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 123

11 diseases · 24 shared-gene connections
11 Diseases
9 Unique genes
0.308 Avg. similarity score
LRP5-related exudative vitreoretinopathy Most-connected disease (7 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 ⇵
LRP5-related exudative vitreoretinopathy 7 7 1
Worth syndrome 7 7 1
polycystic liver disease 4 with or without kidney cysts 7 7 1
Camurati-engelmann syndrome 6 6 2
Bone mineral density quantitative trait locus 5 5 4
Osteopetrosis and infantile neuroaxonal dystrophy 5 5 2
Van buchem disease 5 5 2
Vitamin d deficiency 3 3 3
Bone dysplasia with increased bone density 1 1 1
PLA2G6-associated neurodegeneration 1 1 1
X-linked osteoporosis 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
LRP5 8 / 11 Bone mineral density quantitative trait locus, Camurati-engelmann syndrome, LRP5-related exudative vitreoretinopathy, Osteopetrosis and infantile neuroaxonal dystrophy and 4 more
PLA2G6 2 / 11 Osteopetrosis and infantile neuroaxonal dystrophy, PLA2G6-associated neurodegeneration
PLS3 2 / 11 Bone mineral density quantitative trait locus, X-linked osteoporosis
SOST 2 / 11 Bone dysplasia with increased bone density, Van buchem disease
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 ⇵
Negative regulation of TCF-dependent signaling by WNT ligand antagonists
LRP5, SOST
 Reactome 2 / 8 334× 1.39e-5 4.42e-4 ✓ sig.
Vitamin D (calciferol) metabolism
LRP2, VDR
 Reactome 2 / 11 243× 2.74e-5 7.71e-4 ✓ sig.
Parathyroid hormone synthesis, secretion and action
LRP5, SOST, VDR
 KEGG 3 / 115 34.8× 6.89e-5 1.65e-3 ✓ sig.
Regulation of FZD by ubiquitination
LRP5, LGR4
 Reactome 2 / 21 127× 1.04e-4 2.33e-3 ✓ sig.
Wnt signaling pathway
LRP5, LGR4, SOST
 KEGG 3 / 174 23.0× 2.35e-4 4.44e-3 ✓ sig.
Influenza Virus Induced Apoptosis
TGFB1
 Reactome 1 / 2 667× 1.50e-3 1.85e-2 ✓ sig.
TGFBR2 MSI Frameshift Mutants in Cancer
TGFB1
 Reactome 1 / 2 667× 1.50e-3 1.85e-2 ✓ sig.
TGFBR2 Kinase Domain Mutants in Cancer
TGFB1
 Reactome 1 / 3 445× 2.25e-3 2.48e-2 ✓ sig.
TGFBR1 LBD Mutants in Cancer
TGFB1
 Reactome 1 / 4 334× 2.99e-3 3.07e-2 ✓ sig.
Misspliced LRP5 mutants have enhanced beta-catenin-dependent signaling
LRP5
 Reactome 1 / 6 222× 4.49e-3 4.08e-2 ✓ sig.
SMAD2/3 Phosphorylation Motif Mutants in Cancer
TGFB1
 Reactome 1 / 6 222× 4.49e-3 4.08e-2 ✓ sig.
TGFBR1 KD Mutants in Cancer
TGFB1
 Reactome 1 / 6 222× 4.49e-3 4.08e-2 ✓ sig.
RUNX3 regulates CDKN1A transcription
TGFB1
 Reactome 1 / 7 191× 5.24e-3 4.50e-2 ✓ sig.
Gastric cancer
LRP5, TGFB1
 KEGG 2 / 150 17.8× 5.27e-3 4.53e-2 ✓ sig.
