, PGR, PIK3CA
 KEGG 6 / 148 19.5× 4.62e-7 2.50e-5 ✓ sig.
EGFR tyrosine kinase inhibitor resistance
BRAF, PDGFB, PTEN, AKT1, PIK3CA
 KEGG 5 / 80 30.0× 5.53e-7 2.93e-5 ✓ sig.
Pathways in cancer
BRAF, SMO, PDGFB, PTEN, SUFU, AKT1, HES1, PIK3CA, TERT
 KEGG 9 / 533 8.1× 6.74e-7 3.46e-5 ✓ sig.
Prostate cancer
BRAF, PDGFB, PTEN, AKT1, PIK3CA
 KEGG 5 / 98 24.5× 1.52e-6 7.00e-5 ✓ sig.
Endometrial cancer
BRAF, PTEN, AKT1, PIK3CA
 KEGG 4 / 59 32.6× 6.15e-6 2.23e-4 ✓ sig.
Renal cell carcinoma
BRAF, PDGFB, AKT1, PIK3CA
 KEGG 4 / 70 27.5× 1.22e-5 3.96e-4 ✓ sig.
Focal adhesion
BRAF, PDGFB, PTEN, AKT1, PIK3CA
 KEGG 5 / 203 11.8× 5.30e-5 1.34e-3 ✓ sig.
Proteoglycans in cancer
BRAF, SMO, AKT1, CTSL, PIK3CA
 KEGG 5 / 204 11.8× 5.42e-5 1.37e-3 ✓ sig.
Progesterone-mediated oocyte maturation
BRAF, AKT1, PGR, PIK3CA
 KEGG 4 / 110 17.5× 7.27e-5 1.72e-3 ✓ sig.
Negative regulation of the PI3K/AKT network
PTEN, AKT1
 Reactome 2 / 8 120× 1.16e-4 2.52e-3 ✓ sig.
FoxO signaling pathway
BRAF, PTEN, AKT1, PIK3CA
 KEGG 4 / 133 14.4× 1.52e-4 3.14e-3 ✓ sig.
Estrogen signaling pathway
AKT1, GREB1, PGR, PIK3CA
 KEGG 4 / 139 13.8× 1.80e-4 3.60e-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 ⇵
interleukin-18-mediated signaling pathway
PDGFB, AKT1, NLRP6
 GO:0035655 3 / 14 160× 7.62e-7 6.67e-5 ✓ sig.
negative regulation of gene expression
SMO, PDGFB, AKT1, HES1, PGR, PIK3CA
 GO:0010629 6 / 339 13.2× 4.51e-6 2.76e-4 ✓ sig.
negative regulation of proteolysis
AKT1, CST3, CSTB
 GO:0045861 3 / 27 83.1× 6.06e-6 3.50e-4 ✓ sig.
paracrine signaling
PDGFB, PGR
 GO:0038001 2 / 7 214× 3.59e-5 1.40e-3 ✓ sig.
positive regulation of gene expression
BRAF, SMO, PDGFB, AKT1, HES1, PGR
 GO:0010628 6 / 504 8.9× 4.28e-5 1.60e-3 ✓ sig.
positive regulation of smooth muscle cell proliferation
PDGFB, AKT1, PIK3CA
 GO:0048661 3 / 52 43.1× 4.48e-5 1.66e-3 ✓ sig.
spinal cord dorsal/ventral patterning
SMO, SUFU
 GO:0021513 2 / 8 187× 4.79e-5 1.74e-3 ✓ sig.
forebrain morphogenesis
SMO, PTEN
 GO:0048853 2 / 10 149× 7.68e-5 2.49e-3 ✓ sig.
epidermal growth factor receptor signaling pathway
BRAF, AKT1, PIK3CA
 GO:0007173 3 / 64 35.0× 8.35e-5 2.64e-3 ✓ sig.
anoikis
AKT1, PIK3CA
 GO:0043276 2 / 12 125× 1.12e-4 3.30e-3 ✓ sig.
protein K29-linked ubiquitination
AKT1, TRAF7
 GO:0035519 2 / 12 125× 1.12e-4 3.30e-3 ✓ sig.
positive regulation of organ growth
SMO, AKT1
 GO:0046622 2 / 13 115× 1.33e-4 3.74e-3 ✓ sig.
mammary gland epithelial cell differentiation
SMO, AKT1
 GO:0060644 2 / 14 107× 1.55e-4 4.20e-3 ✓ sig.
negative regulation of macroautophagy
AKT1, PIK3CA
 GO:0016242 2 / 14 107× 1.55e-4 4.20e-3 ✓ sig.
negative regulation of osteoblast proliferation
MN1, NF2
 GO:0033689 2 / 14 107× 1.55e-4 4.20e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Congenital hypothalamic hamartoma syndrome Curry-jones syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Congenital hypothalamic hamartoma syndrome Winter shortland temple syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Congenital hypothalamic hamartoma syndrome mosaic SMO syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Curry-jones syndrome Winter shortland temple syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Curry-jones syndrome mosaic SMO syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
mosaic SMO syndrome Winter shortland temple syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Ameloblastoma Congenital hypothalamic hamartoma syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Ameloblastoma Curry-jones syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Ameloblastoma Winter shortland temple syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Ameloblastoma mosaic SMO syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Congenital hypothalamic hamartoma syndrome Meningioma 0.040 1 1.56e-3 2.36e-3 ✓ sig.
Curry-jones syndrome Meningioma 0.040 1 1.56e-3 2.36e-3 ✓ sig.
Meningioma mosaic SMO syndrome 0.040 1 1.56e-3 2.36e-3 ✓ sig.
Meningioma Winter shortland temple syndrome 0.040 1 1.56e-3 2.36e-3 ✓ sig.