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 125

10 diseases · 19 shared-gene connections
10 Diseases
33 Unique genes
0.214 Avg. similarity score
Cholesterol embolism Most-connected disease (7 links)
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Disease Searched: quebec platelet disorder 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 ⇵
Cholesterol embolism 7 7 2
Intracranial embolism and thrombosis 7 7 2
Arterial occlusive disease 5 5 9
Cardiac injury 4 4 4
quebec platelet disorder 4 4 1
Asthenozoospermia 3 3 3
Brain edema 3 3 10
Intracranial hemorrhage 3 3 13
Hepatic lipase deficiency 1 1 1
dilated cardiomyopathy 1D 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
PLAU 8 / 10 Arterial occlusive disease, Asthenozoospermia, Brain edema, Cardiac injury and 4 more
PLAT 5 / 10 Arterial occlusive disease, Brain edema, Cholesterol embolism, Intracranial embolism and thrombosis and 1 more
LIPC 2 / 10 Arterial occlusive disease, Hepatic lipase deficiency
TNNT2 2 / 10 Cardiac injury, dilated cardiomyopathy 1D
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 ⇵
Complement and coagulation cascades
MBL2, PLAT, PLAU, F7
 KEGG 4 / 88 16.5× 9.36e-5 2.15e-3 ✓ sig.
Interleukin-4 and Interleukin-13 signaling
IL6, MMP9, NOS2, TNF
 Reactome 4 / 108 13.5× 2.07e-4 4.04e-3 ✓ sig.
TNF signaling pathway
DAB2IP, IL6, MMP9, TNF
 KEGG 4 / 119 12.2× 3.00e-4 5.44e-3 ✓ sig.
Eicosanoids
CYP4F3, CYP4F8
 Reactome 2 / 12 60.7× 4.75e-4 7.84e-3 ✓ sig.
Dissolution of Fibrin Clot
PLAT, PLAU
 Reactome 2 / 13 56.0× 5.60e-4 8.88e-3 ✓ sig.
Fluid shear stress and atherosclerosis
PLAT, GSTT1, MMP9, TNF
 KEGG 4 / 141 10.3× 5.72e-4 9.02e-3 ✓ sig.
Fatty acids
CYP4F3, CYP4F8
 Reactome 2 / 15 48.5× 7.52e-4 1.12e-2 ✓ sig.
Pertussis
IL6, NOS2, TNF
 KEGG 3 / 78 14.0× 1.25e-3 1.65e-2 ✓ sig.
Synthesis of Leukotrienes (LT) and Eoxins (EX)
CYP4F3, CYP4F8
 Reactome 2 / 20 36.4× 1.35e-3 1.74e-2 ✓ sig.
RHO GTPases activate PAKs
MYL9, MYLK
 Reactome 2 / 23 31.6× 1.79e-3 2.15e-2 ✓ sig.
Transcriptional misregulation in cancer
IL6, PLAT, PLAU, MMP9
 KEGG 4 / 198 7.4× 2.02e-3 2.34e-2 ✓ sig.
IL-17 signaling pathway
IL6, MMP9, TNF
 KEGG 3 / 94 11.6× 2.14e-3 2.44e-2 ✓ sig.
Prostate cancer
PLAT, PLAU, MMP9
 KEGG 3 / 98 11.1× 2.41e-3 2.67e-2 ✓ sig.
Hypertrophic cardiomyopathy
IL6, TNF, TNNT2
 KEGG 3 / 99 11.0× 2.48e-3 2.73e-2 ✓ sig.
Lipid and atherosclerosis
CYP1A1, IL6, MMP9, TNF
 KEGG 4 / 216 6.7× 2.77e-3 2.96e-2 ✓ sig.

