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 74

13 diseases · 25 shared-gene connections
13 Diseases
18 Unique genes
0.282 Avg. similarity score
Aniridia-cerebellar ataxia-intellectual disability syndrome Most-connected disease (7 links)
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Disease Searched: Ehlers-Danlos syndrome, spondylocheirodysplastic type 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 ⇵
Aniridia-cerebellar ataxia-intellectual disability syndrome 7 7 2
Cataract-corneal dystrophy syndrome 6 6 1
Optic nerve disorder 6 6 2
PAX6-related ocular dysgenesis 6 6 1
Gillespie syndrome 5 5 2
Paranoid schizophrenia 4 4 4
Tooth abnormalities 4 4 10
Bilateral congenital mydriasis 3 3 1
spinocerebellar ataxia type 29 3 3 1
Auriculocondylar syndrome 2 2 4
Urinary retention 2 2 1
Ehlers-Danlos syndrome, spondylocheirodysplastic type 1 1 1
Ulnar-mammary syndrome 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
PAX6 7 / 13 Aniridia-cerebellar ataxia-intellectual disability syndrome, Cataract-corneal dystrophy syndrome, Gillespie syndrome, Optic nerve disorder and 3 more
ITPR1 4 / 13 Aniridia-cerebellar ataxia-intellectual disability syndrome, Bilateral congenital mydriasis, Gillespie syndrome, spinocerebellar ataxia type 29
EDN1 3 / 13 Auriculocondylar syndrome, Optic nerve disorder, Urinary retention
SLC39A13 2 / 13 Ehlers-Danlos syndrome, spondylocheirodysplastic type, Tooth abnormalities
TBX3 2 / 13 Tooth abnormalities, Ulnar-mammary 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 ⇵
Renin secretion
ITPR1, EDN1, GNAI3, PLCB4
 KEGG 4 / 69 38.7× 2.87e-6 1.29e-4 ✓ sig.
Parathyroid hormone synthesis, secretion and action
ITPR1, GNAI3, PLCB4, RUNX2
 KEGG 4 / 115 23.2× 2.20e-5 6.82e-4 ✓ sig.
Estrogen signaling pathway
ITPR1, GNAI3, PLCB4, HSPA1A
 KEGG 4 / 139 19.2× 4.64e-5 1.26e-3 ✓ sig.
Long-term depression
ITPR1, GNAI3, PLCB4
 KEGG 3 / 60 33.4× 9.17e-5 2.16e-3 ✓ sig.
GnRH secretion
ITPR1, PLCB4, KCNN3
 KEGG 3 / 65 30.8× 1.17e-4 2.62e-3 ✓ sig.
PLC beta mediated events
GNAI3, PLCB4
 Reactome 2 / 12 111× 1.39e-4 3.00e-3 ✓ sig.
Gastric acid secretion
ITPR1, GNAI3, PLCB4
 KEGG 3 / 76 26.3× 1.86e-4 3.79e-3 ✓ sig.
Gap junction
ITPR1, GNAI3, PLCB4
 KEGG 3 / 89 22.5× 2.96e-4 5.47e-3 ✓ sig.
Circadian entrainment
ITPR1, GNAI3, PLCB4
 KEGG 3 / 97 20.6× 3.82e-4 6.69e-3 ✓ sig.
Melanogenesis
EDN1, GNAI3, PLCB4
 KEGG 3 / 101 19.8× 4.30e-4 7.37e-3 ✓ sig.
Cholinergic synapse
ITPR1, GNAI3, PLCB4
 KEGG 3 / 115 17.4× 6.28e-4 9.87e-3 ✓ sig.
Serotonergic synapse
ITPR1, GNAI3, PLCB4
 KEGG 3 / 115 17.4× 6.28e-4 9.87e-3 ✓ sig.
Glutamatergic synapse
ITPR1, GNAI3, PLCB4
 KEGG 3 / 116 17.3× 6.44e-4 1.01e-2 ✓ sig.
Growth hormone synthesis, secretion and action
ITPR1, GNAI3, PLCB4
 KEGG 3 / 122 16.4× 7.47e-4 1.13e-2 ✓ sig.
