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 103

12 diseases · 25 shared-gene connections
12 Diseases
175 Unique genes
0.201 Avg. similarity score
Eyelid disease Most-connected disease (7 links)
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Disease Searched: Doyne honeycomb degeneration of retina 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 ⇵
Eyelid disease 7 7 6
Visual impairment 7 7 10
Visual system disorder 7 7 2
Congenital hernia of foramen of bochdalek 6 6 1
Cutis laxa, autosomal recessive, type id 5 5 1
Doyne honeycomb degeneration of retina 5 5 1
Uterine prolapse 4 4 15
Doyne honeycomb retinal dystrophy 3 3 4
Neuropathy 3 3 21
Breast fibrocystic disease 1 1 2
Pelvic organ prolapse 1 1 139
Visual impairment and progressive phthisis bulbi 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
EFEMP1 10 / 12 Congenital hernia of foramen of bochdalek, Cutis laxa, autosomal recessive, type id, Doyne honeycomb degeneration of retina, Doyne honeycomb retinal dystrophy and 6 more
PNPT1 6 / 12 Eyelid disease, Neuropathy, Pelvic organ prolapse, Uterine prolapse and 2 more
CSMD1 2 / 12 Breast fibrocystic disease, Visual impairment
FBN2 2 / 12 Pelvic organ prolapse, Uterine prolapse
GDF7 2 / 12 Pelvic organ prolapse, Uterine prolapse
HNRNPA1L3 2 / 12 Pelvic organ prolapse, Uterine prolapse
MAFF 2 / 12 Pelvic organ prolapse, Uterine prolapse
MARK3 2 / 12 Visual impairment, Visual impairment and progressive phthisis bulbi
MGLL 2 / 12 Pelvic organ prolapse, Uterine prolapse
PLA2G6 2 / 12 Pelvic organ prolapse, Uterine prolapse
POLD3 2 / 12 Pelvic organ prolapse, Uterine prolapse
PSD3 2 / 12 Neuropathy, Pelvic organ prolapse
SLC12A2 2 / 12 Pelvic organ prolapse, Uterine prolapse
SORBS2 2 / 12 Pelvic organ prolapse, Uterine prolapse
WNT4 2 / 12 Pelvic organ prolapse, Uterine prolapse
WT1 2 / 12 Pelvic organ prolapse, Uterine prolapse
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 ⇵
Axon guidance
EPHA4, LIMK2, UNC5D, GDF7, NRP1, NTN4, SLIT3, WNT4
 KEGG 8 / 183 3.0× 5.35e-3 3.81e-2 ✓ sig.
MET activates PTK2 signaling
COL5A1, LAMA4, LAMA5
 Reactome 3 / 30 6.9× 9.25e-3 5.42e-2
Small cell lung cancer
BCL2, CKS2, LAMA4, LAMA5, RXRA
 KEGG 5 / 93 3.7× 1.15e-2 6.20e-2
Presynaptic depolarization and calcium channel opening
CACNA2D3, CACNA2D1
 Reactome 2 / 12 11.4× 1.27e-2 6.57e-2
Signaling by FGFR2 amplification mutants
FGFR2
 Reactome 1 / 1 68.6× 1.46e-2 7.13e-2
Signaling by FGFR2 fusions
FGFR2
 Reactome 1 / 1 68.6× 1.46e-2 7.13e-2
Toxicity of tetanus toxin (TeNT)
VAMP2
 Reactome 1 / 1 68.6× 1.46e-2 7.13e-2
Purine salvage
ADA, ADK
 Reactome 2 / 13 10.6× 1.48e-2 7.22e-2
RAF-independent MAPK1/3 activation
DUSP1, DUSP16
 Reactome 2 / 13 10.6× 1.48e-2 7.22e-2
Negative regulation of MAPK pathway
DUSP1, DUSP16, MARK3
 Reactome 3 / 38 5.4× 1.77e-2 7.98e-2
Insertion of tail-anchored proteins into the endoplasmic reticulum membrane
VAMP2, PRNP
 Reactome 2 / 16 8.6× 2.22e-2 9.10e-2
Gastric cancer
BCL2, DVL2, FGFR2, RXRA, SHC3, WNT4
 KEGG 6 / 150 2.7× 2.25e-2 9.16e-2
Type I diabetes mellitus
IFNG, CPE, PTPRN2
 KEGG 3 / 44 4.7× 2.60e-2 9.98e-2
RORA activates gene expression
CHD9, RXRA
 Reactome 2 / 18 7.6× 2.77e-2 1.03e-1
Elastic fibre formation
FBN2, LOXL1
 Reactome 2 / 18 7.6× 2.77e-2 1.03e-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 ⇵
ureteric bud development
FOXC2, BCL2, EYA1, FGFR2, SPRY1, WT1
 GO:0001657 6 / 41 15.6× 2.12e-6 1.59e-4 ✓ sig.
