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 139

10 diseases · 24 shared-gene connections
10 Diseases
9 Unique genes
0.347 Avg. similarity score
Osteoglophonic dwarfism Most-connected disease (7 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 ⇵
Osteoglophonic dwarfism 7 7 1
Osteoglophonic dysplasia 7 7 1
Craniofaciosynostosis 6 6 2
Hartsfield-Bixler-Demyer syndrome 6 6 1
Pfeiffer syndrome type 1 6 6 1
Trigonocephaly 6 6 3
Encephalocraniocutaneous lipomatosis 4 4 2
Hypereosinophilic syndrome 3 3 6
Bnar syndrome 2 2 1
Eosinophilic leukemia 1 1 2

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

Gene ⇵ Member diseases ⇵ Linked diseases
FGFR1 8 / 10 Craniofaciosynostosis, Encephalocraniocutaneous lipomatosis, Hartsfield-Bixler-Demyer syndrome, Hypereosinophilic syndrome and 4 more
FREM1 3 / 10 Bnar syndrome, Craniofaciosynostosis, Trigonocephaly
FIP1L1 2 / 10 Eosinophilic leukemia, Hypereosinophilic syndrome
PDGFRA 2 / 10 Eosinophilic leukemia, Hypereosinophilic 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 ⇵
Central carbon metabolism in cancer
PDGFRA, FGFR1, KRAS, PDGFRB
 KEGG 4 / 71 75.2× 1.38e-7 8.66e-6 ✓ sig.
Melanoma
PDGFRA, FGFR1, KRAS, PDGFRB
 KEGG 4 / 73 73.1× 1.55e-7 9.56e-6 ✓ sig.
Prostate cancer
PDGFRA, FGFR1, KRAS, PDGFRB
 KEGG 4 / 98 54.5× 5.09e-7 2.72e-5 ✓ sig.
Downstream signal transduction
PDGFRA, KRAS, PDGFRB
 Reactome 3 / 29 138× 1.05e-6 5.11e-5 ✓ sig.
RAF/MAP kinase cascade
PDGFRA, FGFR1, KRAS, PDGFRB
 Reactome 4 / 124 43.0× 1.31e-6 6.18e-5 ✓ sig.
Rap1 signaling pathway
PDGFRA, FGFR1, KRAS, PDGFRB
 KEGG 4 / 211 25.3× 1.09e-5 3.60e-4 ✓ sig.
Regulation of actin cytoskeleton
PDGFRA, FGFR1, KRAS, PDGFRB
 KEGG 4 / 232 23.0× 1.58e-5 4.93e-4 ✓ sig.
Ras signaling pathway
PDGFRA, FGFR1, KRAS, PDGFRB
 KEGG 4 / 237 22.5× 1.72e-5 5.30e-4 ✓ sig.
Constitutive Signaling by Aberrant PI3K in Cancer
PDGFRA, FGFR1, PDGFRB
 Reactome 3 / 75 53.4× 1.91e-5 5.78e-4 ✓ sig.
Glioma
PDGFRA, KRAS, PDGFRB
 KEGG 3 / 76 52.7× 1.99e-5 5.96e-4 ✓ sig.
EGFR tyrosine kinase inhibitor resistance
PDGFRA, KRAS, PDGFRB
 KEGG 3 / 80 50.0× 2.32e-5 6.75e-4 ✓ sig.
Gap junction
PDGFRA, KRAS, PDGFRB
 KEGG 3 / 89 45.0× 3.20e-5 8.81e-4 ✓ sig.
Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants
PDGFRA, KRAS
 Reactome 2 / 12 222× 3.28e-5 9.00e-4 ✓ sig.
Signaling by PDGFRA extracellular domain mutants
PDGFRA, KRAS
 Reactome 2 / 12 222× 3.28e-5 9.00e-4 ✓ sig.
PIP3 activates AKT signaling
PDGFRA, FGFR1, PDGFRB
 Reactome 3 / 93 43.0× 3.65e-5 9.83e-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 ⇵
positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway
PDGFRA, PDGFRB
 GO:0038091 2 / 3 1,384× 6.18e-7 5.59e-5 ✓ sig.
metanephric glomerular capillary formation
PDGFRA, PDGFRB
 GO:0072277 2 / 3 1,384× 6.18e-7 5.59e-5 ✓ sig.
peptidyl-tyrosine phosphorylation
PDGFRA, FGFR1, PDGFRB
 GO:0018108 3 / 39 160× 7.00e-7 6.22e-5 ✓ sig.
cardiac myofibril assembly
PDGFRA, PDGFRB
 GO:0055003 2 / 13 319× 1.60e-5 7.57e-4 ✓ sig.
protein autophosphorylation
PDGFRA, FGFR1, PDGFRB
 GO:0046777 3 / 113 55.1× 1.76e-5 8.12e-4 ✓ sig.
retina vasculature development in camera-type eye
PDGFRA, PDGFRB
 GO:0061298 2 / 15 277× 2.16e-5 9.54e-4 ✓ sig.
positive regulation of chemotaxis
PDGFRA, PDGFRB
 GO:0050921 2 / 21 198× 4.31e-5 1.61e-3 ✓ sig.
