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 84

13 diseases · 27 shared-gene connections
13 Diseases
21 Unique genes
0.260 Avg. similarity score
Congenital factor v deficiency Most-connected disease (8 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 ⇵
Congenital factor v deficiency 8 8 1
East texas bleeding disorder 8 8 1
Venous hypertension 6 6 3
thrombophilia due to activated protein c resistance 6 6 1
Diabetes macrovascular complications 5 5 5
Factor v deficiency 5 5 2
Cerebral venous sinus thrombosis 4 4 3
Budd-chiari syndrome 3 3 4
Hepatic vein thrombosis 3 3 3
Thiamine-responsive megaloblastic anemia 2 2 1
Venous insufficiency 2 2 9
Male infertility motility disorder 1 1 1
protein S deficiency 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
F5 10 / 13 Budd-chiari syndrome, Cerebral venous sinus thrombosis, Congenital factor v deficiency, Diabetes macrovascular complications and 6 more
SLC19A2 3 / 13 Thiamine-responsive megaloblastic anemia, Venous hypertension, Venous insufficiency
CCDC146 2 / 13 Diabetes macrovascular complications, Male infertility motility disorder
JAK2 2 / 13 Budd-chiari syndrome, Hepatic vein thrombosis
PROS1 2 / 13 Cerebral venous sinus thrombosis, protein S deficiency
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
F5, PLAU, PROS1
 KEGG 3 / 88 19.5× 4.60e-4 7.46e-3 ✓ sig.
Common Pathway of Fibrin Clot Formation
F5, PROS1
 Reactome 2 / 22 52.0× 6.59e-4 9.88e-3 ✓ sig.
Cargo concentration in the ER
F5, LMAN1
 Reactome 2 / 33 34.7× 1.49e-3 1.84e-2 ✓ sig.
Efferocytosis
CALR, JAK2, PROS1
 KEGG 3 / 157 10.9× 2.45e-3 2.65e-2 ✓ sig.
Transport to the Golgi and subsequent modification
LMAN1
 Reactome 1 / 2 286× 3.49e-3 3.42e-2 ✓ sig.
Reversal of alkylation damage by DNA dioxygenases
FTO
 Reactome 1 / 2 286× 3.49e-3 3.42e-2 ✓ sig.
Assembly of Viral Components at the Budding Site
CALR
 Reactome 1 / 2 286× 3.49e-3 3.42e-2 ✓ sig.
Glutathione metabolism
NAT8, GSTT1
 KEGG 2 / 59 19.4× 4.69e-3 4.20e-2 ✓ sig.
ABO blood group biosynthesis
ABO
 Reactome 1 / 3 191× 5.24e-3 4.50e-2 ✓ sig.
Chemical carcinogenesis - receptor activation
JAK2, RPS6KA2, GSTT1
 KEGG 3 / 215 8.0× 5.93e-3 4.90e-2 ✓ sig.
COPII-mediated vesicle transport
F5, LMAN1
 Reactome 2 / 68 16.8× 6.19e-3 5.04e-2
RSK activation
RPS6KA2
 Reactome 1 / 4 143× 6.98e-3 5.45e-2
Vitamin B1 (thiamin) metabolism
SLC19A2
 Reactome 1 / 5 114× 8.71e-3 6.31e-2
CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling
RPS6KA2
 Reactome 1 / 5 114× 8.71e-3 6.31e-2
Calnexin/calreticulin cycle
CALR
 Reactome 1 / 5 114× 8.71e-3 6.31e-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 ⇵
blood coagulation
F5, LMAN1, PLAU, PROS1
 GO:0007596 4 / 106 33.6× 5.43e-6 3.21e-4 ✓ sig.
hemostasis
F5, PLAU, PROS1
 GO:0007599 3 / 55 48.5× 3.09e-5 1.25e-3 ✓ sig.
fibrinolysis
PLAU, PROS1
 GO:0042730 2 / 19 93.7× 2.03e-4 5.10e-3 ✓ sig.
