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 294

6 diseases · 12 shared-gene connections
6 Diseases
26 Unique genes
0.197 Avg. similarity score
Bonnevie-ullrich syndrome 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 ⇵
Bonnevie-ullrich syndrome 5 5 7
Turner syndrome 5 5 8
Ureteral calculi 5 5 4
Acatalasia 3 3 1
Aortic disease 3 3 19
amyotrophic lateral sclerosis type 1 3 3 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
CAT 5 / 6 Acatalasia, Aortic disease, Bonnevie-ullrich syndrome, Turner syndrome and 1 more
SOD1 5 / 6 amyotrophic lateral sclerosis type 1, Aortic disease, Bonnevie-ullrich syndrome, Turner syndrome and 1 more
SOD2 3 / 6 Aortic disease, Bonnevie-ullrich syndrome, Turner syndrome
GH1 2 / 6 Bonnevie-ullrich syndrome, Turner syndrome
IGFBP3 2 / 6 Bonnevie-ullrich syndrome, Turner syndrome
NOS2 2 / 6 Bonnevie-ullrich syndrome, Turner syndrome
VDR 2 / 6 Bonnevie-ullrich syndrome, Turner syndrome
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 ⇵
Detoxification of Reactive Oxygen Species
CAT, SOD1, SOD2, GSR, GSTP1
 Reactome 5 / 34 67.9× 8.43e-9 7.55e-7 ✓ sig.
Peroxisome
CAT, SOD1, SOD2, NOS2
 KEGG 4 / 83 22.3× 2.82e-5 7.92e-4 ✓ sig.
Pathways in cancer
LAMC1, MMP2, MMP9, SMAD4, NOS2, PTCH1, GSTP1
 KEGG 7 / 533 6.1× 1.03e-4 2.30e-3 ✓ sig.
Longevity regulating pathway - multiple species
CAT, SOD1, SOD2
 KEGG 3 / 62 22.4× 3.13e-4 5.54e-3 ✓ sig.
Interleukin-4 and Interleukin-13 signaling
MMP2, MMP9, NOS2
 Reactome 3 / 108 12.8× 1.58e-3 1.92e-2 ✓ sig.
Activation of Matrix Metalloproteinases
MMP2, MMP9
 Reactome 2 / 33 28.0× 2.28e-3 2.52e-2 ✓ sig.
Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)
LAMC1, MMP2, IGFBP3
 Reactome 3 / 125 11.1× 2.40e-3 2.61e-2 ✓ sig.
Relaxin signaling pathway
MMP2, MMP9, NOS2
 KEGG 3 / 130 10.7× 2.69e-3 2.84e-2 ✓ sig.
FoxO signaling pathway
CAT, SMAD4, SOD2
 KEGG 3 / 133 10.4× 2.87e-3 2.98e-2 ✓ sig.
Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation
SOD1, SOD2
 Reactome 2 / 38 24.3× 3.02e-3 3.09e-2 ✓ sig.
Fluid shear stress and atherosclerosis
MMP2, MMP9, GSTP1
 KEGG 3 / 141 9.8× 3.38e-3 3.36e-2 ✓ sig.
Bladder cancer
MMP2, MMP9
 KEGG 2 / 41 22.5× 3.51e-3 3.43e-2 ✓ sig.
EPH-ephrin mediated repulsion of cells
MMP2, MMP9
 Reactome 2 / 50 18.5× 5.18e-3 4.47e-2 ✓ sig.
Collagen degradation
MMP2, MMP9
 Reactome 2 / 52 17.8× 5.59e-3 4.71e-2 ✓ sig.
Inhibition of nitric oxide production
NOS2
 Reactome 1 / 3 154× 6.48e-3 5.19e-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 ⇵
response to L-ascorbic acid
CAT, SOD2, GSTP1
 GO:0033591 3 / 4 539× 9.56e-9 1.64e-6 ✓ sig.
response to reactive oxygen species
CAT, SOD1, SOD2, GSTP1
 GO:0000302 4 / 20 144× 1.40e-8 2.30e-6 ✓ sig.
response to hydrogen peroxide
CAT, MMP2, SOD1, SOD2
 GO:0042542 4 / 39 73.7× 2.34e-7 2.47e-5 ✓ sig.
glutathione metabolic process
SOD1, SOD2, GSR, GSTP1
 GO:0006749 4 / 49 58.7× 5.98e-7 5.44e-5 ✓ sig.
response to hyperoxia
CAT, MMP2, SOD2
 GO:0055093 3 / 14 154× 8.62e-7 7.34e-5 ✓ sig.
superoxide metabolic process
SOD1, SOD2, NOS2
 GO:0006801 3 / 22 98.0× 3.62e-6 2.32e-4 ✓ sig.
response to hypoxia
CAT, MMP2, SMAD4, SOD2, NOS2
 GO:0001666 5 / 176 20.4× 3.92e-6 2.47e-4 ✓ sig.
response to nutrient levels
SOD1, SOD2, GH1, GSTP1
 GO:0031667 4 / 79 36.4× 4.12e-6 2.57e-4 ✓ sig.
response to estradiol
CAT, GH1, PTCH1, GSTP1
 GO:0032355 4 / 84 34.2× 5.27e-6 3.13e-4 ✓ sig.
response to superoxide
SOD1, SOD2
 GO:0000303 2 / 5 287× 1.86e-5 8.45e-4 ✓ sig.
response to xenobiotic stimulus
CAT, MMP2, SOD1, SOD2, PTCH1
 GO:0009410 5 / 248 14.5× 2.07e-5 9.23e-4 ✓ sig.
extracellular matrix disassembly
LAMC1, MMP2, MMP9
 GO:0022617 3 / 47 45.9× 3.72e-5 1.44e-3 ✓ sig.
ovarian follicle development
MMP2, SMAD4, SOD1
 GO:0001541 3 / 47 45.9× 3.72e-5 1.44e-3 ✓ sig.
embryo implantation
MMP2, MMP9, SOD1
 GO:0007566 3 / 48 44.9× 3.97e-5 1.51e-3 ✓ sig.
response to oxidative stress
CAT, MMP2, SOD1, SOD2
 GO:0006979 4 / 146 19.7× 4.68e-5 1.71e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Bonnevie-ullrich syndrome Turner syndrome 0.778 7 1.97e-25 5.17e-24 ✓ sig.
Aortic disease Bonnevie-ullrich syndrome 0.125 3 5.56e-8 4.28e-7 ✓ sig.
Aortic disease Turner syndrome 0.120 3 8.89e-8 6.59e-7 ✓ sig.
Bonnevie-ullrich syndrome Ureteral calculi 0.200 2 1.06e-6 6.56e-6 ✓ sig.
Turner syndrome Ureteral calculi 0.182 2 1.42e-6 8.55e-6 ✓ sig.
Aortic disease Ureteral calculi 0.091 2 8.64e-6 4.55e-5 ✓ sig.
Acatalasia Ureteral calculi 0.200 1 2.60e-4 6.40e-4 ✓ sig.
amyotrophic lateral sclerosis type 1 Ureteral calculi 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Acatalasia Bonnevie-ullrich syndrome 0.125 1 4.55e-4 9.55e-4 ✓ sig.
amyotrophic lateral sclerosis type 1 Bonnevie-ullrich syndrome 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Acatalasia Turner syndrome 0.111 1 5.20e-4 1.04e-3 ✓ sig.
amyotrophic lateral sclerosis type 1 Turner syndrome 0.111 1 5.20e-4 1.04e-3 ✓ sig.