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 366

7 diseases · 12 shared-gene connections
7 Diseases
14 Unique genes
0.259 Avg. similarity score
Breast ductal adenoma Most-connected disease (5 links)
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Disease Searched: Intraductal breast papilloma 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 ⇵
Breast ductal adenoma 5 5 3
Breast fibrosis 4 4 1
Intraductal breast papilloma 4 4 4
Overgrowth syndrome 4 4 5
Vascular malformation 4 4 5
Usual ductal breast hyperplasia 2 2 7
Fanconi anemia complementation group D2 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
AKT1 6 / 7 Breast ductal adenoma, Breast fibrosis, Intraductal breast papilloma, Overgrowth syndrome and 2 more
PIK3CA 5 / 7 Breast ductal adenoma, Intraductal breast papilloma, Overgrowth syndrome, Usual ductal breast hyperplasia and 1 more
GNAS 3 / 7 Breast ductal adenoma, Intraductal breast papilloma, Usual ductal breast hyperplasia
FANCD2 2 / 7 Fanconi anemia complementation group D2, Overgrowth syndrome
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 ⇵
Endocrine resistance
PIK3CA, AKT1, BRAF, GNAS, HRAS, MTOR, ESR1, KRAS, PIK3R1
 KEGG 9 / 99 78.0× 2.35e-16 9.15e-14 ✓ sig.
Acute myeloid leukemia
PIK3CA, AKT1, BRAF, HRAS, MTOR, KRAS, PIK3R1
 KEGG 7 / 68 88.3× 4.52e-13 9.28e-11 ✓ sig.
Glioma
PIK3CA, AKT1, BRAF, HRAS, MTOR, KRAS, PIK3R1
 KEGG 7 / 76 79.0× 1.01e-12 1.93e-10 ✓ sig.
Breast cancer
PIK3CA, AKT1, BRAF, HRAS, MTOR, ESR1, KRAS, PIK3R1
 KEGG 8 / 148 46.4× 1.24e-12 2.31e-10 ✓ sig.
EGFR tyrosine kinase inhibitor resistance
PIK3CA, AKT1, BRAF, HRAS, MTOR, KRAS, PIK3R1
 KEGG 7 / 80 75.1× 1.47e-12 2.69e-10 ✓ sig.
ErbB signaling pathway
PIK3CA, AKT1, BRAF, HRAS, MTOR, KRAS, PIK3R1
 KEGG 7 / 86 69.8× 2.48e-12 4.30e-10 ✓ sig.
Colorectal cancer
PIK3CA, AKT1, BRAF, HRAS, MTOR, KRAS, PIK3R1
 KEGG 7 / 87 69.0× 2.70e-12 4.65e-10 ✓ sig.
Prostate cancer
PIK3CA, AKT1, BRAF, HRAS, MTOR, KRAS, PIK3R1
 KEGG 7 / 98 61.3× 6.35e-12 1.01e-9 ✓ sig.
Proteoglycans in cancer
PIK3CA, AKT1, BRAF, HRAS, MTOR, ESR1, KRAS, PIK3R1
 KEGG 8 / 204 33.6× 1.66e-11 2.40e-9 ✓ sig.
Chemical carcinogenesis - receptor activation
PIK3CA, AKT1, GNAS, HRAS, MTOR, ESR1, KRAS, PIK3R1
 KEGG 8 / 215 31.9× 2.54e-11 3.53e-9 ✓ sig.
Thyroid hormone signaling pathway
PIK3CA, AKT1, HRAS, MTOR, ESR1, KRAS, PIK3R1
 KEGG 7 / 122 49.2× 3.04e-11 4.12e-9 ✓ sig.
Growth hormone synthesis, secretion and action
PIK3CA, AKT1, GNAS, HRAS, MTOR, KRAS, PIK3R1
 KEGG 7 / 122 49.2× 3.04e-11 4.12e-9 ✓ sig.
Endometrial cancer
PIK3CA, AKT1, BRAF, HRAS, KRAS, PIK3R1
 KEGG 6 / 59 87.2× 3.15e-11 4.27e-9 ✓ sig.
