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 232

9 diseases · 18 shared-gene connections
9 Diseases
14 Unique genes
0.303 Avg. similarity score
Lung signet ring cell carcinoma Most-connected disease (6 links)
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Disease Searched: Liver solitary fibrous tumor 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 ⇵
Lung signet ring cell carcinoma 6 6 4
Neuroblastic tumor 5 5 1
Neuroblastoma, susceptibility to, 3 5 5 1
Signet ring cell carcinoma 5 5 2
Liver solitary fibrous tumor 4 4 2
Kyphomelic dysplasia 3 3 1
Lymphoepithelioma-like lung carcinoma 3 3 8
Retroperitoneal inflammatory myofibroblastic tumor 3 3 2
Skeletal muscle disorder 2 2 4

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

Gene ⇵ Member diseases ⇵ Linked diseases
ALK 7 / 9 Liver solitary fibrous tumor, Lung signet ring cell carcinoma, Lymphoepithelioma-like lung carcinoma, Neuroblastic tumor and 3 more
KIF5B 4 / 9 Kyphomelic dysplasia, Lung signet ring cell carcinoma, Lymphoepithelioma-like lung carcinoma, Skeletal muscle disorder
EML4 3 / 9 Lung signet ring cell carcinoma, Lymphoepithelioma-like lung carcinoma, Signet ring cell carcinoma
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
KIF5B, ALK, EML4, EGFR, TP53, BRAF, PIK3CA
 KEGG 7 / 73 82.3× 7.57e-13 1.50e-10 ✓ sig.
Pancreatic cancer
TGFBR2, EGFR, TP53, BRAF, PIK3CA
 KEGG 5 / 77 55.7× 1.82e-8 1.25e-6 ✓ sig.
Colorectal cancer
TGFBR2, EGFR, TP53, BRAF, PIK3CA
 KEGG 5 / 87 49.3× 3.38e-8 2.17e-6 ✓ sig.
Endometrial cancer
EGFR, TP53, BRAF, PIK3CA
 KEGG 4 / 59 58.2× 5.07e-7 2.31e-5 ✓ sig.
Gastric cancer
TGFBR2, EGFR, TP53, BRAF, PIK3CA
 KEGG 5 / 150 28.6× 5.20e-7 2.36e-5 ✓ sig.
Pathways in cancer
ALK, TGFBR2, EML4, EGFR, TP53, BRAF, PIK3CA
 KEGG 7 / 533 11.3× 8.53e-7 3.63e-5 ✓ sig.
Hepatocellular carcinoma
TGFBR2, EGFR, TP53, BRAF, PIK3CA
 KEGG 5 / 170 25.2× 9.67e-7 4.05e-5 ✓ sig.
Melanoma
EGFR, TP53, BRAF, PIK3CA
 KEGG 4 / 73 47.0× 1.20e-6 4.89e-5 ✓ sig.
Glioma
EGFR, TP53, BRAF, PIK3CA
 KEGG 4 / 76 45.2× 1.41e-6 5.64e-5 ✓ sig.
Chronic myeloid leukemia
TGFBR2, TP53, BRAF, PIK3CA
 KEGG 4 / 77 44.6× 1.49e-6 5.90e-5 ✓ sig.
PD-L1 expression and PD-1 checkpoint pathway in cancer
ALK, EML4, EGFR, PIK3CA
 KEGG 4 / 90 38.1× 2.79e-6 1.00e-4 ✓ sig.
Prostate cancer
EGFR, TP53, BRAF, PIK3CA
 KEGG 4 / 98 35.0× 3.92e-6 1.34e-4 ✓ sig.
Endocrine resistance
EGFR, TP53, BRAF, PIK3CA
 KEGG 4 / 99 34.7× 4.08e-6 1.39e-4 ✓ sig.
Bladder cancer
EGFR, TP53, BRAF
 KEGG 3 / 41 62.8× 1.31e-5 3.64e-4 ✓ sig.
FoxO signaling pathway
TGFBR2, EGFR, BRAF, PIK3CA
 KEGG 4 / 133 25.8× 1.32e-5 3.67e-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 ⇵
regulation of cell population proliferation
ALK, TGFBR2, EGFR, TP53, BRAF
 GO:0042127 5 / 201 33.2× 2.53e-7 2.76e-5 ✓ sig.
epidermal growth factor receptor signaling pathway
EGFR, BRAF, PIK3CA
 GO:0007173 3 / 64 62.6× 1.36e-5 6.89e-4 ✓ sig.
centrosome localization
KIF5B, RANBP2
 GO:0051642 2 / 18 148× 7.92e-5 2.60e-3 ✓ sig.
response to X-ray
BLM, TP53
 GO:0010165 2 / 19 141× 8.85e-5 2.83e-3 ✓ sig.
positive regulation of peptidyl-serine phosphorylation
