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 390

5 diseases · 9 shared-gene connections
5 Diseases
31 Unique genes
0.295 Avg. similarity score
Amelogenesis imperfecta Most-connected disease (4 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 ⇵
Amelogenesis imperfecta 4 4 25
Dentin dysplasia 4 4 17
Dentinogenesis imperfecta 4 4 16
Enamel-renal syndrome 3 3 1
Hypomaturation amelogenesis imperfecta 3 3 7

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

Gene ⇵ Member diseases ⇵ Linked diseases
AMELX 4 / 5 Amelogenesis imperfecta, Dentin dysplasia, Dentinogenesis imperfecta, Hypomaturation amelogenesis imperfecta
FAM20A 4 / 5 Amelogenesis imperfecta, Dentin dysplasia, Dentinogenesis imperfecta, Enamel-renal syndrome
KLK4 4 / 5 Amelogenesis imperfecta, Dentin dysplasia, Dentinogenesis imperfecta, Hypomaturation amelogenesis imperfecta
MMP20 4 / 5 Amelogenesis imperfecta, Dentin dysplasia, Dentinogenesis imperfecta, Hypomaturation amelogenesis imperfecta
ODAPH 4 / 5 Amelogenesis imperfecta, Dentin dysplasia, Dentinogenesis imperfecta, Hypomaturation amelogenesis imperfecta
SLC24A4 4 / 5 Amelogenesis imperfecta, Dentin dysplasia, Dentinogenesis imperfecta, Hypomaturation amelogenesis imperfecta
WDR72 4 / 5 Amelogenesis imperfecta, Dentin dysplasia, Dentinogenesis imperfecta, Hypomaturation amelogenesis imperfecta
AMBN 3 / 5 Amelogenesis imperfecta, Dentin dysplasia, Dentinogenesis imperfecta
DLX3 3 / 5 Amelogenesis imperfecta, Dentin dysplasia, Dentinogenesis imperfecta
ENAM 3 / 5 Amelogenesis imperfecta, Dentin dysplasia, Dentinogenesis imperfecta
FAM83H 3 / 5 Amelogenesis imperfecta, Dentin dysplasia, Dentinogenesis imperfecta
ITGB6 3 / 5 Amelogenesis imperfecta, Dentin dysplasia, Dentinogenesis imperfecta
LAMB3 3 / 5 Amelogenesis imperfecta, Dentin dysplasia, Dentinogenesis imperfecta
DSPP 2 / 5 Dentin dysplasia, Dentinogenesis imperfecta
GPR68 2 / 5 Amelogenesis imperfecta, Hypomaturation amelogenesis imperfecta
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 ⇵
Assembly of collagen fibrils and other multimeric structures
COL17A1, LAMB3, MMP20, COL7A1, LAMC2, COL1A1, COL1A2
 Reactome 7 / 51 53.2× 3.95e-11 6.23e-9 ✓ sig.
Anchoring fibril formation
LAMB3, COL7A1, LAMC2, COL1A1, COL1A2
 Reactome 5 / 15 129× 2.41e-10 3.17e-8 ✓ sig.
ECM-receptor interaction
ITGB6, LAMB3, LAMC2, DSPP, COL1A1, COL1A2
 KEGG 6 / 89 26.1× 8.86e-8 5.90e-6 ✓ sig.
Post-translational protein phosphorylation
AMBN, AMELX, ENAM, FAM20A, FAM20C, AMTN
 Reactome 6 / 108 21.5× 2.82e-7 1.62e-5 ✓ sig.
Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)
AMBN, AMELX, ENAM, FAM20A, FAM20C, AMTN
 Reactome 6 / 125 18.6× 6.70e-7 3.44e-5 ✓ sig.
MET activates PTK2 signaling
LAMB3, LAMC2, COL1A1, COL1A2
 Reactome 4 / 30 51.7× 9.50e-7 4.65e-5 ✓ sig.
Type I hemidesmosome assembly
COL17A1, LAMB3, LAMC2
 Reactome 3 / 11 106× 2.53e-6 1.08e-4 ✓ sig.
Collagen chain trimerization
COL17A1, COL7A1, COL1A1, COL1A2
 Reactome 4 / 44 35.2× 4.59e-6 1.77e-4 ✓ sig.
Extracellular matrix organization
COL7A1, COL1A1, COL1A2
