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 284

8 diseases · 12 shared-gene connections
8 Diseases
18 Unique genes
0.286 Avg. similarity score
Dysmorphic facies Most-connected disease (6 links)
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Disease Searched: Behavioral problems-intellectual disability-obesity-dysmorphic features 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 ⇵
Dysmorphic facies 6 6 2
Behavioral problems-intellectual disability-obesity-dysmorphic features syndrome 3 3 1
Chung-jansen syndrome 3 3 1
Developmental delay with intellectual disability and obesity 3 3 1
Hepatic fibrosis 3 3 5
Neonatal diabetes-congenital hypothyroidism-congenital glaucoma-hepatic fibrosis-polycystic kidney syndrome 3 3 1
Periprosthetic osteolysis 2 2 12
Hemorrhagic stroke 1 1 2

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

Gene ⇵ Member diseases ⇵ Linked diseases
GLIS3 4 / 8 Dysmorphic facies, Hepatic fibrosis, Neonatal diabetes-congenital hypothyroidism-congenital glaucoma-hepatic fibrosis-polycystic kidney syndrome, Periprosthetic osteolysis
PHIP 4 / 8 Behavioral problems-intellectual disability-obesity-dysmorphic features syndrome, Chung-jansen syndrome, Developmental delay with intellectual disability and obesity, Dysmorphic facies
PDGFA 2 / 8 Hemorrhagic stroke, Hepatic fibrosis
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 ⇵
Hyaluronan biosynthesis and export
CEMIP
 Reactome 1 / 5 133× 7.47e-3 4.73e-2 ✓ sig.
Activation of Ca-permeable Kainate Receptor
NCALD
 Reactome 1 / 12 55.6× 1.78e-2 8.03e-2
Synthesis of IP2, IP, and Ins in the cytosol
INPP5A
 Reactome 1 / 12 55.6× 1.78e-2 8.03e-2
Recycling of bile acids and salts
SLC10A1
 Reactome 1 / 16 41.7× 2.37e-2 9.46e-2
JAK-STAT signaling pathway
PDGFA, IFNL3
 KEGG 2 / 168 7.9× 2.57e-2 9.90e-2
Non-integrin membrane-ECM interactions
PDGFA
 Reactome 1 / 24 27.8× 3.54e-2 1.19e-1
Interleukin-20 family signaling
IFNL3
 Reactome 1 / 25 26.7× 3.68e-2 1.22e-1
Myogenesis
CTNNA2
 Reactome 1 / 27 24.7× 3.97e-2 1.27e-1
Downstream signal transduction
PDGFA
 Reactome 1 / 29 23.0× 4.26e-2 1.32e-1
Signaling by PDGF
PDGFA
 Reactome 1 / 33 20.2× 4.84e-2 1.42e-1
Ovarian tumor domain proteases
OTUD7A
 Reactome 1 / 38 17.6× 5.55e-2 1.54e-1
Virion - Hepatitis viruses
SLC10A1
 KEGG 1 / 48 13.9× 6.96e-2 1.75e-1
ECM proteoglycans
MATN1
 Reactome 1 / 51 13.1× 7.38e-2 1.81e-1
Intraflagellar transport
KIF3B
 Reactome 1 / 54 12.4× 7.80e-2 1.87e-1
Endometrial cancer
CTNNA2
 KEGG 1 / 59 11.3× 8.49e-2 1.96e-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 ⇵
regulation of branching involved in salivary gland morphogenesis by epithelial-mesenchymal signaling
PDGFA
 GO:0060683 1 / 1 1,038× 9.63e-4 1.42e-2 ✓ sig.
regulation of glomerular mesangial cell proliferation
PDGFA
 GO:0072124 1 / 1 1,038× 9.63e-4 1.42e-2 ✓ sig.
growth plate cartilage chondrocyte morphogenesis
MATN1
 GO:0003429 1 / 1 1,038× 9.63e-4 1.42e-2 ✓ sig.
mesoderm morphogenesis
TBX3
 GO:0048332 1 / 1 1,038× 9.63e-4 1.42e-2 ✓ sig.
negative regulation of cell proliferation involved in heart morphogenesis
TBX3
 GO:2000137 1 / 1 1,038× 9.63e-4 1.42e-2 ✓ sig.
limbic system development
TBX3
 GO:0021761 1 / 2 519× 1.93e-3 2.07e-2 ✓ sig.
hepatoblast differentiation
TBX3
 GO:0061017 1 / 2 519× 1.93e-3 2.07e-2 ✓ sig.
negative regulation of phospholipase C-activating G protein-coupled receptor signaling pathway
INPP5A
 GO:1900737 1 / 2 519× 1.93e-3 2.07e-2 ✓ sig.
opsin transport
KIF3B
 GO:0036372 1 / 2 519× 1.93e-3 2.07e-2 ✓ sig.
embryonic lung development
PDGFA
 GO:1990401 1 / 2 519× 1.93e-3 2.07e-2 ✓ sig.
negative regulation of phosphatidylinositol biosynthetic process
PDGFA
 GO:0010512 1 / 2 519× 1.93e-3 2.07e-2 ✓ sig.
platelet-derived growth factor receptor-alpha signaling pathway
PDGFA
 GO:0035790 1 / 2 519× 1.93e-3 2.07e-2 ✓ sig.
follicle-stimulating hormone secretion
TBX3
 GO:0046884 1 / 2 519× 1.93e-3 2.07e-2 ✓ sig.
ureteric peristalsis
TBX3
 GO:0072105 1 / 2 519× 1.93e-3 2.07e-2 ✓ sig.
radial glia guided migration of Purkinje cell
CTNNA2
 GO:0021942 1 / 3 346× 2.89e-3 2.55e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Behavioral problems-intellectual disability-obesity-dysmorphic features syndrome Chung-jansen syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Behavioral problems-intellectual disability-obesity-dysmorphic features syndrome Developmental delay with intellectual disability and obesity 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Chung-jansen syndrome Developmental delay with intellectual disability and obesity 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Behavioral problems-intellectual disability-obesity-dysmorphic features syndrome Dysmorphic facies 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Chung-jansen syndrome Dysmorphic facies 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Developmental delay with intellectual disability and obesity Dysmorphic facies 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Dysmorphic facies Neonatal diabetes-congenital hypothyroidism-congenital glaucoma-hepatic fibrosis-polycystic kidney syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Hepatic fibrosis Neonatal diabetes-congenital hypothyroidism-congenital glaucoma-hepatic fibrosis-polycystic kidney syndrome 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Hemorrhagic stroke Hepatic fibrosis 0.143 1 6.46e-4 1.09e-3 ✓ sig.
Dysmorphic facies Hepatic fibrosis 0.143 1 6.46e-4 1.09e-3 ✓ sig.
Neonatal diabetes-congenital hypothyroidism-congenital glaucoma-hepatic fibrosis-polycystic kidney syndrome Periprosthetic osteolysis 0.077 1 7.75e-4 1.25e-3 ✓ sig.
Dysmorphic facies Periprosthetic osteolysis 0.071 1 1.55e-3 2.19e-3 ✓ sig.