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 203

8 diseases · 14 shared-gene connections
8 Diseases
9 Unique genes
0.258 Avg. similarity score
Tessier facial cleft Most-connected disease (6 links)
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Disease Searched: nevoid basal cell carcinoma syndrome 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 ⇵
Tessier facial cleft 6 6 2
Commissural facial cleft 4 4 5
Duplication of pituitary gland 4 4 1
Gorlin syndrome 4 4 4
Opitz g/bbb syndrome 3 3 1
Teebi syndrome 3 3 2
nevoid basal cell carcinoma syndrome 3 3 2
Arthrogryposis with oculomotor limitation and retinal anomalies 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
PTCH2 5 / 8 Commissural facial cleft, Duplication of pituitary gland, Gorlin syndrome, nevoid basal cell carcinoma syndrome and 1 more
SPECC1L 4 / 8 Commissural facial cleft, Opitz g/bbb syndrome, Teebi syndrome, Tessier facial cleft
PIEZO2 2 / 8 Arthrogryposis with oculomotor limitation and retinal anomalies, Gorlin syndrome
PTCH1 2 / 8 Gorlin syndrome, nevoid basal cell carcinoma 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 ⇵
Hedgehog signaling pathway
PTCH2, PTCH1, SUFU
 KEGG 3 / 56 71.5× 7.91e-6 2.94e-4 ✓ sig.
Basal cell carcinoma
PTCH2, PTCH1, SUFU
 KEGG 3 / 63 63.5× 1.13e-5 3.92e-4 ✓ sig.
Pathways in cancer
MITF, PTCH2, PTCH1, SUFU
 KEGG 4 / 533 10.0× 4.04e-4 7.01e-3 ✓ sig.
Hedgehog 'off' state
PTCH1, SUFU
 Reactome 2 / 56 47.7× 7.53e-4 1.13e-2 ✓ sig.
Hedgehog 'on' state
PTCH1, SUFU
 Reactome 2 / 70 38.1× 1.17e-3 1.59e-2 ✓ sig.
Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP)
PAX6
 Reactome 1 / 7 191× 5.24e-3 4.67e-2 ✓ sig.
Ligand-receptor interactions
PTCH1
 Reactome 1 / 7 191× 5.24e-3 4.67e-2 ✓ sig.
Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1)
PAX6
 Reactome 1 / 14 95.3× 1.04e-2 7.29e-2
SUMOylation of transcription factors
MITF
 Reactome 1 / 18 74.1× 1.34e-2 8.46e-2
Activation of SMO
PTCH1
 Reactome 1 / 18 74.1× 1.34e-2 8.46e-2
Maturity onset diabetes of the young
PAX6
 KEGG 1 / 26 51.3× 1.93e-2 1.05e-1
Adherens junctions interactions
CDH11
 Reactome 1 / 32 41.7× 2.37e-2 1.18e-1
Degradation of GLI1 by the proteasome
SUFU
 Reactome 1 / 57 23.4× 4.19e-2 1.61e-1
GLI3 is processed to GLI3R by the proteasome
SUFU
 Reactome 1 / 60 22.2× 4.41e-2 1.65e-1
Melanoma
MITF
 KEGG 1 / 73 18.3× 5.34e-2 1.83e-1

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

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
cell fate determination
PAX6, PTCH2, PTCH1
 GO:0001709 3 / 18 346× 6.28e-8 8.26e-6 ✓ sig.
negative regulation of smoothened signaling pathway
PTCH2, PTCH1, SUFU
 GO:0045879 3 / 35 178× 5.02e-7 4.81e-5 ✓ sig.
epidermal cell fate specification
PTCH2, PTCH1
 GO:0009957 2 / 5 831× 2.06e-6 1.52e-4 ✓ sig.
positive regulation of epidermal cell differentiation
PTCH2, PTCH1
 GO:0045606 2 / 8 519× 5.76e-6 3.48e-4 ✓ sig.
adherens junction organization
SPECC1L, CDH11
 GO:0034332 2 / 34 122× 1.15e-4 3.46e-3 ✓ sig.
dorsal/ventral pattern formation
PAX6, PTCH1
 GO:0009953 2 / 47 88.4× 2.20e-4 5.57e-3 ✓ sig.
eye development
PAX6, SALL2
 GO:0001654 2 / 49 84.7× 2.40e-4 5.93e-3 ✓ sig.
skin development
PTCH2, SUFU
 GO:0043588 2 / 55 75.5× 3.02e-4 7.00e-3 ✓ sig.
negative regulation of epithelial cell proliferation
PAX6, PTCH1
 GO:0050680 2 / 62 67.0× 3.84e-4 8.24e-3 ✓ sig.
response to mechanical stimulus
PIEZO2, PTCH1
 GO:0009612 2 / 67 62.0× 4.49e-4 9.20e-3 ✓ sig.
pancreatic A cell development
PAX6
 GO:0003322 1 / 1 2,076× 4.82e-4 9.61e-3 ✓ sig.
forebrain-midbrain boundary formation
PAX6
 GO:0021905 1 / 1 2,076× 4.82e-4 9.61e-3 ✓ sig.
positive regulation of cellular response to drug
SUFU
 GO:2001040 1 / 1 2,076× 4.82e-4 9.61e-3 ✓ sig.
neural crest cell delamination
SPECC1L
 GO:0036032 1 / 1 2,076× 4.82e-4 9.61e-3 ✓ sig.
negative regulation of osteoblast differentiation
PTCH1, SUFU
 GO:0045668 2 / 71 58.5× 5.04e-4 9.93e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Gorlin syndrome nevoid basal cell carcinoma syndrome 0.400 2 5.06e-8 3.71e-7 ✓ sig.
Commissural facial cleft Tessier facial cleft 0.333 2 8.44e-8 5.94e-7 ✓ sig.
Duplication of pituitary gland Tessier facial cleft 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Duplication of pituitary gland nevoid basal cell carcinoma syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Opitz g/bbb syndrome Teebi syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Opitz g/bbb syndrome Tessier facial cleft 0.333 1 1.30e-4 3.93e-4 ✓ sig.
nevoid basal cell carcinoma syndrome Tessier facial cleft 0.250 1 2.60e-4 6.51e-4 ✓ sig.
Teebi syndrome Tessier facial cleft 0.250 1 2.60e-4 6.51e-4 ✓ sig.
Arthrogryposis with oculomotor limitation and retinal anomalies Gorlin syndrome 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Duplication of pituitary gland Gorlin syndrome 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Commissural facial cleft Duplication of pituitary gland 0.167 1 3.25e-4 7.71e-4 ✓ sig.
Commissural facial cleft Opitz g/bbb syndrome 0.167 1 3.25e-4 7.71e-4 ✓ sig.
Gorlin syndrome Tessier facial cleft 0.167 1 5.19e-4 1.06e-3 ✓ sig.
Commissural facial cleft Teebi syndrome 0.143 1 6.49e-4 1.24e-3 ✓ sig.