Efferocytosis
TGFB1, PLA2G6
 KEGG 2 / 157 17.0× 5.76e-3 4.81e-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 ⇵
canonical Wnt signaling pathway
LRP5, TGFB1, SOST
 GO:0060070 3 / 105 59.3× 1.41e-5 6.84e-4 ✓ sig.
retina vasculature development in camera-type eye
LRP5, TGFB1
 GO:0061298 2 / 15 277× 2.16e-5 9.54e-4 ✓ sig.
positive regulation of branching involved in ureteric bud morphogenesis
LGR4, TGFB1
 GO:0090190 2 / 18 231× 3.14e-5 1.27e-3 ✓ sig.
bone remodeling
LRP5, LGR4
 GO:0046849 2 / 18 231× 3.14e-5 1.27e-3 ✓ sig.
negative regulation of ossification
TGFB1, SOST
 GO:0030279 2 / 27 154× 7.19e-5 2.36e-3 ✓ sig.
digestive tract development
LGR4, TGFB1
 GO:0048565 2 / 34 122× 1.15e-4 3.35e-3 ✓ sig.
Wnt signaling pathway
LRP5, LGR4, SOST
 GO:0016055 3 / 232 26.8× 1.50e-4 4.10e-3 ✓ sig.
gene expression
LRP5, TGFB1, LRP2
 GO:0010467 3 / 269 23.2× 2.32e-4 5.61e-3 ✓ sig.
diol metabolic process
LRP2
 GO:0034311 1 / 1 2,076× 4.82e-4 9.31e-3 ✓ sig.
columnar/cuboidal epithelial cell maturation
TGFB1
 GO:0002069 1 / 1 2,076× 4.82e-4 9.31e-3 ✓ sig.
adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
TGFB1
 GO:0002460 1 / 1 2,076× 4.82e-4 9.31e-3 ✓ sig.
positive regulation of microglia differentiation
TGFB1
 GO:0014008 1 / 1 2,076× 4.82e-4 9.31e-3 ✓ sig.
regulation of interleukin-23 production
TGFB1
 GO:0032667 1 / 1 2,076× 4.82e-4 9.31e-3 ✓ sig.
branch elongation involved in mammary gland duct branching
TGFB1
 GO:0060751 1 / 1 2,076× 4.82e-4 9.31e-3 ✓ sig.
cellular response to acetaldehyde
TGFB1
 GO:1905641 1 / 1 2,076× 4.82e-4 9.31e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
polycystic liver disease 4 with or without kidney cysts Worth syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
LRP5-related exudative vitreoretinopathy polycystic liver disease 4 with or without kidney cysts 0.500 1 6.49e-5 2.34e-4 ✓ sig.
LRP5-related exudative vitreoretinopathy Worth syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Camurati-engelmann syndrome LRP5-related exudative vitreoretinopathy 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Van buchem disease Worth syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Osteopetrosis and infantile neuroaxonal dystrophy polycystic liver disease 4 with or without kidney cysts 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Osteopetrosis and infantile neuroaxonal dystrophy Worth syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Osteopetrosis and infantile neuroaxonal dystrophy PLA2G6-associated neurodegeneration 0.333 1 1.30e-4 3.90e-4 ✓ sig.
LRP5-related exudative vitreoretinopathy Osteopetrosis and infantile neuroaxonal dystrophy 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Camurati-engelmann syndrome polycystic liver disease 4 with or without kidney cysts 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Camurati-engelmann syndrome Worth syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
polycystic liver disease 4 with or without kidney cysts Van buchem disease 0.333 1 1.30e-4 3.90e-4 ✓ sig.
LRP5-related exudative vitreoretinopathy Van buchem disease 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Bone dysplasia with increased bone density Van buchem disease 0.333 1 1.30e-4 3.90e-4 ✓ sig.
LRP5-related exudative vitreoretinopathy Vitamin d deficiency 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Vitamin d deficiency Worth syndrome 0.250 1 1.95e-4 5.28e-4 ✓ sig.
polycystic liver disease 4 with or without kidney cysts Vitamin d deficiency 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Camurati-engelmann syndrome Osteopetrosis and infantile neuroaxonal dystrophy 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Camurati-engelmann syndrome Van buchem disease 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Bone mineral density quantitative trait locus X-linked osteoporosis 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Bone mineral density quantitative trait locus LRP5-related exudative vitreoretinopathy 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Bone mineral density quantitative trait locus polycystic liver disease 4 with or without kidney cysts 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Bone mineral density quantitative trait locus Worth syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Bone mineral density quantitative trait locus Camurati-engelmann syndrome 0.167 1 5.19e-4 1.04e-3 ✓ sig.