EGFR, BRAF
 GO:0033138 2 / 20 133× 9.83e-5 3.05e-3 ✓ sig.
positive regulation of reactive oxygen species metabolic process
TGFBR2, TP53
 GO:2000379 2 / 34 78.5× 2.88e-4 6.59e-3 ✓ sig.
gastrulation
TGFBR2, TP53
 GO:0007369 2 / 38 70.3× 3.61e-4 7.64e-3 ✓ sig.
T cell differentiation in thymus
TP53, BRAF
 GO:0033077 2 / 41 65.1× 4.20e-4 8.48e-3 ✓ sig.
cellular response to ionizing radiation
BLM, TP53
 GO:0071479 2 / 41 65.1× 4.20e-4 8.48e-3 ✓ sig.
negative regulation of cardiocyte differentiation
EGFR
 GO:1905208 1 / 1 1,335× 7.49e-4 1.23e-2 ✓ sig.
negative regulation of helicase activity
TP53
 GO:0051097 1 / 1 1,335× 7.49e-4 1.23e-2 ✓ sig.
regulation of intrinsic apoptotic signaling pathway by p53 class mediator
TP53
 GO:1902253 1 / 1 1,335× 7.49e-4 1.23e-2 ✓ sig.
negative regulation of G1 to G0 transition
TP53
 GO:1903451 1 / 1 1,335× 7.49e-4 1.23e-2 ✓ sig.
positive regulation of tolerance induction to self antigen
TGFBR2
 GO:0002651 1 / 1 1,335× 7.49e-4 1.23e-2 ✓ sig.
positive regulation of B cell tolerance induction
TGFBR2
 GO:0002663 1 / 1 1,335× 7.49e-4 1.23e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Lung signet ring cell carcinoma Lymphoepithelioma-like lung carcinoma 0.429 3 3.23e-11 3.15e-10 ✓ sig.
Lung signet ring cell carcinoma Signet ring cell carcinoma 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Lymphoepithelioma-like lung carcinoma Signet ring cell carcinoma 0.286 2 1.25e-7 8.63e-7 ✓ sig.
Neuroblastic tumor Neuroblastoma, susceptibility to, 3 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Neuroblastoma, susceptibility to, 3 Retroperitoneal inflammatory myofibroblastic tumor 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Liver solitary fibrous tumor Neuroblastoma, susceptibility to, 3 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Liver solitary fibrous tumor Neuroblastic tumor 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Neuroblastic tumor Signet ring cell carcinoma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Neuroblastic tumor Retroperitoneal inflammatory myofibroblastic tumor 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Neuroblastoma, susceptibility to, 3 Signet ring cell carcinoma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Kyphomelic dysplasia Lung signet ring cell carcinoma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Lung signet ring cell carcinoma Neuroblastoma, susceptibility to, 3 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Lung signet ring cell carcinoma Neuroblastic tumor 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Liver solitary fibrous tumor Signet ring cell carcinoma 0.250 1 2.58e-4 5.38e-4 ✓ sig.
Liver solitary fibrous tumor Retroperitoneal inflammatory myofibroblastic tumor 0.250 1 2.58e-4 5.38e-4 ✓ sig.
Kyphomelic dysplasia Skeletal muscle disorder 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Kyphomelic dysplasia Lymphoepithelioma-like lung carcinoma 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Lung signet ring cell carcinoma Skeletal muscle disorder 0.143 1 7.75e-4 1.25e-3 ✓ sig.