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 594

5 diseases · 10 shared-gene connections
5 Diseases
14 Unique genes
0.278 Avg. similarity score
Byzanthine arch palate Most-connected disease (4 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 ⇵
Byzanthine arch palate 4 4 13
Child syndrome xld 4 4 1
Ck syndrome 4 4 1
Congenital hemidysplasia with ichthyosiform erythroderma and limb defects 4 4 1
Perisylvian polymicrogyria 4 4 2

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

Gene ⇵ Member diseases ⇵ Linked diseases
NSDHL 5 / 5 Byzanthine arch palate, Child syndrome xld, Ck syndrome, Congenital hemidysplasia with ichthyosiform erythroderma and limb defects and 1 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 ⇵
Yersinia infection
IRAK1, MAP2K2, PTK2
 KEGG 3 / 138 18.6× 4.92e-4 6.61e-3 ✓ sig.
Gastric cancer
FGFR2, MAP2K2, SHH
 KEGG 3 / 150 17.2× 6.28e-4 7.98e-3 ✓ sig.
Signaling by FGFR2 amplification mutants
FGFR2
 Reactome 1 / 1 858× 1.17e-3 1.27e-2 ✓ sig.
Signaling by FGFR2 fusions
FGFR2
 Reactome 1 / 1 858× 1.17e-3 1.27e-2 ✓ sig.
Proteoglycans in cancer
MAP2K2, PTK2, SHH
 KEGG 3 / 204 12.6× 1.53e-3 1.56e-2 ✓ sig.
Human immunodeficiency virus 1 infection
IRAK1, MAP2K2, PTK2
 KEGG 3 / 213 12.1× 1.73e-3 1.72e-2 ✓ sig.
VEGF signaling pathway
MAP2K2, PTK2
 KEGG 2 / 60 28.6× 2.15e-3 2.01e-2 ✓ sig.
Regulation of actin cytoskeleton
FGFR2, MAP2K2, PTK2
 KEGG 3 / 232 11.1× 2.21e-3 2.05e-2 ✓ sig.
Pathways in cancer
FGFR2, MAP2K2, PTK2, SHH
 KEGG 4 / 533 6.4× 2.69e-3 2.36e-2 ✓ sig.
Central carbon metabolism in cancer
FGFR2, MAP2K2
 KEGG 2 / 71 24.2× 2.99e-3 2.54e-2 ✓ sig.
Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors
TFAP2A
 Reactome 1 / 3 286× 3.49e-3 2.83e-2 ✓ sig.
EGFR tyrosine kinase inhibitor resistance
FGFR2, MAP2K2
 KEGG 2 / 80 21.4× 3.79e-3 3.01e-2 ✓ sig.
ErbB signaling pathway
MAP2K2, PTK2
 KEGG 2 / 86 20.0× 4.36e-3 3.33e-2 ✓ sig.
MAPK signaling pathway
FGFR2, IRAK1, MAP2K2
 KEGG 3 / 299 8.6× 4.54e-3 3.42e-2 ✓ sig.
TFAP2 (AP-2) family regulates transcription of other transcription factors
TFAP2A
 Reactome 1 / 4 214× 4.66e-3 3.48e-2 ✓ 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 ⇵
prostate epithelial cord elongation
FGFR2, SHH
 GO:0060523 2 / 3 890× 1.56e-6 1.24e-4 ✓ sig.
epithelial cell proliferation involved in salivary gland morphogenesis
FGFR2, SHH
 GO:0060664 2 / 5 534× 5.21e-6 3.27e-4 ✓ sig.
mesenchymal cell proliferation involved in lung development
FGFR2, SHH
 GO:0060916 2 / 5 534× 5.21e-6 3.27e-4 ✓ sig.
branching involved in prostate gland morphogenesis
FGFR2, SHH
 GO:0060442 2 / 6 445× 7.80e-6 4.51e-4 ✓ sig.
regulation of cell differentiation
FGFR2, PTK2, TFAP2A
 GO:0045595 3 / 54 74.2× 8.12e-6 4.64e-4 ✓ sig.
lung lobe morphogenesis
FGFR2, SHH
 GO:0060463 2 / 8 334× 1.46e-5 7.28e-4 ✓ sig.
limb bud formation
FGFR2, SHH
 GO:0060174 2 / 9 297× 1.87e-5 8.78e-4 ✓ sig.
lung-associated mesenchyme development
FGFR2, SHH
 GO:0060484 2 / 9 297× 1.87e-5 8.78e-4 ✓ sig.
branching involved in salivary gland morphogenesis
FGFR2, SHH
 GO:0060445 2 / 12 222× 3.43e-5 1.39e-3 ✓ sig.
lung development
FBN1, FGFR2, SHH
 GO:0030324 3 / 108 37.1× 6.52e-5 2.25e-3 ✓ sig.
regulation of osteoblast differentiation
FGFR2, PTK2
 GO:0045667 2 / 17 157× 7.04e-5 2.38e-3 ✓ sig.
protein autophosphorylation
FGFR2, IRAK1, PTK2
 GO:0046777 3 / 113 35.4× 7.47e-5 2.49e-3 ✓ sig.
embryonic digestive tract morphogenesis
FGFR2, SHH
 GO:0048557 2 / 18 148× 7.92e-5 2.60e-3 ✓ sig.
lung morphogenesis
MAP2K2, SHH
 GO:0060425 2 / 25 107× 1.55e-4 4.24e-3 ✓ sig.
kidney development
FBN1, SHH, TFAP2A
 GO:0001822 3 / 146 27.4× 1.60e-4 4.33e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Child syndrome xld Ck syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Child syndrome xld Congenital hemidysplasia with ichthyosiform erythroderma and limb defects 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Ck syndrome Congenital hemidysplasia with ichthyosiform erythroderma and limb defects 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Child syndrome xld Perisylvian polymicrogyria 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Ck syndrome Perisylvian polymicrogyria 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital hemidysplasia with ichthyosiform erythroderma and limb defects Perisylvian polymicrogyria 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Byzanthine arch palate Child syndrome xld 0.071 1 8.39e-4 1.34e-3 ✓ sig.
Byzanthine arch palate Ck syndrome 0.071 1 8.39e-4 1.34e-3 ✓ sig.
Byzanthine arch palate Congenital hemidysplasia with ichthyosiform erythroderma and limb defects 0.071 1 8.39e-4 1.34e-3 ✓ sig.
Byzanthine arch palate Perisylvian polymicrogyria 0.067 1 1.68e-3 2.34e-3 ✓ sig.