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 352

5 diseases · 6 shared-gene connections
5 Diseases
39 Unique genes
0.054 Avg. similarity score
Syndactyly Most-connected disease (4 links)
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Disease Searched: leber congenital amaurosis 15 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 ⇵
Syndactyly 4 4 22
Brachydactyly 3 3 21
Acrocapitofemoral dysplasia 2 2 1
leber congenital amaurosis 15 2 2 1
Cernunnos-XLF deficiency 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
IHH 3 / 5 Acrocapitofemoral dysplasia, Brachydactyly, Syndactyly
TULP1 3 / 5 Brachydactyly, leber congenital amaurosis 15, Syndactyly
HOXD13 2 / 5 Brachydactyly, Syndactyly
IQCE 2 / 5 Brachydactyly, Syndactyly
NHEJ1 2 / 5 Cernunnos-XLF deficiency, Syndactyly
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 ⇵
Basal cell carcinoma
BMP2, FZD4, GLI3, APC, SHH
 KEGG 5 / 63 24.4× 1.70e-6 8.27e-5 ✓ sig.
Signaling by BMP
BMPR1B, SMAD4, BMP2, NOG
 Reactome 4 / 28 44.0× 1.84e-6 8.83e-5 ✓ sig.
Pathways in cancer
GNAS, SMAD4, BMP2, DLL3, FZD4, GLI3, JAG2, APC, SHH, FGF16
 KEGG 10 / 533 5.8× 5.40e-6 2.16e-4 ✓ sig.
Hippo signaling pathway
BMPR1B, GDF5, SMAD4, BMP2, FZD4, APC
 KEGG 6 / 157 11.8× 1.04e-5 3.65e-4 ✓ sig.
TGF-beta signaling pathway
BMPR1B, GDF5, SMAD4, BMP2, NOG
 KEGG 5 / 108 14.3× 2.42e-5 7.40e-4 ✓ sig.
Activation of SMO
IHH, IQCE, SHH
 Reactome 3 / 18 51.3× 2.50e-5 7.59e-4 ✓ sig.
Hedgehog signaling pathway
IHH, IQCE, GLI3, SHH
 KEGG 4 / 56 22.0× 3.09e-5 8.99e-4 ✓ sig.
HHAT G278V abrogates palmitoylation of Hh-Np
IHH, SHH
 Reactome 2 / 4 154× 6.14e-5 1.57e-3 ✓ sig.
Breast cancer
DLL3, FZD4, JAG2, APC, FGF16
 KEGG 5 / 148 10.4× 1.09e-4 2.49e-3 ✓ sig.
Gastric cancer
SMAD4, FZD4, APC, SHH, FGF16
 KEGG 5 / 150 10.3× 1.16e-4 2.61e-3 ✓ sig.
Release of Hh-Np from the secreting cell
IHH, SHH
 Reactome 2 / 7 88.0× 2.14e-4 4.21e-3 ✓ sig.
Ligand-receptor interactions
IHH, SHH
 Reactome 2 / 7 88.0× 2.14e-4 4.21e-3 ✓ sig.
Wnt signaling pathway
SMAD4, ROR2, CSNK2B, FZD4, APC
 KEGG 5 / 174 8.8× 2.33e-4 4.51e-3 ✓ sig.
Hormone signaling
BMPR1B, GNAS, SMAD4, PTHLH, PTH1R
 KEGG 5 / 219 7.0× 6.69e-4 1.03e-2 ✓ sig.
G alpha (s) signalling events
GNAS, PTHLH, PDE3A, PTH1R
 Reactome 4 / 140 8.8× 1.06e-3 1.47e-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 ⇵
embryonic digit morphogenesis
IHH, CHST11, HOXD13, SMAD4, NOG, GLI3, LRP4, FREM2, LMBR1, SHH
 GO:0042733 10 / 57 84.1× 1.80e-17 1.93e-14 ✓ sig.
skeletal system development
IHH, HOXD13, TRPS1, BMP2, NOG, PTHLH, PTH1R, DLL3, JAG2
 GO:0001501 9 / 151 28.6× 1.99e-11 6.89e-9 ✓ sig.
developmental growth
CHST11, GNAS, NIPBL, SMAD4, GLI3, SHH
 GO:0048589 6 / 30 95.8× 3.16e-11 1.05e-8 ✓ sig.
chondrocyte differentiation
IHH, BMPR1B, GDF5, SLC26A2, BMP2, PTH1R, GLI3
 GO:0002062 7 / 61 55.0× 3.92e-11 1.26e-8 ✓ sig.
embryonic limb morphogenesis
CHST11, GDF5, HOXD13, GLI3, LRP4, SHH
 GO:0030326 6 / 59 48.7× 2.30e-9 4.70e-7 ✓ sig.
pattern specification process
IHH, HOXD13, NOG, GLI3, APC, SHH
 GO:0007389 6 / 60 47.9× 2.55e-9 5.14e-7 ✓ sig.
negative regulation of alpha-beta T cell differentiation
IHH, GLI3, SHH
 GO:0046639 3 / 3 479× 8.40e-9 1.46e-6 ✓ sig.
negative regulation of canonical Wnt signaling pathway
SMAD4, BMP2, NOG, GLI3, LRP4, APC, SHH
 GO:0090090 7 / 150 22.4× 2.31e-8 3.55e-6 ✓ sig.
cartilage development
IHH, BMPR1B, CHST11, GDF5, BMP2, NOG
 GO:0051216 6 / 89 32.3× 2.83e-8 4.21e-6 ✓ sig.
in utero embryonic development
IHH, CHST11, SMAD4, BMP2, NOG, PTH1R, GLI3, JAG2
 GO:0001701 8 / 252 15.2× 4.20e-8 5.87e-6 ✓ sig.
dorsal/ventral pattern formation
BMPR1B, NOG, GLI3, LRP4, SHH
 GO:0009953 5 / 47 51.0× 4.37e-8 6.08e-6 ✓ sig.
embryonic digestive tract morphogenesis
IHH, NIPBL, GLI3, SHH
 GO:0048557 4 / 18 106× 4.85e-8 6.68e-6 ✓ sig.
cell population proliferation
IHH, SMAD4, NOG, PTH1R, FZD4, GLI3, IRF6, SHH
 GO:0008283 8 / 263 14.6× 5.84e-8 7.76e-6 ✓ sig.
odontogenesis of dentin-containing tooth
BMP2, GLI3, JAG2, LRP4, SHH
 GO:0042475 5 / 56 42.8× 1.07e-7 1.30e-5 ✓ sig.
limb development
NOG, GLI3, IRF6, LRP4, SHH
 GO:0060173 5 / 56 42.8× 1.07e-7 1.30e-5 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Brachydactyly Syndactyly 0.100 4 1.84e-8 1.44e-7 ✓ sig.
Acrocapitofemoral dysplasia Brachydactyly 0.045 1 1.36e-3 2.15e-3 ✓ sig.
Brachydactyly leber congenital amaurosis 15 0.045 1 1.36e-3 2.15e-3 ✓ sig.
Acrocapitofemoral dysplasia Syndactyly 0.043 1 1.43e-3 2.23e-3 ✓ sig.
Cernunnos-XLF deficiency Syndactyly 0.043 1 1.43e-3 2.23e-3 ✓ sig.
leber congenital amaurosis 15 Syndactyly 0.043 1 1.43e-3 2.23e-3 ✓ sig.