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 247

7 diseases · 13 shared-gene connections
7 Diseases
25 Unique genes
0.229 Avg. similarity score
Atrophoderma vermiculata Most-connected disease (5 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 ⇵
Atrophoderma vermiculata 5 5 1
Burnett schwartz berberian syndrome 5 5 1
Tricuspid atresia 5 5 1
Keratosis follicularis spinulosa decalvans 4 4 3
Common migraine 3 3 10
Developmental dysplasia of the hip 3 3 14
pediatric systemic lupus erythematosus 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
LRP1 6 / 7 Atrophoderma vermiculata, Burnett schwartz berberian syndrome, Common migraine, Developmental dysplasia of the hip and 2 more
SAT1 2 / 7 Keratosis follicularis spinulosa decalvans, pediatric systemic lupus erythematosus
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 ⇵
Degradation of GABA
ABAT
 Reactome 1 / 2 240× 4.16e-3 3.87e-2 ✓ sig.
Malaria
LRP1, TNF
 KEGG 2 / 50 19.2× 4.79e-3 4.27e-2 ✓ sig.
Cholesterol metabolism
LRP1, LDLR
 KEGG 2 / 51 18.8× 4.98e-3 4.37e-2 ✓ sig.
Interconversion of polyamines
SAT1
 Reactome 1 / 3 160× 6.23e-3 5.06e-2
ATF6 (ATF6-alpha) activates chaperones
MBTPS2
 Reactome 1 / 4 120× 8.30e-3 6.10e-2
CREB3 factors activate genes
MBTPS2
 Reactome 1 / 5 96.1× 1.04e-2 7.02e-2
Chylomicron clearance
LDLR
 Reactome 1 / 5 96.1× 1.04e-2 7.02e-2
Defective LFNG causes SCDO3
NOTCH3
 Reactome 1 / 5 96.1× 1.04e-2 7.02e-2
Tachykinin receptors bind tachykinins
TAC1
 Reactome 1 / 5 96.1× 1.04e-2 7.02e-2
TNFR1-mediated ceramide production
TNF
 Reactome 1 / 6 80.1× 1.24e-2 7.78e-2
Pre-NOTCH Processing in Golgi
NOTCH3
 Reactome 1 / 6 80.1× 1.24e-2 7.78e-2
Regulation of cholesterol biosynthesis by SREBP (SREBF)
MBTPS2
 Reactome 1 / 7 68.6× 1.45e-2 8.53e-2
TNF signaling
TNF
 Reactome 1 / 7 68.6× 1.45e-2 8.53e-2
Noncanonical activation of NOTCH3
NOTCH3
 Reactome 1 / 8 60.1× 1.65e-2 9.23e-2
Cargo recognition for clathrin-mediated endocytosis
LDLR, SH3GL3
 Reactome 2 / 106 9.1× 2.03e-2 1.04e-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 ⇵
positive regulation of lysosomal protein catabolic process
LRP1, LDLR
 GO:1905167 2 / 5 299× 1.71e-5 7.95e-4 ✓ sig.
defense response to Gram-positive bacterium
CALCA, TAC1, TNF, REG3G
 GO:0050830 4 / 135 22.1× 2.93e-5 1.20e-3 ✓ sig.
positive regulation of action potential
TAC1, TNF
 GO:0045760 2 / 7 214× 3.59e-5 1.40e-3 ✓ sig.
negative regulation of macromolecule metabolic process
LRP1, LDLR
 GO:0010605 2 / 7 214× 3.59e-5 1.40e-3 ✓ sig.
amyloid-beta clearance by cellular catabolic process
LRP1, LDLR
 GO:0150094 2 / 8 187× 4.79e-5 1.74e-3 ✓ sig.
negative regulation of heart rate
TAC1, TNF
 GO:0010459 2 / 12 125× 1.12e-4 3.30e-3 ✓ sig.
antifungal humoral response
CALCA, TAC1
 GO:0019732 2 / 13 115× 1.33e-4 3.74e-3 ✓ sig.
response to yeast
CALCA, TAC1
 GO:0001878 2 / 16 93.4× 2.04e-4 5.11e-3 ✓ sig.
amyloid-beta clearance
LRP1, LDLR
 GO:0097242 2 / 17 87.9× 2.31e-4 5.58e-3 ✓ sig.
negative regulation of systemic arterial blood pressure
TAC1, TNF
 GO:0003085 2 / 18 83.1× 2.59e-4 6.07e-3 ✓ sig.
regulation of protein metabolic process
LRP1, LDLR
 GO:0051246 2 / 24 62.3× 4.66e-4 9.12e-3 ✓ sig.
lysosomal transport
LRP1, VPS53
 GO:0007041 2 / 26 57.5× 5.48e-4 1.01e-2 ✓ sig.
antimicrobial humoral immune response mediated by antimicrobial peptide
CALCA, TAC1, REG3G
 GO:0061844 3 / 124 18.1× 5.90e-4 1.07e-2 ✓ sig.
artery morphogenesis
LDLR, NOTCH3
 GO:0048844 2 / 27 55.4× 5.91e-4 1.07e-2 ✓ sig.
negative regulation of blood pressure
CALCA, ABAT
 GO:0045776 2 / 28 53.4× 6.36e-4 1.13e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Atrophoderma vermiculata Burnett schwartz berberian syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Atrophoderma vermiculata Tricuspid atresia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Burnett schwartz berberian syndrome Tricuspid atresia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Atrophoderma vermiculata Keratosis follicularis spinulosa decalvans 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Burnett schwartz berberian syndrome Keratosis follicularis spinulosa decalvans 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Keratosis follicularis spinulosa decalvans Tricuspid atresia 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Keratosis follicularis spinulosa decalvans pediatric systemic lupus erythematosus 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Atrophoderma vermiculata Common migraine 0.091 1 6.49e-4 1.22e-3 ✓ sig.
Burnett schwartz berberian syndrome Common migraine 0.091 1 6.49e-4 1.22e-3 ✓ sig.
Common migraine Tricuspid atresia 0.091 1 6.49e-4 1.22e-3 ✓ sig.
Atrophoderma vermiculata Developmental dysplasia of the hip 0.067 1 9.09e-4 1.56e-3 ✓ sig.
Burnett schwartz berberian syndrome Developmental dysplasia of the hip 0.067 1 9.09e-4 1.56e-3 ✓ sig.
Developmental dysplasia of the hip Tricuspid atresia 0.067 1 9.09e-4 1.56e-3 ✓ sig.