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 145

11 diseases · 36 shared-gene connections
11 Diseases
5 Unique genes
0.412 Avg. similarity score
Colon inflammatory polyp Most-connected disease (9 links)
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Disease Searched: Thymoma type b1 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 ⇵
Colon inflammatory polyp 9 9 1
Gastrointestinal polyp 9 9 1
Gastrointestinal stromal tumor/gist-plus syndrome, somatic or familial 9 9 1
Hyper eosinophilic advanced snydrome 9 9 1
Nasal cavity and paranasal sinus neoplasm 9 9 1
Congenital respiratory system anomaly 6 6 3
Eosinophilic leukemia 5 5 2
Gist-plus syndrome 5 5 1
Polyps, multiple and recurrent inflammatory fibroid, gastrointestinal 5 5 1
Thymoma type b1 5 5 2
Rienhoff syndrome 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
PDGFRA 10 / 11 Colon inflammatory polyp, Congenital respiratory system anomaly, Eosinophilic leukemia, Gastrointestinal polyp and 6 more
TGFB3 2 / 11 Congenital respiratory system anomaly, Rienhoff 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 ⇵
Molecules associated with elastic fibres
TGFB2, TGFB3
 Reactome 2 / 38 126× 9.69e-5 1.85e-3 ✓ sig.
MAPK signaling pathway
PDGFRA, TGFB2, TGFB3
 KEGG 3 / 299 24.1× 1.47e-4 2.58e-3 ✓ sig.
Malaria
TGFB2, TGFB3
 KEGG 2 / 50 96.1× 1.69e-4 2.87e-3 ✓ sig.
Inflammatory bowel disease
TGFB2, TGFB3
 KEGG 2 / 66 72.8× 2.94e-4 4.44e-3 ✓ sig.
Renal cell carcinoma
TGFB2, TGFB3
 KEGG 2 / 70 68.6× 3.31e-4 4.86e-3 ✓ sig.
Pancreatic cancer
TGFB2, TGFB3
 KEGG 2 / 77 62.4× 4.01e-4 5.63e-3 ✓ sig.
Chronic myeloid leukemia
TGFB2, TGFB3
 KEGG 2 / 77 62.4× 4.01e-4 5.63e-3 ✓ sig.
Leishmaniasis
TGFB2, TGFB3
 KEGG 2 / 78 61.6× 4.11e-4 5.74e-3 ✓ sig.
Imatinib-resistant PDGFR mutants
PDGFRA
 Reactome 1 / 1 2,402× 4.16e-4 5.79e-3 ✓ sig.
Sunitinib-resistant PDGFR mutants
PDGFRA
 Reactome 1 / 1 2,402× 4.16e-4 5.79e-3 ✓ sig.
Regorafenib-resistant PDGFR mutants
PDGFRA
 Reactome 1 / 1 2,402× 4.16e-4 5.79e-3 ✓ sig.
Sorafenib-resistant PDGFR mutants
PDGFRA
 Reactome 1 / 1 2,402× 4.16e-4 5.79e-3 ✓ sig.
PDGFR mutants bind TKIs
PDGFRA
 Reactome 1 / 1 2,402× 4.16e-4 5.79e-3 ✓ sig.
Colorectal cancer
TGFB2, TGFB3
 KEGG 2 / 87 55.2× 5.11e-4 6.78e-3 ✓ sig.
Rheumatoid arthritis
TGFB2, TGFB3
 KEGG 2 / 95 50.6× 6.10e-4 7.79e-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 ⇵
face morphogenesis
PDGFRA, TGFB2, TGFB3
 GO:0060325 3 / 33 340× 5.01e-8 7.08e-6 ✓ sig.
uterine wall breakdown
TGFB2, TGFB3
 GO:0042704 2 / 2 3,737× 5.73e-8 7.95e-6 ✓ sig.
salivary gland morphogenesis
TGFB2, TGFB3
 GO:0007435 2 / 10 747× 2.58e-6 1.86e-4 ✓ sig.
transforming growth factor beta receptor superfamily signaling pathway
TGFB2, TGFB3
 GO:0141091 2 / 11 680× 3.15e-6 2.18e-4 ✓ sig.
negative regulation of macrophage cytokine production
TGFB2, TGFB3
 GO:0010936 2 / 12 623× 3.78e-6 2.53e-4 ✓ sig.
secondary palate development
TGFB2, TGFB3
 GO:0062009 2 / 14 534× 5.21e-6 3.27e-4 ✓ sig.