branching involved in ureteric bud morphogenesis
BCL2, EYA1, LAMA5, WNT4, WT1, PAX2
 GO:0001658 6 / 45 14.2× 3.72e-6 2.50e-4 ✓ sig.
metanephros development
FOXC2, BCL2, EYA1, SPRY1, WNT4
 GO:0001656 5 / 38 14.1× 2.66e-5 1.14e-3 ✓ sig.
animal organ morphogenesis
BCL2, EYA1, FGFR2, GREM1, LAMA5, NRP1, NTN4, SLIT3
 GO:0009887 8 / 130 6.6× 3.10e-5 1.28e-3 ✓ sig.
gland morphogenesis
BCL2, FGFR2, GDF7
 GO:0022612 3 / 9 35.6× 6.51e-5 2.24e-3 ✓ sig.
camera-type eye development
EFEMP1, FOXC2, FBN2, FOXP2, WT1, PAX2
 GO:0043010 6 / 74 8.7× 6.77e-5 2.31e-3 ✓ sig.
mesenchymal to epithelial transition
WNT4, WT1, PAX2
 GO:0060231 3 / 11 29.1× 1.26e-4 3.65e-3 ✓ sig.
protein homooligomerization
PNPT1, PRPH2, OTOL1, KCTD14, KCTD18, PRMT8, PRNP
 GO:0051260 7 / 130 5.7× 2.25e-4 5.52e-3 ✓ sig.
ventricular zone neuroblast division
DCT, FGFR2
 GO:0021847 2 / 3 71.2× 2.60e-4 6.13e-3 ✓ sig.
calcium ion transport into cytosol
BCL2, JPH2, CACNA2D1
 GO:0060402 3 / 14 22.9× 2.72e-4 6.32e-3 ✓ sig.
mucus secretion
ADA, HTR4, VAMP2
 GO:0070254 3 / 15 21.4× 3.38e-4 7.30e-3 ✓ sig.
regulation of signal transduction
CSF2, GPC6, GUCA1C, MGLL, SPRY1, WWOX
 GO:0009966 6 / 101 6.3× 3.76e-4 7.83e-3 ✓ sig.
axon guidance
EPHA4, TRIO, UNC5D, GDF7, KLF7, NRP1, NTN4, SLIT3
 GO:0007411 8 / 192 4.4× 4.62e-4 9.03e-3 ✓ sig.
eye morphogenesis
COL5A1, STAU2
 GO:0048592 2 / 4 53.4× 5.17e-4 9.73e-3 ✓ sig.
regulation of epidermal cell differentiation
KLF7, MAFF
 GO:0045604 2 / 4 53.4× 5.17e-4 9.73e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Pelvic organ prolapse Uterine prolapse 0.092 13 1.43e-25 2.48e-24 ✓ sig.
Eyelid disease Visual system disorder 0.286 2 1.25e-7 8.63e-7 ✓ sig.
Visual impairment Visual system disorder 0.182 2 3.75e-7 2.42e-6 ✓ sig.
Uterine prolapse Visual system disorder 0.125 2 8.76e-7 5.37e-6 ✓ sig.
Neuropathy Visual system disorder 0.091 2 1.75e-6 1.03e-5 ✓ sig.
Eyelid disease Visual impairment 0.133 2 5.62e-6 3.11e-5 ✓ sig.
Eyelid disease Uterine prolapse 0.100 2 1.31e-5 7.00e-5 ✓ sig.
Eyelid disease Neuropathy 0.077 2 2.62e-5 1.36e-4 ✓ sig.
Cutis laxa, autosomal recessive, type id Doyne honeycomb degeneration of retina 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital hernia of foramen of bochdalek Cutis laxa, autosomal recessive, type id 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital hernia of foramen of bochdalek Doyne honeycomb degeneration of retina 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Uterine prolapse Visual impairment 0.083 2 3.92e-5 1.98e-4 ✓ sig.
Neuropathy Visual impairment 0.067 2 7.83e-5 2.40e-4 ✓ sig.
Doyne honeycomb degeneration of retina Visual system disorder 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Cutis laxa, autosomal recessive, type id Visual system disorder 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital hernia of foramen of bochdalek Visual system disorder 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Cutis laxa, autosomal recessive, type id Doyne honeycomb retinal dystrophy 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Doyne honeycomb degeneration of retina Doyne honeycomb retinal dystrophy 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Congenital hernia of foramen of bochdalek Doyne honeycomb retinal dystrophy 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Doyne honeycomb degeneration of retina Eyelid disease 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Cutis laxa, autosomal recessive, type id Eyelid disease 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Congenital hernia of foramen of bochdalek Eyelid disease 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Congenital hernia of foramen of bochdalek Visual impairment 0.091 1 6.46e-4 1.09e-3 ✓ sig.
Visual impairment Visual impairment and progressive phthisis bulbi 0.091 1 6.46e-4 1.09e-3 ✓ sig.
Breast fibrocystic disease Visual impairment 0.083 1 1.29e-3 1.89e-3 ✓ sig.