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 62

15 diseases · 39 shared-gene connections
15 Diseases
16 Unique genes
0.336 Avg. similarity score
Osteoporosis-pseudoglioma syndrome on a spectrum with fevr with osteopenia Most-connected disease (10 links)
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Disease Searched: Polycystic liver disease 4 with or without kidney cysts 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 ⇵
Osteoporosis-pseudoglioma syndrome on a spectrum with fevr with osteopenia 10 10 1
Polycystic liver disease 4 with or without kidney cysts 10 10 1
Worth syndrome 10 10 1
Endosteal hyperostosis, worth type 9 9 1
Osteopetrosis, autosomal dominant 1 6 6 1
Bone mineral density quantitative trait locus 5 5 4
Camurati-engelmann syndrome 5 5 2
Van buchem disease 5 5 2
Osteopetrosis and infantile neuroaxonal dystrophy 4 4 2
Retinopathy background 4 4 2
Vitamin d deficiency 4 4 3
Vitreoretinal degeneration 3 3 8
Cleft palate proliferative retinopathy developmental delay 1 1 1
Delayed puberty, self-limited 1 1 1
Snowflake vitreoretinal degeneration 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
LRP5 12 / 15 Bone mineral density quantitative trait locus, Camurati-engelmann syndrome, Endosteal hyperostosis, worth type, Osteopetrosis and infantile neuroaxonal dystrophy and 8 more
ABCA4 2 / 15 Retinopathy background, Vitreoretinal degeneration
KCNJ13 2 / 15 Snowflake vitreoretinal degeneration, Vitreoretinal degeneration
LGR4 2 / 15 Bone mineral density quantitative trait locus, Delayed puberty, self-limited
LRRC32 2 / 15 Cleft palate proliferative retinopathy developmental delay, Vitreoretinal degeneration
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 / 8 188× 4.64e-5 1.03e-3 ✓ sig.
Vitamin D (calciferol) metabolism
LRP2, VDR
 Reactome 2 / 11 136× 9.09e-5 1.76e-3 ✓ sig.
Regulation of FZD by ubiquitination
LRP5, LGR4
 Reactome 2 / 21 71.5× 3.44e-4 5.01e-3 ✓ sig.
Parathyroid hormone synthesis, secretion and action
LRP5, SOST, VDR
 KEGG 3 / 115 19.6× 4.37e-4 6.02e-3 ✓ sig.
Wnt signaling pathway
LRP5, LGR4, SOST
 KEGG 3 / 174 12.9× 1.46e-3 1.51e-2 ✓ sig.
Influenza Virus Induced Apoptosis
TGFB1
 Reactome 1 / 2 375× 2.66e-3 2.34e-2 ✓ sig.
TGFBR2 MSI Frameshift Mutants in Cancer
TGFB1
 Reactome 1 / 2 375× 2.66e-3 2.34e-2 ✓ sig.
TGFBR2 Kinase Domain Mutants in Cancer
TGFB1
 Reactome 1 / 3 250× 3.99e-3 3.12e-2 ✓ sig.
TGFBR1 LBD Mutants in Cancer
TGFB1
 Reactome 1 / 4 188× 5.32e-3 3.80e-2 ✓ sig.
Misspliced LRP5 mutants have enhanced beta-catenin-dependent signaling
LRP5
 Reactome 1 / 6 125× 7.97e-3 4.94e-2 ✓ sig.
SMAD2/3 Phosphorylation Motif Mutants in Cancer
TGFB1
 Reactome 1 / 6 125× 7.97e-3 4.94e-2 ✓ sig.
TGFBR1 KD Mutants in Cancer
TGFB1
 Reactome 1 / 6 125× 7.97e-3 4.94e-2 ✓ sig.
TGF-beta signaling pathway
TGFB1, LRRC32
 KEGG 2 / 108 13.9× 8.86e-3 5.28e-2
RUNX3 regulates CDKN1A transcription
TGFB1
 Reactome 1 / 7 107× 9.29e-3 5.43e-2
Defective CHST3 causes SEDCJD
VCAN
 Reactome 1 / 8 93.8× 1.06e-2 5.90e-2

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
Norrin signaling pathway
LRP5, TSPAN12
 GO:0110135 2 / 4 584× 4.12e-6 2.71e-4 ✓ sig.
retina vasculature development in camera-type eye
LRP5, TGFB1
 GO:0061298 2 / 15 156× 7.17e-5 2.41e-3 ✓ sig.
canonical Wnt signaling pathway
LRP5, TGFB1, SOST
 GO:0060070 3 / 105 33.4× 9.15e-5 2.90e-3 ✓ sig.
positive regulation of branching involved in ureteric bud morphogenesis
LGR4, TGFB1
 GO:0090190 2 / 18 130× 1.04e-4 3.19e-3 ✓ sig.
bone remodeling
LRP5, LGR4
 GO:0046849 2 / 18 130× 1.04e-4 3.19e-3 ✓ sig.