positive regulation of cellular component organization
TGFB2, TGFB3
 GO:0051130 2 / 16 467× 6.86e-6 4.06e-4 ✓ sig.
cell-cell junction organization
TGFB2, TGFB3
 GO:0045216 2 / 29 258× 2.32e-5 1.03e-3 ✓ sig.
response to progesterone
TGFB2, TGFB3
 GO:0032570 2 / 31 241× 2.66e-5 1.14e-3 ✓ sig.
positive regulation of multicellular organismal process
TGFB2, TGFB3
 GO:0051240 2 / 35 214× 3.40e-5 1.38e-3 ✓ sig.
odontogenesis
TGFB2, TGFB3
 GO:0042476 2 / 36 208× 3.60e-5 1.44e-3 ✓ sig.
positive regulation of SMAD protein signal transduction
TGFB2, TGFB3
 GO:0060391 2 / 42 178× 4.91e-5 1.82e-3 ✓ sig.
positive regulation of cell division
TGFB2, TGFB3
 GO:0051781 2 / 48 156× 6.43e-5 2.23e-3 ✓ sig.
positive regulation of protein secretion
TGFB2, TGFB3
 GO:0050714 2 / 49 153× 6.70e-5 2.29e-3 ✓ sig.
positive regulation of epithelial to mesenchymal transition
TGFB2, TGFB3
 GO:0010718 2 / 59 127× 9.74e-5 3.03e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Colon inflammatory polyp Nasal cavity and paranasal sinus neoplasm 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Nasal cavity and paranasal sinus neoplasm Polyps, multiple and recurrent inflammatory fibroid, gastrointestinal 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hyper eosinophilic advanced snydrome Polyps, multiple and recurrent inflammatory fibroid, gastrointestinal 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hyper eosinophilic advanced snydrome Nasal cavity and paranasal sinus neoplasm 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Gastrointestinal stromal tumor/gist-plus syndrome, somatic or familial Gist-plus syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colon inflammatory polyp Gist-plus syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Gastrointestinal polyp Gist-plus syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Gist-plus syndrome Nasal cavity and paranasal sinus neoplasm 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Gist-plus syndrome Hyper eosinophilic advanced snydrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Gastrointestinal stromal tumor/gist-plus syndrome, somatic or familial Polyps, multiple and recurrent inflammatory fibroid, gastrointestinal 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Gastrointestinal stromal tumor/gist-plus syndrome, somatic or familial Nasal cavity and paranasal sinus neoplasm 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Gastrointestinal stromal tumor/gist-plus syndrome, somatic or familial Hyper eosinophilic advanced snydrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Gastrointestinal polyp Polyps, multiple and recurrent inflammatory fibroid, gastrointestinal 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Gastrointestinal polyp Gastrointestinal stromal tumor/gist-plus syndrome, somatic or familial 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Gastrointestinal polyp Nasal cavity and paranasal sinus neoplasm 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Gastrointestinal polyp Hyper eosinophilic advanced snydrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colon inflammatory polyp Hyper eosinophilic advanced snydrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colon inflammatory polyp Gastrointestinal polyp 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colon inflammatory polyp Gastrointestinal stromal tumor/gist-plus syndrome, somatic or familial 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colon inflammatory polyp Polyps, multiple and recurrent inflammatory fibroid, gastrointestinal 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Eosinophilic leukemia Gastrointestinal stromal tumor/gist-plus syndrome, somatic or familial 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Gastrointestinal stromal tumor/gist-plus syndrome, somatic or familial Thymoma type b1 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Colon inflammatory polyp Thymoma type b1 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Gastrointestinal polyp Thymoma type b1 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Nasal cavity and paranasal sinus neoplasm Thymoma type b1 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Hyper eosinophilic advanced snydrome Thymoma type b1 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Eosinophilic leukemia Hyper eosinophilic advanced snydrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Eosinophilic leukemia Nasal cavity and paranasal sinus neoplasm 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Eosinophilic leukemia Gastrointestinal polyp 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Colon inflammatory polyp Eosinophilic leukemia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital respiratory system anomaly Hyper eosinophilic advanced snydrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Congenital respiratory system anomaly Nasal cavity and paranasal sinus neoplasm 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Congenital respiratory system anomaly Gastrointestinal polyp 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Colon inflammatory polyp Congenital respiratory system anomaly 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Congenital respiratory system anomaly Rienhoff syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Congenital respiratory system anomaly Gastrointestinal stromal tumor/gist-plus syndrome, somatic or familial 0.250 1 1.94e-4 4.41e-4 ✓ sig.