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 37

17 diseases · 34 shared-gene connections
17 Diseases
63 Unique genes
0.223 Avg. similarity score
Congenital factor v deficiency Most-connected disease (8 links)
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Disease Searched: Benign prostatic hyperplasia 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 7 7 3
thrombophilia due to activated protein c resistance 6 6 1
Diabetes macrovascular complications 5 5 5
Factor v deficiency 5 5 2
Lipoma 5 5 12
Cerebral venous sinus thrombosis 4 4 3
Benign prostatic hyperplasia 3 3 35
Budd-chiari syndrome 3 3 4
Hepatic vein thrombosis 3 3 3
Thiamine-responsive megaloblastic anemia 3 3 1
Venous insufficiency 3 3 9
Uterine benign neoplasm 2 2 1
Cervical polyp 1 1 2
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 11 / 17 Budd-chiari syndrome, Cerebral venous sinus thrombosis, Congenital factor v deficiency, Diabetes macrovascular complications and 7 more
SLC19A2 4 / 17 Lipoma, Thiamine-responsive megaloblastic anemia, Venous hypertension, Venous insufficiency
BET1L 3 / 17 Benign prostatic hyperplasia, Lipoma, Uterine benign neoplasm
CCDC146 2 / 17 Diabetes macrovascular complications, Male infertility motility disorder
IRAK1BP1 2 / 17 Benign prostatic hyperplasia, Cervical polyp
JAK2 2 / 17 Budd-chiari syndrome, Hepatic vein thrombosis
MEI4 2 / 17 Benign prostatic hyperplasia, Cervical polyp
PROS1 2 / 17 Cerebral venous sinus thrombosis, protein S deficiency
STN1 2 / 17 Benign prostatic hyperplasia, Lipoma
TERT 2 / 17 Benign prostatic hyperplasia, Lipoma
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 ⇵
Gamma-carboxylation of protein precursors
GGCX, PROS1
 Reactome 2 / 9 42.4× 9.52e-4 1.29e-2 ✓ sig.
Glutathione metabolism
GCLC, NAT8, GSTT1
 KEGG 3 / 59 9.7× 3.63e-3 3.51e-2 ✓ sig.
Signaling by FGFR2 amplification mutants
FGFR2
 Reactome 1 / 1 191× 5.25e-3 4.51e-2 ✓ sig.
Signaling by FGFR2 fusions
FGFR2
 Reactome 1 / 1 191× 5.25e-3 4.51e-2 ✓ sig.
PTEN Loss of Function in Cancer
PTEN
 Reactome 1 / 1 191× 5.25e-3 4.51e-2 ✓ sig.
Common Pathway of Fibrin Clot Formation
F5, PROS1
 Reactome 2 / 22 17.3× 5.85e-3 4.86e-2 ✓ sig.
Central carbon metabolism in cancer
FGFR2, SIRT3, PTEN
 KEGG 3 / 71 8.1× 6.10e-3 5.01e-2
EGFR tyrosine kinase inhibitor resistance
FGFR2, JAK2, PTEN
 KEGG 3 / 80 7.1× 8.48e-3 6.24e-2
Defective GCLC causes Hemolytic anemia due to gamma-glutamylcysteine synthetase deficiency (HAGGSD)
GCLC
 Reactome 1 / 2 95.3× 1.05e-2 7.13e-2
Transport to the Golgi and subsequent modification
LMAN1
 Reactome 1 / 2 95.3× 1.05e-2 7.13e-2
Reversal of alkylation damage by DNA dioxygenases
FTO
 Reactome 1 / 2 95.3× 1.05e-2 7.13e-2
Assembly of Viral Components at the Budding Site
CALR
 Reactome 1 / 2 95.3× 1.05e-2 7.13e-2
Complement and coagulation cascades
F5, PLAU, PROS1
 KEGG 3 / 88 6.5× 1.10e-2 7.36e-2
Cargo concentration in the ER
F5, LMAN1
 Reactome 2 / 33 11.6× 1.29e-2 8.10e-2
Prostate cancer
FGFR2, PTEN, PLAU
 KEGG 3 / 98 5.8× 1.47e-2 8.76e-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 ⇵
cardiac muscle cell differentiation
GATA6, MYOCD, TBX3, CALR
 GO:0055007 4 / 30 39.5× 3.01e-6 2.01e-4 ✓ sig.
intestinal epithelial cell differentiation
CBFA2T2, GATA5, GATA6
 GO:0060575 3 / 11 80.9× 5.91e-6 3.46e-4 ✓ sig.
hepatoblast differentiation
HNF1B, TBX3
 GO:0061017 2 / 2 297× 1.12e-5 5.73e-4 ✓ sig.
smooth muscle cell differentiation
GATA6, MYOCD, TBX3
 GO:0051145 3 / 18 49.4× 2.87e-5 1.19e-3 ✓ sig.
blood coagulation
GGCX, F5, LMAN1, PLAU, PROS1
 GO:0007596 5 / 106 14.0× 2.89e-5 1.19e-3 ✓ sig.
cardiac vascular smooth muscle cell differentiation
GATA6, MYOCD
 GO:0060947 2 / 4 148× 6.68e-5 2.24e-3 ✓ sig.