Platelet activation
ITPR1, GNAI3, PLCB4
 KEGG 3 / 126 15.9× 8.20e-4 1.21e-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 ⇵
animal organ morphogenesis
PAX6, FGFR2, MSX1, PITX2, TBX3
 GO:0009887 5 / 130 39.9× 1.20e-7 1.44e-5 ✓ sig.
negative regulation of transcription by RNA polymerase II
PAX6, EDN1, HDAC9, HSPA1A, FGFR2, MSX1, PITX2, TBX3
 GO:0000122 8 / 1,002 8.3× 1.80e-6 1.37e-4 ✓ sig.
embryonic hindlimb morphogenesis
MSX1, PITX2, TBX3
 GO:0035116 3 / 29 107× 2.70e-6 1.89e-4 ✓ sig.
pituitary gland development
PAX6, MSX1, PITX2
 GO:0021983 3 / 30 104× 3.00e-6 2.05e-4 ✓ sig.
in utero embryonic development
EDN1, FGFR2, MSX1, PITX2, TBX3
 GO:0001701 5 / 252 20.6× 3.18e-6 2.15e-4 ✓ sig.
embryonic forelimb morphogenesis
MSX1, RUNX2, TBX3
 GO:0035115 3 / 33 94.4× 4.02e-6 2.60e-4 ✓ sig.
odontogenesis
FGFR2, MSX1, PITX2
 GO:0042476 3 / 36 86.5× 5.25e-6 3.22e-4 ✓ sig.
signal transduction involved in regulation of gene expression
PAX6, EDN1, MSX1
 GO:0023019 3 / 39 79.9× 6.71e-6 3.93e-4 ✓ sig.
positive regulation of odontogenesis
EDN1, MSX1
 GO:0042482 2 / 5 415× 8.75e-6 4.88e-4 ✓ sig.
positive regulation of cell cycle
FGFR2, MSX1, TBX3
 GO:0045787 3 / 44 70.8× 9.70e-6 5.28e-4 ✓ sig.
skeletal system development
EDN1, ANKH, RUNX2, TBX3
 GO:0001501 4 / 151 27.5× 1.15e-5 6.02e-4 ✓ sig.
dorsal/ventral pattern formation
PAX6, EDN1, LRP4
 GO:0009953 3 / 47 66.3× 1.18e-5 6.17e-4 ✓ sig.
lacrimal gland development
PAX6, FGFR2
 GO:0032808 2 / 7 297× 1.84e-5 8.67e-4 ✓ sig.
cardiac neural crest cell migration involved in outflow tract morphogenesis
EDN1, PITX2
 GO:0003253 2 / 7 297× 1.84e-5 8.67e-4 ✓ sig.
bone mineralization
ANKH, FGFR2, RUNX2
 GO:0030282 3 / 56 55.6× 2.01e-5 9.34e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Aniridia-cerebellar ataxia-intellectual disability syndrome Gillespie syndrome 0.667 2 8.44e-9 6.82e-8 ✓ sig.
Bilateral congenital mydriasis spinocerebellar ataxia type 29 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Cataract-corneal dystrophy syndrome PAX6-related ocular dysgenesis 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Aniridia-cerebellar ataxia-intellectual disability syndrome Bilateral congenital mydriasis 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Optic nerve disorder Urinary retention 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Optic nerve disorder PAX6-related ocular dysgenesis 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Gillespie syndrome PAX6-related ocular dysgenesis 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Gillespie syndrome spinocerebellar ataxia type 29 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Cataract-corneal dystrophy syndrome Gillespie syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Cataract-corneal dystrophy syndrome Optic nerve disorder 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Bilateral congenital mydriasis Gillespie syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Aniridia-cerebellar ataxia-intellectual disability syndrome PAX6-related ocular dysgenesis 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Aniridia-cerebellar ataxia-intellectual disability syndrome Cataract-corneal dystrophy syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Aniridia-cerebellar ataxia-intellectual disability syndrome spinocerebellar ataxia type 29 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Aniridia-cerebellar ataxia-intellectual disability syndrome Optic nerve disorder 0.250 1 2.60e-4 6.51e-4 ✓ sig.
Auriculocondylar syndrome Urinary retention 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Cataract-corneal dystrophy syndrome Paranoid schizophrenia 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Paranoid schizophrenia PAX6-related ocular dysgenesis 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Auriculocondylar syndrome Optic nerve disorder 0.167 1 5.19e-4 1.06e-3 ✓ sig.
Aniridia-cerebellar ataxia-intellectual disability syndrome Paranoid schizophrenia 0.167 1 5.19e-4 1.06e-3 ✓ sig.
Optic nerve disorder Paranoid schizophrenia 0.167 1 5.19e-4 1.06e-3 ✓ sig.
Tooth abnormalities Ulnar-mammary syndrome 0.091 1 6.49e-4 1.24e-3 ✓ sig.
PAX6-related ocular dysgenesis Tooth abnormalities 0.091 1 6.49e-4 1.24e-3 ✓ sig.
Cataract-corneal dystrophy syndrome Tooth abnormalities 0.091 1 6.49e-4 1.24e-3 ✓ sig.
Ehlers-Danlos syndrome, spondylocheirodysplastic type Tooth abnormalities 0.091 1 6.49e-4 1.24e-3 ✓ sig.