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 hypoxia
CYP1A1, PLAT, PLAU, NOS2, TNF, F7
 GO:0001666 6 / 176 19.3× 5.75e-7 5.31e-5 ✓ sig.
cellular response to lipopolysaccharide
DAB2IP, IL6, ZC3H12A, MMP9, NOS2, TNF
 GO:0071222 6 / 187 18.2× 8.20e-7 7.12e-5 ✓ sig.
plasminogen activation
APOH, PLAT, PLAU
 GO:0031639 3 / 12 142× 1.09e-6 8.99e-5 ✓ sig.
negative regulation of fibrinolysis
APOH, PLAT, PLAU
 GO:0051918 3 / 12 142× 1.09e-6 8.99e-5 ✓ sig.
positive regulation of glial cell proliferation
IL6, NTN1, TNF
 GO:0060252 3 / 22 77.2× 7.55e-6 4.27e-4 ✓ sig.
response to genistein
CYP1A1, F7
 GO:0033595 2 / 3 378× 9.06e-6 4.93e-4 ✓ sig.
regulation of fibrinolysis
APOH, PLAU
 GO:0051917 2 / 4 283× 1.81e-5 8.43e-4 ✓ sig.
response to 2,3,7,8-tetrachlorodibenzodioxine
CYP1A1, F7
 GO:1904612 2 / 5 227× 3.01e-5 1.24e-3 ✓ sig.
menaquinone catabolic process
CYP4F3, CYP4F8
 GO:0042361 2 / 5 227× 3.01e-5 1.24e-3 ✓ sig.
vascular endothelial growth factor production
IL6, TNF
 GO:0010573 2 / 6 189× 4.52e-5 1.70e-3 ✓ sig.
phylloquinone catabolic process
CYP4F3, CYP4F8
 GO:0042376 2 / 6 189× 4.52e-5 1.70e-3 ✓ sig.
negative regulation of plasminogen activation
PLAT, PLAU
 GO:0010757 2 / 7 162× 6.32e-5 2.19e-3 ✓ sig.
regulation of insulin secretion
IL6, NOS2, TNF
 GO:0050796 3 / 46 36.9× 7.23e-5 2.43e-3 ✓ sig.
very-low-density lipoprotein particle remodeling
APOH, LIPC
 GO:0034372 2 / 8 142× 8.41e-5 2.72e-3 ✓ sig.
smooth muscle cell migration
PLAT, PLAU
 GO:0014909 2 / 9 126× 1.08e-4 3.27e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Cholesterol embolism Intracranial embolism and thrombosis 0.667 2 8.44e-9 6.84e-8 ✓ sig.
Arterial occlusive disease Intracranial embolism and thrombosis 0.200 2 3.04e-7 1.96e-6 ✓ sig.
Arterial occlusive disease Cholesterol embolism 0.200 2 3.04e-7 1.96e-6 ✓ sig.
Brain edema Cholesterol embolism 0.182 2 3.80e-7 2.40e-6 ✓ sig.
Brain edema Intracranial embolism and thrombosis 0.182 2 3.80e-7 2.40e-6 ✓ sig.
Intracranial embolism and thrombosis Intracranial hemorrhage 0.143 2 6.58e-7 4.00e-6 ✓ sig.
Cholesterol embolism Intracranial hemorrhage 0.143 2 6.58e-7 4.00e-6 ✓ sig.
Arterial occlusive disease Brain edema 0.111 2 1.36e-5 6.63e-5 ✓ sig.
Arterial occlusive disease Intracranial hemorrhage 0.095 2 2.36e-5 1.11e-4 ✓ sig.
Cholesterol embolism quebec platelet disorder 0.333 1 1.30e-4 3.91e-4 ✓ sig.
Intracranial embolism and thrombosis quebec platelet disorder 0.333 1 1.30e-4 3.91e-4 ✓ sig.
Asthenozoospermia quebec platelet disorder 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Cardiac injury quebec platelet disorder 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Cardiac injury dilated cardiomyopathy 1D 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Asthenozoospermia Intracranial embolism and thrombosis 0.200 1 3.90e-4 8.64e-4 ✓ sig.
Asthenozoospermia Cholesterol embolism 0.200 1 3.90e-4 8.64e-4 ✓ sig.
Cardiac injury Cholesterol embolism 0.167 1 5.19e-4 1.06e-3 ✓ sig.
Cardiac injury Intracranial embolism and thrombosis 0.167 1 5.19e-4 1.06e-3 ✓ sig.
Arterial occlusive disease Hepatic lipase deficiency 0.100 1 5.84e-4 1.15e-3 ✓ sig.