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 29

19 diseases · 53 shared-gene connections
19 Diseases
37 Unique genes
0.330 Avg. similarity score
Cholesterol embolism Most-connected disease (11 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 ⇵
Cholesterol embolism 11 11 2
Aphasia 10 10 2
Intracranial embolism and thrombosis 10 10 2
Postictal aphasia 9 9 2
Cardiac tamponade 8 8 1
Commisural aphasia 6 6 2
Dejerine-lichtheim phenomenon 6 6 2
Arterial occlusive disease 5 5 9
Brain edema 5 5 10
Dysphasia 5 5 4
Spinal cord compression 5 5 3
Syntactic aphasia 5 5 2
Cardiac injury 4 4 4
Hematoma 4 4 3
Intracranial hemorrhage 4 4 13
quebec platelet disorder 4 4 1
Asthenozoospermia 3 3 3
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
PLAT 14 / 19 Aphasia, Arterial occlusive disease, Brain edema, Cardiac tamponade and 10 more
PLAU 8 / 19 Arterial occlusive disease, Asthenozoospermia, Brain edema, Cardiac injury and 4 more
L1CAM 6 / 19 Aphasia, Commisural aphasia, Dejerine-lichtheim phenomenon, Dysphasia and 2 more
F7 2 / 19 Hematoma, Intracranial hemorrhage
LIPC 2 / 19 Arterial occlusive disease, Hepatic lipase deficiency
S100B 2 / 19 Brain edema, Hematoma
TNF 2 / 19 Brain edema, Spinal cord compression
TNNT2 2 / 19 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 ⇵
Interleukin-4 and Interleukin-13 signaling
IL6, MMP9, NOS2, TNF, CCL2
 Reactome 5 / 108 15.0× 1.86e-5 5.64e-4 ✓ sig.
TNF signaling pathway
DAB2IP, IL6, MMP9, TNF, CCL2
 KEGG 5 / 119 13.6× 2.97e-5 8.27e-4 ✓ sig.
Fluid shear stress and atherosclerosis
PLAT, GSTT1, MMP9, TNF, CCL2
 KEGG 5 / 141 11.5× 6.69e-5 1.62e-3 ✓ sig.
Complement and coagulation cascades
PLAT, MBL2, PLAU, F7
 KEGG 4 / 88 14.8× 1.48e-4 3.08e-3 ✓ sig.
IL-17 signaling pathway
IL6, MMP9, TNF, CCL2
 KEGG 4 / 94 13.8× 1.91e-4 3.77e-3 ✓ sig.
Chagas disease
IL6, NOS2, TNF, CCL2
 KEGG 4 / 103 12.6× 2.71e-4 4.96e-3 ✓ sig.
Interleukin-10 signaling
IL6, TNF, CCL2
 Reactome 3 / 47 20.7× 3.98e-4 6.68e-3 ✓ sig.
Malaria
IL6, TNF, CCL2
 KEGG 3 / 50 19.5× 4.78e-4 7.69e-3 ✓ sig.
Lipid and atherosclerosis
CYP1A1, IL6, MMP9, TNF, CCL2
 KEGG 5 / 216 7.5× 4.90e-4 7.85e-3 ✓ sig.
Eicosanoids
CYP4F3, CYP4F8
 Reactome 2 / 12 54.1× 5.98e-4 9.16e-3 ✓ sig.
Dissolution of Fibrin Clot
PLAT, PLAU
 Reactome 2 / 13 49.9× 7.05e-4 1.04e-2 ✓ sig.
Fatty acids
CYP4F3, CYP4F8
 Reactome 2 / 15 43.3× 9.46e-4 1.30e-2 ✓ sig.
Synthesis of Leukotrienes (LT) and Eoxins (EX)
CYP4F3, CYP4F8
 Reactome 2 / 20 32.5× 1.69e-3 2.02e-2 ✓ sig.
Pertussis
IL6, NOS2, TNF
 KEGG 3 / 78 12.5× 1.75e-3 2.07e-2 ✓ sig.
RHO GTPases activate PAKs
MYL9, MYLK
 Reactome 2 / 23 28.2× 2.24e-3 2.48e-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 ⇵
cellular response to lipopolysaccharide
DAB2IP, IL6, ZC3H12A, MMP9, NOS2, TNF, CCL2
 GO:0071222 7 / 187 18.9× 7.17e-8 9.13e-6 ✓ sig.
response to hypoxia
PLAT, CYP1A1, PLAU, NOS2, TNF, F7
 GO:0001666 6 / 176 17.2× 1.17e-6 9.40e-5 ✓ sig.
plasminogen activation
PLAT, APOH, PLAU
 GO:0031639 3 / 12 126× 1.55e-6 1.18e-4 ✓ sig.
negative regulation of fibrinolysis
PLAT, APOH, PLAU
 GO:0051918 3 / 12 126× 1.55e-6 1.18e-4 ✓ sig.
regulation of muscle contraction
MYL9, ATP1A2, TNNT2
 GO:0006937 3 / 16 94.7× 3.93e-6 2.48e-4 ✓ sig.
positive regulation of glial cell proliferation
IL6, NTN1, TNF
 GO:0060252 3 / 22 68.9× 1.07e-5 5.50e-4 ✓ sig.
response to genistein
CYP1A1, F7
 GO:0033595 2 / 3 337× 1.14e-5 5.77e-4 ✓ sig.
regulation of fibrinolysis
APOH, PLAU
 GO:0051917 2 / 4 253× 2.28e-5 9.94e-4 ✓ sig.
response to 2,3,7,8-tetrachlorodibenzodioxine
CYP1A1, F7
 GO:1904612 2 / 5 202× 3.80e-5 1.46e-3 ✓ sig.