regulation of white fat cell proliferation
FTO
 GO:0070350 1 / 1 890× 1.12e-3 1.62e-2 ✓ sig.
nuclear receptor-mediated mineralocorticoid signaling pathway
JAK2
 GO:0031959 1 / 1 890× 1.12e-3 1.62e-2 ✓ sig.
symbiont-induced defense-related programmed cell death
JAK2
 GO:0034050 1 / 1 890× 1.12e-3 1.62e-2 ✓ sig.
interleukin-35-mediated signaling pathway
JAK2
 GO:0070757 1 / 1 890× 1.12e-3 1.62e-2 ✓ sig.
regulation of smooth muscle cell-matrix adhesion
PLAU
 GO:2000097 1 / 1 890× 1.12e-3 1.62e-2 ✓ sig.
glutathione metabolic process
NAT8, GSTT1
 GO:0006749 2 / 49 36.3× 1.37e-3 1.83e-2 ✓ sig.
response to vitamin B2
MTHFR
 GO:0033274 1 / 2 445× 2.25e-3 2.41e-2 ✓ sig.
brain renin-angiotensin system
RPS6KA2
 GO:0002035 1 / 2 445× 2.25e-3 2.41e-2 ✓ sig.
cellular response to carbohydrate stimulus
RPS6KA2
 GO:0071322 1 / 2 445× 2.25e-3 2.41e-2 ✓ sig.
response to interleukin-12
JAK2
 GO:0070671 1 / 2 445× 2.25e-3 2.41e-2 ✓ sig.
positive regulation of growth factor dependent skeletal muscle satellite cell proliferation
JAK2
 GO:1902728 1 / 2 445× 2.25e-3 2.41e-2 ✓ sig.
regulation of postsynapse to nucleus signaling pathway
JAK2
 GO:1905539 1 / 2 445× 2.25e-3 2.41e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Budd-chiari syndrome Hepatic vein thrombosis 0.333 2 1.52e-7 1.09e-6 ✓ sig.
Venous hypertension Venous insufficiency 0.182 2 9.11e-7 5.67e-6 ✓ sig.
East texas bleeding disorder thrombophilia due to activated protein c resistance 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Congenital factor v deficiency thrombophilia due to activated protein c resistance 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Congenital factor v deficiency East texas bleeding disorder 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Congenital factor v deficiency Factor v deficiency 0.333 1 1.30e-4 3.90e-4 ✓ sig.
East texas bleeding disorder Factor v deficiency 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Factor v deficiency thrombophilia due to activated protein c resistance 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Cerebral venous sinus thrombosis protein S deficiency 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Congenital factor v deficiency Venous hypertension 0.250 1 1.95e-4 5.28e-4 ✓ sig.
thrombophilia due to activated protein c resistance Venous hypertension 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Thiamine-responsive megaloblastic anemia Venous hypertension 0.250 1 1.95e-4 5.28e-4 ✓ sig.
East texas bleeding disorder Hepatic vein thrombosis 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Congenital factor v deficiency Hepatic vein thrombosis 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Cerebral venous sinus thrombosis thrombophilia due to activated protein c resistance 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Cerebral venous sinus thrombosis East texas bleeding disorder 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Cerebral venous sinus thrombosis Congenital factor v deficiency 0.250 1 1.95e-4 5.28e-4 ✓ sig.
East texas bleeding disorder Venous hypertension 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Budd-chiari syndrome Congenital factor v deficiency 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Budd-chiari syndrome East texas bleeding disorder 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Diabetes macrovascular complications Male infertility motility disorder 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Diabetes macrovascular complications thrombophilia due to activated protein c resistance 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Diabetes macrovascular complications East texas bleeding disorder 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Congenital factor v deficiency Diabetes macrovascular complications 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Factor v deficiency Venous hypertension 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Thiamine-responsive megaloblastic anemia Venous insufficiency 0.100 1 5.84e-4 1.14e-3 ✓ sig.
Diabetes macrovascular complications Factor v deficiency 0.143 1 6.49e-4 1.22e-3 ✓ sig.