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 296

6 diseases · 11 shared-gene connections
6 Diseases
17 Unique genes
0.192 Avg. similarity score
Bicuspid aortic valve Most-connected disease (5 links)
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Disease Searched: Keratosis palmoplantaris striata 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 ⇵
Bicuspid aortic valve 5 5 14
Congenital erythroderma with palmoplantar keratoderma, hypotrichosis, and hyper-ige 4 4 1
Diffuse palmoplantar keratoderma 4 4 2
Focal palmoplantar keratoderma with joint keratoses 4 4 1
Keratosis palmoplantaris striata 4 4 4
aortic valve disease 3 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
DSG1 5 / 6 Bicuspid aortic valve, Congenital erythroderma with palmoplantar keratoderma, hypotrichosis, and hyper-ige, Diffuse palmoplantar keratoderma, Focal palmoplantar keratoderma with joint keratoses and 1 more
DSP 2 / 6 Bicuspid aortic valve, Keratosis palmoplantaris striata
ROBO4 2 / 6 aortic valve disease 3, Bicuspid aortic valve
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 ⇵
Apoptotic cleavage of cell adhesion proteins
DSG1, DSP
 Reactome 2 / 11 128× 1.03e-4 2.24e-3 ✓ sig.
Formation of ATP by chemiosmotic coupling
ATP6, ATP8
 Reactome 2 / 18 78.5× 2.85e-4 5.04e-3 ✓ sig.
Cristae formation
ATP6, ATP8
 Reactome 2 / 18 78.5× 2.85e-4 5.04e-3 ✓ sig.
Formation of the cornified envelope
DSG1, DSP, KRT1
 Reactome 3 / 130 16.3× 7.54e-4 1.08e-2 ✓ sig.
Keratinization
DSG1, DSP, KRT1
 Reactome 3 / 152 13.9× 1.19e-3 1.53e-2 ✓ sig.
Defective SLC2A10 causes arterial tortuosity syndrome (ATS)
SLC2A10
 Reactome 1 / 1 706× 1.42e-3 1.75e-2 ✓ sig.
Prion disease
ATP6, ATP8, NOTCH1
 KEGG 3 / 275 7.7× 6.37e-3 5.16e-2
Defective LFNG causes SCDO3
NOTCH1
 Reactome 1 / 5 141× 7.06e-3 5.50e-2
Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling
NOTCH1
 Reactome 1 / 5 141× 7.06e-3 5.50e-2
Pre-NOTCH Processing in Golgi
NOTCH1
 Reactome 1 / 6 118× 8.46e-3 6.23e-2
RUNX2 regulates bone development
SMAD6
 Reactome 1 / 7 101× 9.87e-3 6.88e-2
Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant
NOTCH1
 Reactome 1 / 7 101× 9.87e-3 6.88e-2
IRAK2 mediated activation of TAK1 complex
TAB2
 Reactome 1 / 10 70.6× 1.41e-2 8.52e-2
Activated NOTCH1 Transmits Signal to the Nucleus
NOTCH1
 Reactome 1 / 10 70.6× 1.41e-2 8.52e-2
TICAM1,TRAF6-dependent induction of TAK1 complex
TAB2
 Reactome 1 / 11 64.2× 1.55e-2 9.04e-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 ⇵
aortic valve morphogenesis
GATA5, NOTCH1, SMAD6, NKX2-5
 GO:0003180 4 / 37 119× 3.04e-8 4.39e-6 ✓ sig.
atrioventricular node development
NOTCH1, NKX2-5
 GO:0003162 2 / 6 366× 1.17e-5 5.91e-4 ✓ sig.
cardiac ventricle morphogenesis
NOTCH1, NKX2-5
 GO:0003208 2 / 10 220× 3.49e-5 1.38e-3 ✓ sig.
cardiac muscle tissue morphogenesis
NOTCH1, NKX2-5
 GO:0055008 2 / 13 169× 6.04e-5 2.08e-3 ✓ sig.
ventricular trabecula myocardium morphogenesis
NOTCH1, NKX2-5
 GO:0003222 2 / 15 147× 8.12e-5 2.60e-3 ✓ sig.
heart development
GATA5, NOTCH1, TAB2, NKX2-5
 GO:0007507 4 / 273 16.1× 9.13e-5 2.83e-3 ✓ sig.
cardiac septum morphogenesis
NOTCH1, NKX2-5
 GO:0060411 2 / 16 137× 9.28e-5 2.87e-3 ✓ sig.
pulmonary valve morphogenesis
NOTCH1, SMAD6
 GO:0003184 2 / 18 122× 1.18e-4 3.43e-3 ✓ sig.
negative regulation of cardiac muscle hypertrophy
GATA5, NOTCH1
 GO:0010614 2 / 18 122× 1.18e-4 3.43e-3 ✓ sig.
negative regulation of myotube differentiation
NOTCH1, NKX2-5
 GO:0010832 2 / 18 122× 1.18e-4 3.43e-3 ✓ sig.
peptide cross-linking
DSP, KRT1
 GO:0018149 2 / 19 116× 1.32e-4 3.74e-3 ✓ sig.
proton motive force-driven ATP synthesis
ATP6, ATP8
 GO:0015986 2 / 23 95.6× 1.95e-4 4.96e-3 ✓ sig.
cardiac muscle tissue development
GATA5, NKX2-5
 GO:0048738 2 / 24 91.6× 2.12e-4 5.27e-3 ✓ sig.
cell differentiation
GATA5, MGP, NOTCH1, ROBO4, SMAD6, NKX2-5
 GO:0030154 6 / 1,051 6.3× 2.26e-4 5.48e-3 ✓ sig.
cardiac muscle cell development
MYH11, NKX2-5
 GO:0055013 2 / 25 87.9× 2.31e-4 5.57e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Bicuspid aortic valve Keratosis palmoplantaris striata 0.118 2 4.60e-6 2.40e-5 ✓ sig.
Congenital erythroderma with palmoplantar keratoderma, hypotrichosis, and hyper-ige Focal palmoplantar keratoderma with joint keratoses 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Congenital erythroderma with palmoplantar keratoderma, hypotrichosis, and hyper-ige Diffuse palmoplantar keratoderma 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Diffuse palmoplantar keratoderma Focal palmoplantar keratoderma with joint keratoses 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Congenital erythroderma with palmoplantar keratoderma, hypotrichosis, and hyper-ige Keratosis palmoplantaris striata 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Focal palmoplantar keratoderma with joint keratoses Keratosis palmoplantaris striata 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Diffuse palmoplantar keratoderma Keratosis palmoplantaris striata 0.167 1 5.19e-4 1.06e-3 ✓ sig.
aortic valve disease 3 Bicuspid aortic valve 0.067 1 9.09e-4 1.58e-3 ✓ sig.
Bicuspid aortic valve Congenital erythroderma with palmoplantar keratoderma, hypotrichosis, and hyper-ige 0.067 1 9.09e-4 1.58e-3 ✓ sig.
Bicuspid aortic valve Focal palmoplantar keratoderma with joint keratoses 0.067 1 9.09e-4 1.58e-3 ✓ sig.
Bicuspid aortic valve Diffuse palmoplantar keratoderma 0.063 1 1.82e-3 2.68e-3 ✓ sig.