regulation of smooth muscle cell differentiation
FGFR2, MYOCD
 GO:0051150 2 / 5 119× 1.11e-4 3.28e-3 ✓ sig.
in utero embryonic development
FGFR2, GATA6, RNASEH2B, TBX3, LMAN1, BAP1
 GO:0001701 6 / 252 7.1× 2.02e-4 5.09e-3 ✓ sig.
gene expression
GATA6, HNF1B, RNASEH2B, LMAN1, BAP1, CCDC146
 GO:0010467 6 / 269 6.6× 2.88e-4 6.56e-3 ✓ sig.
heart development
GATA5, MYOCD, TERT, WDR11, PTEN, RPS6KA2
 GO:0007507 6 / 273 6.5× 3.11e-4 6.95e-3 ✓ sig.
positive regulation of cell cycle
FGFR2, TBX3, CALR
 GO:0045787 3 / 44 20.2× 4.38e-4 8.79e-3 ✓ sig.
negative regulation of transcription by RNA polymerase II
BCL11A, CBFA2T2, FGFR2, GATA5, GATA6, HNF1B, MBD2, MYOCD, TBX3, CALR, TCERG1
 GO:0000122 11 / 1,002 3.3× 4.72e-4 9.29e-3 ✓ sig.
positive regulation of Wnt signaling pathway
FGFR2, MBD2, TERT
 GO:0030177 3 / 48 18.5× 5.67e-4 1.05e-2 ✓ sig.
glutathione metabolic process
GCLC, NAT8, GSTT1
 GO:0006749 3 / 49 18.2× 6.02e-4 1.10e-2 ✓ sig.
atrioventricular canal development
GATA6, TBX3
 GO:0036302 2 / 11 53.9× 6.03e-4 1.10e-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 1.03e-6 ✓ sig.
Venous hypertension Venous insufficiency 0.182 2 9.11e-7 5.37e-6 ✓ sig.
Lipoma Venous hypertension 0.143 2 1.67e-6 9.44e-6 ✓ sig.
Benign prostatic hyperplasia Lipoma 0.067 3 2.33e-6 1.28e-5 ✓ sig.
Benign prostatic hyperplasia Cervical polyp 0.056 2 5.02e-6 2.60e-5 ✓ sig.
Lipoma Venous insufficiency 0.100 2 2.00e-5 9.48e-5 ✓ sig.
Congenital factor v deficiency East texas bleeding disorder 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Congenital factor v deficiency thrombophilia due to activated protein c resistance 0.500 1 6.49e-5 2.33e-4 ✓ sig.
East texas bleeding disorder thrombophilia due to activated protein c resistance 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Congenital factor v deficiency Factor v deficiency 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Factor v deficiency thrombophilia due to activated protein c resistance 0.333 1 1.30e-4 3.93e-4 ✓ sig.
East texas bleeding disorder Factor v deficiency 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Cerebral venous sinus thrombosis East texas bleeding disorder 0.250 1 1.95e-4 5.35e-4 ✓ sig.
thrombophilia due to activated protein c resistance Venous hypertension 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Thiamine-responsive megaloblastic anemia Venous hypertension 0.250 1 1.95e-4 5.35e-4 ✓ sig.
East texas bleeding disorder Hepatic vein thrombosis 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Congenital factor v deficiency Hepatic vein thrombosis 0.250 1 1.95e-4 5.35e-4 ✓ sig.
East texas bleeding disorder Venous hypertension 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Congenital factor v deficiency Venous hypertension 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Cerebral venous sinus thrombosis protein S deficiency 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Cerebral venous sinus thrombosis thrombophilia due to activated protein c resistance 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Cerebral venous sinus thrombosis Congenital factor v deficiency 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Budd-chiari syndrome East texas bleeding disorder 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Budd-chiari syndrome Congenital factor v deficiency 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Diabetes macrovascular complications Male infertility motility disorder 0.167 1 3.25e-4 7.70e-4 ✓ sig.
Diabetes macrovascular complications thrombophilia due to activated protein c resistance 0.167 1 3.25e-4 7.70e-4 ✓ sig.
Diabetes macrovascular complications East texas bleeding disorder 0.167 1 3.25e-4 7.70e-4 ✓ sig.
Congenital factor v deficiency Diabetes macrovascular complications 0.167 1 3.25e-4 7.70e-4 ✓ sig.
Factor v deficiency Venous hypertension 0.200 1 3.90e-4 8.66e-4 ✓ sig.
Thiamine-responsive megaloblastic anemia Venous insufficiency 0.100 1 5.84e-4 1.16e-3 ✓ sig.
Diabetes macrovascular complications Factor v deficiency 0.143 1 6.49e-4 1.24e-3 ✓ sig.
Lipoma Thiamine-responsive megaloblastic anemia 0.077 1 7.79e-4 1.40e-3 ✓ sig.
Lipoma Uterine benign neoplasm 0.077 1 7.79e-4 1.40e-3 ✓ sig.
Benign prostatic hyperplasia Uterine benign neoplasm 0.028 1 2.27e-3 3.19e-3 ✓ sig.