Longevity regulating pathway - multiple species
PIK3CA, AKT1, HRAS, MTOR, KRAS, PIK3R1
 KEGG 6 / 62 83.0× 4.29e-11 5.60e-9 ✓ sig.
Insulin signaling pathway
PIK3CA, AKT1, BRAF, HRAS, MTOR, KRAS, PIK3R1
 KEGG 7 / 138 43.5× 7.28e-11 8.92e-9 ✓ 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 ⇵
insulin receptor signaling pathway
PIK3CA, AKT1, HRAS, MTOR, PIK3R1
 GO:0008286 5 / 80 83.4× 2.46e-9 5.10e-7 ✓ sig.
vascular endothelial cell response to laminar fluid shear stress
AKT1, GNAS, MTOR
 GO:0097700 3 / 9 445× 2.80e-8 4.33e-6 ✓ sig.
anoikis
PIK3CA, AKT1, MTOR
 GO:0043276 3 / 12 334× 7.33e-8 9.83e-6 ✓ sig.
negative regulation of macroautophagy
PIK3CA, AKT1, MTOR
 GO:0016242 3 / 14 286× 1.21e-7 1.49e-5 ✓ sig.
phosphatidylinositol 3-kinase/protein kinase B signal transduction
PIK3CA, AKT1, MTOR, PIK3R1
 GO:0043491 4 / 92 58.0× 5.30e-7 5.12e-5 ✓ sig.
cellular response to insulin stimulus
PIK3CA, AKT1, MTOR, PIK3R1
 GO:0032869 4 / 102 52.3× 8.03e-7 7.17e-5 ✓ sig.
positive regulation of lamellipodium assembly
PIK3CA, MTOR, PIK3R1
 GO:0010592 3 / 28 143× 1.08e-6 9.19e-5 ✓ sig.
insulin-like growth factor receptor signaling pathway
PIK3CA, AKT1, PIK3R1
 GO:0048009 3 / 33 121× 1.80e-6 1.39e-4 ✓ sig.
T cell costimulation
YES1, AKT1, MTOR
 GO:0031295 3 / 45 89.0× 4.66e-6 3.00e-4 ✓ sig.
negative regulation of neuron apoptotic process
PIK3CA, BRAF, HRAS, KRAS
 GO:0043524 4 / 160 33.4× 4.85e-6 3.10e-4 ✓ sig.
positive regulation of smooth muscle cell proliferation
PIK3CA, AKT1, PIK3R1
 GO:0048661 3 / 52 77.0× 7.24e-6 4.23e-4 ✓ sig.
epidermal growth factor receptor signaling pathway
PIK3CA, AKT1, BRAF
 GO:0007173 3 / 64 62.6× 1.36e-5 6.89e-4 ✓ sig.
interleukin-18-mediated signaling pathway
AKT1, PIK3R1
 GO:0035655 2 / 14 191× 4.72e-5 1.77e-3 ✓ sig.
regulation of long-term neuronal synaptic plasticity
HRAS, KRAS
 GO:0048169 2 / 18 148× 7.92e-5 2.60e-3 ✓ sig.
behavioral response to pain
AKT1, MTOR
 GO:0048266 2 / 18 148× 7.92e-5 2.60e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Breast ductal adenoma Intraductal breast papilloma 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Breast ductal adenoma Usual ductal breast hyperplasia 0.286 2 1.25e-7 8.63e-7 ✓ sig.
Intraductal breast papilloma Usual ductal breast hyperplasia 0.250 2 3.75e-7 2.42e-6 ✓ sig.
Breast ductal adenoma Breast fibrosis 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Breast fibrosis Vascular malformation 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Breast fibrosis Intraductal breast papilloma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Breast fibrosis Overgrowth syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Fanconi anemia complementation group D2 Overgrowth syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Breast ductal adenoma Overgrowth syndrome 0.200 1 3.87e-4 7.33e-4 ✓ sig.
Breast ductal adenoma Vascular malformation 0.200 1 3.87e-4 7.33e-4 ✓ sig.
Overgrowth syndrome Vascular malformation 0.167 1 5.81e-4 1.00e-3 ✓ sig.
Intraductal breast papilloma Vascular malformation 0.167 1 5.81e-4 1.00e-3 ✓ sig.