 Reactome 3 / 15 77.5× 6.94e-6 2.47e-4 ✓ sig.
ECM proteoglycans
ITGB6, DSPP, COL1A1, COL1A2
 Reactome 4 / 51 30.4× 8.34e-6 2.88e-4 ✓ sig.
Collagen degradation
MMP20, COL7A1, COL1A1, COL1A2
 Reactome 4 / 52 29.8× 9.02e-6 3.08e-4 ✓ sig.
Collagen biosynthesis and modifying enzymes
COL17A1, COL7A1, COL1A1, COL1A2
 Reactome 4 / 67 23.1× 2.48e-5 7.13e-4 ✓ sig.
Laminin interactions
LAMB3, COL7A1, LAMC2
 Reactome 3 / 28 41.5× 4.88e-5 1.25e-3 ✓ sig.
Integrin cell surface interactions
ITGB6, COL7A1, COL1A1, COL1A2
 Reactome 4 / 81 19.1× 5.26e-5 1.33e-3 ✓ sig.
Protein digestion and absorption
COL17A1, COL7A1, COL1A1, COL1A2
 KEGG 4 / 103 15.0× 1.34e-4 2.85e-3 ✓ 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 ⇵
biomineral tissue development
AMBN, AMELX, ENAM, FAM20A, FAM20C, FAM83H, KLK4, WDR72, AMTN, DSPP
 GO:0031214 10 / 35 172× 5.56e-21 1.03e-17 ✓ sig.
amelogenesis
AMELX, ENAM, KLK4, MMP20, RELT, SLC24A4
 GO:0097186 6 / 12 301× 1.14e-14 7.38e-12 ✓ sig.
enamel mineralization
AMELX, FAM20A, FAM20C, ITGB6, SLC24A4
 GO:0070166 5 / 14 215× 1.77e-11 6.14e-9 ✓ sig.
positive regulation of enamel mineralization
ENAM, ODAPH, AMTN
 GO:0070175 3 / 5 362× 4.12e-8 5.75e-6 ✓ sig.
odontoblast differentiation
DLX3, FAM20C, DSPP
 GO:0071895 3 / 8 226× 2.30e-7 2.44e-5 ✓ sig.
odontogenesis
ACP4, SP6, SSUH2, COL1A2
 GO:0042476 4 / 36 67.0× 3.52e-7 3.47e-5 ✓ sig.
odontogenesis of dentin-containing tooth
AMBN, AMELX, DLX3, AMTN
 GO:0042475 4 / 56 43.1× 2.14e-6 1.52e-4 ✓ sig.
tooth mineralization
AMELX, COL1A1
 GO:0034505 2 / 3 402× 7.98e-6 4.37e-4 ✓ sig.
positive regulation of biomineral tissue development
ODAPH, AMTN
 GO:0070169 2 / 5 241× 2.66e-5 1.11e-3 ✓ sig.
epidermis development
COL17A1, LAMB3, COL7A1, LAMC2
 GO:0008544 4 / 114 21.2× 3.64e-5 1.42e-3 ✓ sig.
dentinogenesis
FAM20C, DSPP
 GO:0097187 2 / 7 172× 5.56e-5 1.95e-3 ✓ sig.
cell adhesion
AMBN, AMELX, ITGB6, LAMB3, COL7A1, LAMC2, AMTN
 GO:0007155 7 / 665 6.3× 8.73e-5 2.74e-3 ✓ sig.
skeletal system development
FAM20C, LTBP3, COL1A1, COL1A2
 GO:0001501 4 / 151 16.0× 1.09e-4 3.22e-3 ✓ sig.
skin morphogenesis
COL1A1, COL1A2
 GO:0043589 2 / 13 92.7× 2.05e-4 5.14e-3 ✓ sig.
blood vessel development
DLX3, COL1A1, COL1A2
 GO:0001568 3 / 70 25.8× 2.10e-4 5.21e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Dentin dysplasia Dentinogenesis imperfecta 0.700 14 1.70e-43 8.14e-42 ✓ sig.
Amelogenesis imperfecta Dentinogenesis imperfecta 0.448 13 6.65e-36 2.63e-34 ✓ sig.
Amelogenesis imperfecta Dentin dysplasia 0.433 13 2.82e-35 1.08e-33 ✓ sig.
Amelogenesis imperfecta Hypomaturation amelogenesis imperfecta 0.269 7 1.18e-20 2.46e-19 ✓ sig.
Dentinogenesis imperfecta Hypomaturation amelogenesis imperfecta 0.333 6 3.03e-18 5.57e-17 ✓ sig.
Dentin dysplasia Hypomaturation amelogenesis imperfecta 0.316 6 4.68e-18 8.55e-17 ✓ sig.
Dentinogenesis imperfecta Enamel-renal syndrome 0.059 1 1.04e-3 1.72e-3 ✓ sig.
Dentin dysplasia Enamel-renal syndrome 0.056 1 1.10e-3 1.81e-3 ✓ sig.
Amelogenesis imperfecta Enamel-renal syndrome 0.038 1 1.62e-3 2.44e-3 ✓ sig.