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 396

5 diseases · 7 shared-gene connections
5 Diseases
23 Unique genes
0.229 Avg. similarity score
Congenital skin anomaly 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 ⇵
Congenital skin anomaly 4 4 10
Skin abnormalities 4 4 10
Brittle cornea syndrome 2 2 2
Congenital anomaly of limb 2 2 16
geroderma osteodysplastica 2 2 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
CHUK 3 / 5 Congenital anomaly of limb, Congenital skin anomaly, Skin abnormalities
FGFR2 3 / 5 Congenital anomaly of limb, Congenital skin anomaly, Skin abnormalities
GORAB 3 / 5 Congenital skin anomaly, geroderma osteodysplastica, Skin abnormalities
IRF6 3 / 5 Congenital anomaly of limb, Congenital skin anomaly, Skin abnormalities
TP63 3 / 5 Congenital anomaly of limb, Congenital skin anomaly, Skin abnormalities
ZNF469 3 / 5 Brittle cornea syndrome, Congenital skin anomaly, Skin abnormalities
APAF1 2 / 5 Congenital skin anomaly, Skin abnormalities
ERCC2 2 / 5 Congenital skin anomaly, Skin abnormalities
SOD2 2 / 5 Congenital skin anomaly, Skin abnormalities
SUPV3L1 2 / 5 Congenital skin anomaly, Skin abnormalities
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 ⇵
TP53 Regulates Transcription of Caspase Activators and Caspases
APAF1, TP63
 Reactome 2 / 12 87.0× 2.29e-4 4.35e-3 ✓ sig.
POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation
SALL1, SALL4
 Reactome 2 / 13 80.3× 2.70e-4 4.95e-3 ✓ sig.
Signaling by FGFR2 amplification mutants
FGFR2
 Reactome 1 / 1 522× 1.92e-3 2.20e-2 ✓ sig.
Signaling by FGFR2 fusions
FGFR2
 Reactome 1 / 1 522× 1.92e-3 2.20e-2 ✓ sig.
FoxO signaling pathway
CHUK, SOD2, TGFB2
 KEGG 3 / 133 11.8× 2.00e-3 2.28e-2 ✓ sig.
MAPK signaling pathway
CHUK, FGFR2, CACNA1C, TGFB2
 KEGG 4 / 299 7.0× 2.29e-3 2.53e-2 ✓ sig.
Hepatitis B
APAF1, CHUK, TGFB2
 KEGG 3 / 163 9.6× 3.56e-3 3.47e-2 ✓ sig.
IKBKB deficiency causes SCID
CHUK
 Reactome 1 / 3 174× 5.73e-3 4.80e-2 ✓ sig.
IKBKG deficiency causes anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) (via TLR)
CHUK
 Reactome 1 / 3 174× 5.73e-3 4.80e-2 ✓ sig.
Lipid and atherosclerosis
APAF1, CHUK, SOD2
 KEGG 3 / 216 7.3× 7.79e-3 5.87e-2
p53 signaling pathway
APAF1, GORAB
 KEGG 2 / 75 13.9× 8.94e-3 6.42e-2
Pancreatic cancer
CHUK, TGFB2
 KEGG 2 / 77 13.6× 9.41e-3 6.62e-2
Chronic myeloid leukemia
CHUK, TGFB2
 KEGG 2 / 77 13.6× 9.41e-3 6.62e-2
Formation of apoptosome
APAF1
 Reactome 1 / 6 87.0× 1.14e-2 7.44e-2
Activation of caspases through apoptosome-mediated cleavage
APAF1
 Reactome 1 / 6 87.0× 1.14e-2 7.44e-2

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
skeletal system development
TP63, COL11A2, HAPLN1, HOXA11, HOXD12, HOXD13, TBX3, TGFB2
 GO:0001501 8 / 151 43.0× 6.67e-12 2.56e-9 ✓ sig.
cranial skeletal system development
FGFR2, IRF6, TP63, TGFB2
 GO:1904888 4 / 18 181× 5.27e-9 9.78e-7 ✓ sig.
embryonic digit morphogenesis
HOXA11, HOXD12, HOXD13, SALL1, TBX3
 GO:0042733 5 / 57 71.3× 7.12e-9 1.28e-6 ✓ sig.
embryonic limb morphogenesis
TP63, HOXA11, HOXD13, SALL4, TGFB2
 GO:0030326 5 / 59 68.9× 8.50e-9 1.49e-6 ✓ sig.
embryonic forelimb morphogenesis
TP63, CACNA1C, HOXA11, TBX3
 GO:0035115 4 / 33 98.5× 6.97e-8 8.94e-6 ✓ sig.
hair follicle morphogenesis
FGFR2, GORAB, TP63, TGFB2
 GO:0031069 4 / 34 95.6× 7.89e-8 9.86e-6 ✓ sig.
regulation of extracellular matrix organization
PRDM5, ZNF469, TGFB2
 GO:1903053 3 / 12 203× 3.56e-7 3.51e-5 ✓ sig.
prostate gland development
TP63, HOXA11, HOXD13
 GO:0030850 3 / 16 152× 9.03e-7 7.62e-5 ✓ sig.
regulation of transcription by RNA polymerase II
CHUK, ERCC2, IRF6, SOD2, HOXA11, HOXD11, HOXD12, HOXD13, SALL1, SALL4, TBX3
 GO:0006357 11 / 1,602 5.6× 9.11e-7 7.69e-5 ✓ sig.
squamous basal epithelial stem cell differentiation involved in prostate gland acinus development
FGFR2, TP63
 GO:0060529 2 / 2 812× 1.45e-6 1.11e-4 ✓ sig.
positive regulation of transcription by RNA polymerase II
PRDM5, CHUK, FGFR2, IRF6, TP63, HOXD13, SALL1, SALL4, TBX3
 GO:0045944 9 / 1,208 6.1× 6.83e-6 3.85e-4 ✓ sig.
heart development
SOD2, CACNA1C, SALL1, SALL4, TGFB2
 GO:0007507 5 / 273 14.9× 1.74e-5 8.04e-4 ✓ sig.
positive regulation of cell cycle
FGFR2, TBX3, TGFB2
 GO:0045787 3 / 44 55.4× 2.09e-5 9.29e-4 ✓ sig.
branching involved in ureteric bud morphogenesis
HOXA11, HOXD11, SALL1
 GO:0001658 3 / 45 54.2× 2.23e-5 9.79e-4 ✓ sig.
prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis
FGFR2, HOXD13
 GO:0060527 2 / 7 232× 3.03e-5 1.23e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Congenital skin anomaly Skin abnormalities 0.909 10 4.86e-36 1.94e-34 ✓ sig.
Congenital anomaly of limb Congenital skin anomaly 0.174 4 1.63e-10 1.68e-9 ✓ sig.
Congenital anomaly of limb Skin abnormalities 0.174 4 1.63e-10 1.68e-9 ✓ sig.
Congenital skin anomaly geroderma osteodysplastica 0.091 1 6.49e-4 1.22e-3 ✓ sig.
geroderma osteodysplastica Skin abnormalities 0.091 1 6.49e-4 1.22e-3 ✓ sig.
Brittle cornea syndrome Congenital skin anomaly 0.083 1 1.30e-3 2.04e-3 ✓ sig.
Brittle cornea syndrome Skin abnormalities 0.083 1 1.30e-3 2.04e-3 ✓ sig.