positive regulation of MAP kinase activity
FGFR1, PDGFRB
 GO:0043406 2 / 25 166× 6.15e-5 2.10e-3 ✓ sig.
cardiac muscle cell proliferation
FGFR1, KRAS
 GO:0060038 2 / 28 148× 7.74e-5 2.50e-3 ✓ sig.
platelet-derived growth factor receptor signaling pathway
PDGFRA, PDGFRB
 GO:0048008 2 / 33 126× 1.08e-4 3.20e-3 ✓ sig.
positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
PDGFRA, FGFR1, PDGFRB
 GO:0051897 3 / 217 28.7× 1.23e-4 3.54e-3 ✓ sig.
positive regulation of calcium-mediated signaling
PDGFRA, PDGFRB
 GO:0050850 2 / 38 109× 1.44e-4 3.97e-3 ✓ sig.
skeletal system morphogenesis
PDGFRA, FGFR1
 GO:0048705 2 / 45 92.3× 2.02e-4 5.08e-3 ✓ sig.
cell migration
PDGFRA, FGFR1, PDGFRB
 GO:0016477 3 / 303 20.6× 3.30e-4 7.16e-3 ✓ sig.
positive regulation of mitotic cell cycle DNA replication
FGFR1
 GO:1903465 1 / 1 2,076× 4.82e-4 9.31e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Craniofaciosynostosis Trigonocephaly 0.500 2 2.53e-8 2.03e-7 ✓ sig.
Eosinophilic leukemia Hypereosinophilic syndrome 0.286 2 1.27e-7 9.20e-7 ✓ sig.
Osteoglophonic dysplasia Pfeiffer syndrome type 1 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Osteoglophonic dwarfism Pfeiffer syndrome type 1 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Osteoglophonic dwarfism Osteoglophonic dysplasia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Hartsfield-Bixler-Demyer syndrome Pfeiffer syndrome type 1 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Hartsfield-Bixler-Demyer syndrome Osteoglophonic dysplasia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Hartsfield-Bixler-Demyer syndrome Osteoglophonic dwarfism 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Encephalocraniocutaneous lipomatosis Hartsfield-Bixler-Demyer syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Encephalocraniocutaneous lipomatosis Pfeiffer syndrome type 1 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Encephalocraniocutaneous lipomatosis Osteoglophonic dysplasia 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Encephalocraniocutaneous lipomatosis Osteoglophonic dwarfism 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Craniofaciosynostosis Hartsfield-Bixler-Demyer syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Craniofaciosynostosis Pfeiffer syndrome type 1 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Craniofaciosynostosis Osteoglophonic dysplasia 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Craniofaciosynostosis Osteoglophonic dwarfism 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Bnar syndrome Craniofaciosynostosis 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Hartsfield-Bixler-Demyer syndrome Trigonocephaly 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Pfeiffer syndrome type 1 Trigonocephaly 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Osteoglophonic dysplasia Trigonocephaly 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Osteoglophonic dwarfism Trigonocephaly 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Bnar syndrome Trigonocephaly 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Hypereosinophilic syndrome Osteoglophonic dysplasia 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Hypereosinophilic syndrome Osteoglophonic dwarfism 0.143 1 3.90e-4 8.52e-4 ✓ sig.