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 169

9 diseases · 15 shared-gene connections
9 Diseases
15 Unique genes
0.234 Avg. similarity score
Cleft face Most-connected disease (5 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 ⇵
Cleft face 5 5 2
Culler-jones syndrome 5 5 1
Postaxial polydactyly–anterior pituitary anomalies–facial dysmorphism syndrome 5 5 1
Basal cell nevus syndrome 4 4 4
Bifid nose 4 4 2
Facial dysmorphism syndrome 4 4 10
Desanto-shinawi syndrome 1 1 1
facial dysmorphism, hypertrichosis, epilepsy, intellectual/developmental delay, and gingival overgrowth syndrome 1 1 1
familial meningioma 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
GLI2 6 / 9 Basal cell nevus syndrome, Bifid nose, Cleft face, Culler-jones syndrome and 2 more
KCNK4 2 / 9 Facial dysmorphism syndrome, facial dysmorphism, hypertrichosis, epilepsy, intellectual/developmental delay, and gingival overgrowth syndrome
SMARCE1 2 / 9 Cleft face, familial meningioma
WAC 2 / 9 Desanto-shinawi syndrome, Facial dysmorphism 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
GLI2, PTCH1, SUFU, SHH
 KEGG 4 / 56 57.2× 5.57e-7 2.94e-5 ✓ sig.
Basal cell carcinoma
GLI2, PTCH1, SUFU, SHH
 KEGG 4 / 63 50.8× 8.99e-7 4.44e-5 ✓ sig.
Ligand-receptor interactions
PTCH1, SHH
 Reactome 2 / 7 229× 3.05e-5 8.46e-4 ✓ sig.
Hedgehog 'off' state
GLI2, PTCH1, SUFU
 Reactome 3 / 56 42.9× 4.20e-5 1.11e-3 ✓ sig.
Hedgehog 'on' state
GLI2, PTCH1, SUFU
 Reactome 3 / 70 34.3× 8.21e-5 1.91e-3 ✓ sig.
Activation of SMO
PTCH1, SHH
 Reactome 2 / 18 89.0× 2.20e-4 4.22e-3 ✓ sig.
Pathways in cancer
GLI2, PTCH1, SUFU, SHH, RAC3
 KEGG 5 / 533 7.5× 3.50e-4 6.06e-3 ✓ sig.
Axon guidance
PTCH1, SHH, RAC3
 KEGG 3 / 183 13.1× 1.38e-3 1.73e-2 ✓ sig.
GLI proteins bind promoters of Hh responsive genes to promote transcription
GLI2
 Reactome 1 / 3 267× 3.74e-3 3.59e-2 ✓ sig.
TWIK related potassium channel (TREK)
KCNK4
 Reactome 1 / 3 267× 3.74e-3 3.59e-2 ✓ sig.
HHAT G278V abrogates palmitoylation of Hh-Np
SHH
 Reactome 1 / 4 200× 4.99e-3 4.37e-2 ✓ sig.
Release of Hh-Np from the secreting cell
SHH
 Reactome 1 / 7 114× 8.71e-3 6.31e-2
DNA replication initiation
POLE
 Reactome 1 / 8 100× 9.95e-3 6.82e-2
Insulin processing
EXOC4
 Reactome 1 / 14 57.2× 1.74e-2 9.50e-2
Class B/2 (Secretin family receptors)
PTH
 Reactome 1 / 18 44.5× 2.23e-2 1.09e-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 ⇵
spinal cord dorsal/ventral patterning
GLI2, SUFU, SHH
 GO:0021513 3 / 8 467× 2.34e-8 3.57e-6 ✓ sig.
pattern specification process
GLI2, PTCH1, SHH, ASPH
 GO:0007389 4 / 60 83.1× 1.28e-7 1.48e-5 ✓ sig.
ventral midline development
GLI2, SHH
 GO:0007418 2 / 3 831× 1.80e-6 1.33e-4 ✓ sig.
smoothened signaling pathway involved in ventral spinal cord interneuron specification
GLI2, SUFU
 GO:0021775 2 / 3 831× 1.80e-6 1.33e-4 ✓ sig.
hindgut morphogenesis
GLI2, SHH
 GO:0007442 2 / 4 623× 3.61e-6 2.31e-4 ✓ sig.
embryonic organ development
PTCH1, SHH, POLE
 GO:0048568 3 / 42 89.0× 4.71e-6 2.87e-4 ✓ sig.
positive regulation of DNA-templated transcription
GLI2, PTCH1, SMARCE1, WAC, SHH, ASPH
 GO:0045893 6 / 778 9.6× 1.85e-5 8.45e-4 ✓ sig.
metanephric collecting duct development
PTCH1, SHH
 GO:0072205 2 / 9 277× 2.16e-5 9.54e-4 ✓ sig.
positive regulation of T cell differentiation in thymus
GLI2, SHH
 GO:0033089 2 / 11 227× 3.29e-5 1.31e-3 ✓ sig.
tube development
GLI2, SHH
 GO:0035295 2 / 13 192× 4.67e-5 1.71e-3 ✓ sig.
dorsal/ventral neural tube patterning
PTCH1, SHH
 GO:0021904 2 / 13 192× 4.67e-5 1.71e-3 ✓ sig.
smoothened signaling pathway
GLI2, SUFU, SHH
 GO:0007224 3 / 94 39.8× 5.37e-5 1.90e-3 ✓ sig.
osteoblast development
GLI2, SHH
 GO:0002076 2 / 16 156× 7.17e-5 2.36e-3 ✓ sig.
smooth muscle tissue development
PTCH1, SHH
 GO:0048745 2 / 16 156× 7.17e-5 2.36e-3 ✓ sig.
somite development
PTCH1, SHH
 GO:0061053 2 / 16 156× 7.17e-5 2.36e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Culler-jones syndrome Postaxial polydactyly–anterior pituitary anomalies–facial dysmorphism syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Bifid nose Culler-jones syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Bifid nose Postaxial polydactyly–anterior pituitary anomalies–facial dysmorphism syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Cleft face Culler-jones syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Cleft face Postaxial polydactyly–anterior pituitary anomalies–facial dysmorphism syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Cleft face familial meningioma 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Bifid nose Cleft face 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Basal cell nevus syndrome Culler-jones syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Basal cell nevus syndrome Postaxial polydactyly–anterior pituitary anomalies–facial dysmorphism syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Basal cell nevus syndrome Bifid nose 0.167 1 5.19e-4 1.04e-3 ✓ sig.
Basal cell nevus syndrome Cleft face 0.167 1 5.19e-4 1.04e-3 ✓ sig.
Desanto-shinawi syndrome Facial dysmorphism syndrome 0.091 1 6.49e-4 1.22e-3 ✓ sig.
Culler-jones syndrome Facial dysmorphism syndrome 0.091 1 6.49e-4 1.22e-3 ✓ sig.
Facial dysmorphism syndrome Postaxial polydactyly–anterior pituitary anomalies–facial dysmorphism syndrome 0.091 1 6.49e-4 1.22e-3 ✓ sig.
Facial dysmorphism syndrome facial dysmorphism, hypertrichosis, epilepsy, intellectual/developmental delay, and gingival overgrowth syndrome 0.091 1 6.49e-4 1.22e-3 ✓ sig.