negative regulation of ossification
TGFB1, SOST
 GO:0030279 2 / 27 86.5× 2.38e-4 5.74e-3 ✓ sig.
digestive tract development
LGR4, TGFB1
 GO:0048565 2 / 34 68.7× 3.79e-4 7.88e-3 ✓ sig.
retinoid metabolic process
ABCA4, LRP2
 GO:0001523 2 / 38 61.5× 4.75e-4 9.19e-3 ✓ sig.
photoreceptor cell maintenance
ABCA4, CDH23
 GO:0045494 2 / 45 51.9× 6.66e-4 1.14e-2 ✓ sig.
negative regulation of cytokine production
LGR4, LRRC32
 GO:0001818 2 / 47 49.7× 7.26e-4 1.22e-2 ✓ sig.
diol metabolic process
LRP2
 GO:0034311 1 / 1 1,168× 8.56e-4 1.33e-2 ✓ sig.
columnar/cuboidal epithelial cell maturation
TGFB1
 GO:0002069 1 / 1 1,168× 8.56e-4 1.33e-2 ✓ sig.
adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
TGFB1
 GO:0002460 1 / 1 1,168× 8.56e-4 1.33e-2 ✓ sig.
positive regulation of microglia differentiation
TGFB1
 GO:0014008 1 / 1 1,168× 8.56e-4 1.33e-2 ✓ sig.
regulation of interleukin-23 production
TGFB1
 GO:0032667 1 / 1 1,168× 8.56e-4 1.33e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Retinopathy background Vitreoretinal degeneration 0.222 2 2.33e-7 1.55e-6 ✓ sig.
Osteopetrosis, autosomal dominant 1 Polycystic liver disease 4 with or without kidney cysts 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Polycystic liver disease 4 with or without kidney cysts Worth syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Osteoporosis-pseudoglioma syndrome on a spectrum with fevr with osteopenia Polycystic liver disease 4 with or without kidney cysts 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Osteoporosis-pseudoglioma syndrome on a spectrum with fevr with osteopenia Worth syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Osteopetrosis, autosomal dominant 1 Osteoporosis-pseudoglioma syndrome on a spectrum with fevr with osteopenia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Osteopetrosis, autosomal dominant 1 Worth syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Endosteal hyperostosis, worth type Osteopetrosis, autosomal dominant 1 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Endosteal hyperostosis, worth type Osteoporosis-pseudoglioma syndrome on a spectrum with fevr with osteopenia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Endosteal hyperostosis, worth type Polycystic liver disease 4 with or without kidney cysts 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Endosteal hyperostosis, worth type Worth syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Endosteal hyperostosis, worth type Van buchem disease 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Van buchem disease Worth syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Osteoporosis-pseudoglioma syndrome on a spectrum with fevr with osteopenia Retinopathy background 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Polycystic liver disease 4 with or without kidney cysts Retinopathy background 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Retinopathy background Worth syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Polycystic liver disease 4 with or without kidney cysts Van buchem disease 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Osteoporosis-pseudoglioma syndrome on a spectrum with fevr with osteopenia Van buchem disease 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Camurati-engelmann syndrome Osteopetrosis, autosomal dominant 1 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Camurati-engelmann syndrome Worth syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Camurati-engelmann syndrome Polycystic liver disease 4 with or without kidney cysts 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Endosteal hyperostosis, worth type Osteopetrosis and infantile neuroaxonal dystrophy 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Osteopetrosis and infantile neuroaxonal dystrophy Osteoporosis-pseudoglioma syndrome on a spectrum with fevr with osteopenia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Osteopetrosis and infantile neuroaxonal dystrophy Polycystic liver disease 4 with or without kidney cysts 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Osteopetrosis and infantile neuroaxonal dystrophy Worth syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Camurati-engelmann syndrome Endosteal hyperostosis, worth type 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Camurati-engelmann syndrome Osteoporosis-pseudoglioma syndrome on a spectrum with fevr with osteopenia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Osteopetrosis, autosomal dominant 1 Van buchem disease 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Osteoporosis-pseudoglioma syndrome on a spectrum with fevr with osteopenia Vitamin d deficiency 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Vitamin d deficiency Worth syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Polycystic liver disease 4 with or without kidney cysts Vitamin d deficiency 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Endosteal hyperostosis, worth type Vitamin d deficiency 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Bone mineral density quantitative trait locus Polycystic liver disease 4 with or without kidney cysts 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Bone mineral density quantitative trait locus Worth syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Bone mineral density quantitative trait locus Osteoporosis-pseudoglioma syndrome on a spectrum with fevr with osteopenia 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Bone mineral density quantitative trait locus Endosteal hyperostosis, worth type 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Bone mineral density quantitative trait locus Delayed puberty, self-limited 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Snowflake vitreoretinal degeneration Vitreoretinal degeneration 0.111 1 5.17e-4 9.13e-4 ✓ sig.
Cleft palate proliferative retinopathy developmental delay Vitreoretinal degeneration 0.111 1 5.17e-4 9.13e-4 ✓ sig.