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 47

16 diseases · 43 shared-gene connections
16 Diseases
32 Unique genes
0.330 Avg. similarity score
Cronkhite-canada syndrome Most-connected disease (9 links)
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Disease Searched: Polydactyly, preaxial 4 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 ⇵
Cronkhite-canada syndrome 9 9 1
Greig cephalo-poly-syndactyly syndrome 9 9 1
Pallister-hall syndrome 9 9 1
Tibial hemimelia 9 9 1
Acrocallosal syndrome 8 8 2
Polydactyly, preaxial 4 8 8 1
White sutton syndrome 6 6 3
Anorectal malformation 5 5 24
Pilosebaceous disorder 5 5 2
Polydactyly, postaxial, types a1 and b 5 5 1
Hydrolethalus syndrome 4 4 3
Al-gazali-bakalinova syndrome 3 3 1
Male infertility testicular dysgenesis 3 3 3
Intellectual developmental disorder microcephaly strabismus behaviora 1 1 1
Neurodevelopmental disorder with microcephaly and gray sclerae 1 1 1
Urocanate hydratase deficiency 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
GLI3 10 / 16 Acrocallosal syndrome, Anorectal malformation, Cronkhite-canada syndrome, Greig cephalo-poly-syndactyly syndrome and 6 more
KIF7 4 / 16 Acrocallosal syndrome, Al-gazali-bakalinova syndrome, Hydrolethalus syndrome, Male infertility testicular dysgenesis
POGZ 2 / 16 Intellectual developmental disorder microcephaly strabismus behaviora, White sutton syndrome
PUS3 2 / 16 Hydrolethalus syndrome, Neurodevelopmental disorder with microcephaly and gray sclerae
UROC1 2 / 16 Anorectal malformation, Urocanate hydratase deficiency
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 ⇵
GLI proteins bind promoters of Hh responsive genes to promote transcription
GLI3, GLI2
 Reactome 2 / 3 250× 2.06e-5 5.34e-4 ✓ sig.
Hedgehog signaling pathway
GLI3, KIF7, GLI2
 KEGG 3 / 56 20.1× 4.33e-4 5.97e-3 ✓ sig.
Hedgehog 'off' state
GLI3, KIF7, GLI2
 Reactome 3 / 56 20.1× 4.33e-4 5.97e-3 ✓ sig.
Basal cell carcinoma
GLI3, KIF7, GLI2
 KEGG 3 / 63 17.9× 6.12e-4 7.82e-3 ✓ sig.
Hedgehog 'on' state
GLI3, KIF7, GLI2
 Reactome 3 / 70 16.1× 8.33e-4 9.86e-3 ✓ sig.
Leukotriene receptors
LTB4R2
 Reactome 1 / 5 75.1× 1.33e-2 6.74e-2
EGFR tyrosine kinase inhibitor resistance
GAS6, SOS2
 KEGG 2 / 80 9.4× 1.91e-2 8.34e-2
Histidine catabolism
UROC1
 Reactome 1 / 8 46.9× 2.11e-2 8.84e-2
Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus
GAS6
 Reactome 1 / 9 41.7× 2.37e-2 9.46e-2
Removal of aminoterminal propeptides from gamma-carboxylated proteins
GAS6
 Reactome 1 / 10 37.5× 2.63e-2 1.00e-1
POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation
ZIC3
 Reactome 1 / 13 28.9× 3.41e-2 1.16e-1
Interleukin-15 signaling
SOS2
 Reactome 1 / 13 28.9× 3.41e-2 1.16e-1
Thyroid hormone signaling pathway
PLCD1, MED12
 KEGG 2 / 122 6.2× 4.16e-2 1.30e-1
Telomere Extension By Telomerase
RTEL1
 Reactome 1 / 16 23.5× 4.18e-2 1.31e-1
Defective GALNT3 causes familial hyperphosphatemic tumoral calcinosis (HFTC)
MUC5B
 Reactome 1 / 17 22.1× 4.44e-2 1.35e-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 ⇵
lung development
GLI3, GLI2, MYCN, ZIC3, FOXF1
 GO:0030324 5 / 108 27.0× 1.04e-6 8.90e-5 ✓ sig.
pattern specification process
GLI3, GLI2, ZIC3, CDX1
 GO:0007389 4 / 60 38.9× 3.23e-6 2.22e-4 ✓ sig.
embryonic digestive tract development
GLI3, GLI2, FOXF1
 GO:0048566 3 / 19 92.2× 4.34e-6 2.83e-4 ✓ sig.
smoothened signaling pathway involved in ventral spinal cord interneuron specification
GLI3, GLI2
 GO:0021775 2 / 3 389× 8.51e-6 4.80e-4 ✓ sig.
branching morphogenesis of an epithelial tube
GLI3, GLI2, MYCN
 GO:0048754 3 / 29 60.4× 1.62e-5 7.89e-4 ✓ sig.
hindgut morphogenesis
GLI3, GLI2
 GO:0007442 2 / 4 292× 1.70e-5 8.18e-4 ✓ sig.