menaquinone catabolic process
CYP4F3, CYP4F8
 GO:0042361 2 / 5 202× 3.80e-5 1.46e-3 ✓ sig.
vascular endothelial growth factor production
IL6, TNF
 GO:0010573 2 / 6 168× 5.69e-5 1.98e-3 ✓ sig.
phylloquinone catabolic process
CYP4F3, CYP4F8
 GO:0042376 2 / 6 168× 5.69e-5 1.98e-3 ✓ sig.
negative regulation of plasminogen activation
PLAT, PLAU
 GO:0010757 2 / 7 144× 7.96e-5 2.55e-3 ✓ sig.
regulation of insulin secretion
IL6, NOS2, TNF
 GO:0050796 3 / 46 32.9× 1.02e-4 3.07e-3 ✓ sig.
very-low-density lipoprotein particle remodeling
APOH, LIPC
 GO:0034372 2 / 8 126× 1.06e-4 3.16e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Aphasia Commisural aphasia 0.667 2 8.44e-9 7.20e-8 ✓ sig.
Commisural aphasia Postictal aphasia 0.667 2 8.44e-9 7.20e-8 ✓ sig.
Commisural aphasia Dejerine-lichtheim phenomenon 0.667 2 8.44e-9 7.20e-8 ✓ sig.
Commisural aphasia Syntactic aphasia 0.667 2 8.44e-9 7.20e-8 ✓ sig.
Aphasia Postictal aphasia 0.667 2 8.44e-9 7.20e-8 ✓ sig.
Cholesterol embolism Intracranial embolism and thrombosis 0.667 2 8.44e-9 7.20e-8 ✓ sig.
Dejerine-lichtheim phenomenon Postictal aphasia 0.667 2 8.44e-9 7.20e-8 ✓ sig.
Dejerine-lichtheim phenomenon Syntactic aphasia 0.667 2 8.44e-9 7.20e-8 ✓ sig.
Postictal aphasia Syntactic aphasia 0.667 2 8.44e-9 7.20e-8 ✓ sig.
Aphasia Syntactic aphasia 0.667 2 8.44e-9 7.20e-8 ✓ sig.
Aphasia Dejerine-lichtheim phenomenon 0.667 2 8.44e-9 7.20e-8 ✓ sig.
Dysphasia Syntactic aphasia 0.400 2 5.06e-8 3.92e-7 ✓ sig.
Dysphasia Postictal aphasia 0.400 2 5.06e-8 3.92e-7 ✓ sig.
Dejerine-lichtheim phenomenon Dysphasia 0.400 2 5.06e-8 3.92e-7 ✓ sig.
Commisural aphasia Dysphasia 0.400 2 5.06e-8 3.92e-7 ✓ sig.
Aphasia Dysphasia 0.400 2 5.06e-8 3.92e-7 ✓ sig.
Arterial occlusive disease Intracranial embolism and thrombosis 0.200 2 3.04e-7 2.06e-6 ✓ sig.
Arterial occlusive disease Cholesterol embolism 0.200 2 3.04e-7 2.06e-6 ✓ sig.
Brain edema Cholesterol embolism 0.182 2 3.80e-7 2.53e-6 ✓ sig.
Brain edema Intracranial embolism and thrombosis 0.182 2 3.80e-7 2.53e-6 ✓ sig.
Intracranial embolism and thrombosis Intracranial hemorrhage 0.143 2 6.58e-7 4.21e-6 ✓ sig.
Cholesterol embolism Intracranial hemorrhage 0.143 2 6.58e-7 4.21e-6 ✓ sig.
Brain edema Hematoma 0.167 2 1.14e-6 6.99e-6 ✓ sig.
Brain edema Spinal cord compression 0.167 2 1.14e-6 6.99e-6 ✓ sig.
Hematoma Intracranial hemorrhage 0.133 2 1.97e-6 1.16e-5 ✓ sig.
Arterial occlusive disease Brain edema 0.111 2 1.36e-5 6.99e-5 ✓ sig.
Arterial occlusive disease Intracranial hemorrhage 0.095 2 2.36e-5 1.18e-4 ✓ sig.
Intracranial embolism and thrombosis quebec platelet disorder 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Cardiac tamponade Intracranial embolism and thrombosis 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Cholesterol embolism quebec platelet disorder 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Cardiac tamponade Dejerine-lichtheim phenomenon 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Cardiac tamponade Commisural aphasia 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Cardiac tamponade Cholesterol embolism 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Cardiac tamponade Postictal aphasia 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Aphasia Cardiac tamponade 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Cardiac tamponade Spinal cord compression 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Cardiac tamponade Hematoma 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Asthenozoospermia quebec platelet disorder 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Aphasia Cholesterol embolism 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Cholesterol embolism Postictal aphasia 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Aphasia Intracranial embolism and thrombosis 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Intracranial embolism and thrombosis Postictal aphasia 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Cardiac injury dilated cardiomyopathy 1D 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Cardiac injury quebec platelet disorder 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Asthenozoospermia Intracranial embolism and thrombosis 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Asthenozoospermia Cholesterol embolism 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Aphasia Hematoma 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Aphasia Spinal cord compression 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Postictal aphasia Spinal cord compression 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Cholesterol embolism Spinal cord compression 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Cardiac injury Cholesterol embolism 0.167 1 5.19e-4 1.04e-3 ✓ sig.
Cardiac injury Intracranial embolism and thrombosis 0.167 1 5.19e-4 1.04e-3 ✓ sig.
Arterial occlusive disease Hepatic lipase deficiency 0.100 1 5.84e-4 1.14e-3 ✓ sig.