smoothened signaling pathway
GLI3, GLI2, ZIC3, FOXF1
 GO:0007224 4 / 94 24.8× 1.94e-5 9.01e-4 ✓ sig.
positive regulation of transcription by RNA polymerase II
GLI3, ZNF507, POGZ, GLI2, MYCN, ZIC3, CASK, CDX1, MED12, FOXF1
 GO:0045944 10 / 1,208 4.8× 2.13e-5 9.72e-4 ✓ sig.
spinal cord dorsal/ventral patterning
GLI3, GLI2
 GO:0021513 2 / 8 146× 7.90e-5 2.60e-3 ✓ sig.
embryonic neurocranium morphogenesis
GLI3, MED12
 GO:0048702 2 / 8 146× 7.90e-5 2.60e-3 ✓ sig.
heart development
GLI3, GLI2, ZIC3, MED12, FOXF1
 GO:0007507 5 / 273 10.7× 9.35e-5 2.94e-3 ✓ sig.
tube development
GLI3, GLI2
 GO:0035295 2 / 13 89.8× 2.19e-4 5.40e-3 ✓ sig.
dendritic cell differentiation
GAS6, TRPM2
 GO:0097028 2 / 16 73.0× 3.36e-4 7.26e-3 ✓ sig.
embryonic digestive tract morphogenesis
GLI3, FOXF1
 GO:0048557 2 / 18 64.9× 4.27e-4 8.53e-3 ✓ sig.
regulation of double-strand break repair via homologous recombination
RTEL1, CHEK1
 GO:0010569 2 / 18 64.9× 4.27e-4 8.53e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Greig cephalo-poly-syndactyly syndrome Polydactyly, postaxial, types a1 and b 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Greig cephalo-poly-syndactyly syndrome Polydactyly, preaxial 4 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Greig cephalo-poly-syndactyly syndrome Pallister-hall syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Greig cephalo-poly-syndactyly syndrome Tibial hemimelia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cronkhite-canada syndrome Polydactyly, postaxial, types a1 and b 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cronkhite-canada syndrome Polydactyly, preaxial 4 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cronkhite-canada syndrome Pallister-hall syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cronkhite-canada syndrome Greig cephalo-poly-syndactyly syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cronkhite-canada syndrome Tibial hemimelia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Polydactyly, preaxial 4 Tibial hemimelia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Polydactyly, postaxial, types a1 and b Polydactyly, preaxial 4 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Polydactyly, postaxial, types a1 and b Tibial hemimelia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Pallister-hall syndrome Tibial hemimelia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Pallister-hall syndrome Polydactyly, preaxial 4 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Pallister-hall syndrome Polydactyly, postaxial, types a1 and b 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cronkhite-canada syndrome Pilosebaceous disorder 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Pilosebaceous disorder Polydactyly, preaxial 4 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Pallister-hall syndrome Pilosebaceous disorder 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Greig cephalo-poly-syndactyly syndrome Pilosebaceous disorder 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Pilosebaceous disorder Tibial hemimelia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Acrocallosal syndrome Tibial hemimelia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Acrocallosal syndrome Al-gazali-bakalinova syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Acrocallosal syndrome Polydactyly, preaxial 4 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Acrocallosal syndrome Pallister-hall syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Acrocallosal syndrome Greig cephalo-poly-syndactyly syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Acrocallosal syndrome Cronkhite-canada syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Tibial hemimelia White sutton syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Cronkhite-canada syndrome White sutton syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Greig cephalo-poly-syndactyly syndrome White sutton syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Pallister-hall syndrome White sutton syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Polydactyly, preaxial 4 White sutton syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Intellectual developmental disorder microcephaly strabismus behaviora White sutton syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Hydrolethalus syndrome Neurodevelopmental disorder with microcephaly and gray sclerae 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Al-gazali-bakalinova syndrome Male infertility testicular dysgenesis 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Al-gazali-bakalinova syndrome Hydrolethalus syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Acrocallosal syndrome Male infertility testicular dysgenesis 0.200 1 3.87e-4 7.33e-4 ✓ sig.
Acrocallosal syndrome Hydrolethalus syndrome 0.200 1 3.87e-4 7.33e-4 ✓ sig.
Hydrolethalus syndrome Male infertility testicular dysgenesis 0.167 1 5.81e-4 1.00e-3 ✓ sig.
Anorectal malformation Pallister-hall syndrome 0.040 1 1.55e-3 2.19e-3 ✓ sig.
Anorectal malformation Urocanate hydratase deficiency 0.040 1 1.55e-3 2.19e-3 ✓ sig.
Anorectal malformation Greig cephalo-poly-syndactyly syndrome 0.040 1 1.55e-3 2.19e-3 ✓ sig.
Anorectal malformation Cronkhite-canada syndrome 0.040 1 1.55e-3 2.19e-3 ✓ sig.
Anorectal malformation Tibial hemimelia 0.040 1 1.55e-3 2.19e-3 ✓ sig.