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 288

8 diseases · 16 shared-gene connections
8 Diseases
91 Unique genes
0.218 Avg. similarity score
Heritable pulmonary arterial hypertension Most-connected disease (6 links)
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Disease Searched: Heritable pulmonary arterial hypertension 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 ⇵
Heritable pulmonary arterial hypertension 6 6 8
Idiopathic pulmonary arterial hypertension 5 5 3
Pulmonary arterial hypertension 4 4 45
Pulmonary capillary hemangiomatosis 4 4 1
Pulmonary veno-occlusive disease and/or pulmonary capillary hemangiomatosis 4 4 1
Pulmonary venoocclusive disease 2 4 4 1
Pulmonary hypertension 3 3 62
Pulmonary hypertension, primary, autosomal recessive 2 2 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
EIF2AK4 7 / 8 Heritable pulmonary arterial hypertension, Idiopathic pulmonary arterial hypertension, Pulmonary arterial hypertension, Pulmonary capillary hemangiomatosis and 3 more
BMPR2 4 / 8 Heritable pulmonary arterial hypertension, Idiopathic pulmonary arterial hypertension, Pulmonary arterial hypertension, Pulmonary hypertension
SMAD9 4 / 8 Heritable pulmonary arterial hypertension, Idiopathic pulmonary arterial hypertension, Pulmonary arterial hypertension, Pulmonary hypertension
ACVRL1 3 / 8 Heritable pulmonary arterial hypertension, Pulmonary arterial hypertension, Pulmonary hypertension
ATP13A3 3 / 8 Pulmonary arterial hypertension, Pulmonary hypertension, Pulmonary hypertension, primary, autosomal recessive
CAV1 3 / 8 Heritable pulmonary arterial hypertension, Pulmonary arterial hypertension, Pulmonary hypertension
ENG 3 / 8 Heritable pulmonary arterial hypertension, Pulmonary arterial hypertension, Pulmonary hypertension
GDF2 3 / 8 Heritable pulmonary arterial hypertension, Pulmonary arterial hypertension, Pulmonary hypertension
SOX17 3 / 8 Heritable pulmonary arterial hypertension, Pulmonary arterial hypertension, Pulmonary hypertension
BMPR1B 2 / 8 Pulmonary arterial hypertension, Pulmonary hypertension
CBLN2 2 / 8 Pulmonary arterial hypertension, Pulmonary hypertension
KCNA5 2 / 8 Pulmonary arterial hypertension, Pulmonary hypertension
KCNK3 2 / 8 Pulmonary arterial hypertension, Pulmonary hypertension
SMAD1 2 / 8 Pulmonary arterial hypertension, Pulmonary hypertension
SMAD4 2 / 8 Pulmonary arterial hypertension, Pulmonary hypertension
TBX4 2 / 8 Pulmonary arterial hypertension, Pulmonary hypertension
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 ⇵
Signaling by BMP
BMPR2, ACVRL1, GDF2, SMAD9, BMP10, BMPR1A, BMPR1B, SMAD1, SMAD4
 Reactome 9 / 28 42.4× 3.37e-13 7.00e-11 ✓ sig.
Fluid shear stress and atherosclerosis
BMPR2, CAV1, CCL2, EDN1, NOS3, TNF, BMPR1A, BMPR1B, KDR, KLF2
 KEGG 10 / 141 9.4× 1.03e-7 5.75e-6 ✓ sig.
TGF-beta signaling pathway
BMPR2, HDAC1, SMAD9, TNF, BMPR1A, BMPR1B, FBN1, SMAD1, SMAD4
 KEGG 9 / 108 11.0× 1.17e-7 6.40e-6 ✓ sig.
AGE-RAGE signaling pathway in diabetic complications
CCL2, CXCL8, EDN1, FOXO1, NOS3, TNF, PIM1, SMAD4
 KEGG 8 / 101 10.5× 9.04e-7 3.82e-5 ✓ sig.
Notch-HLH transcription pathway
HDAC1, HDAC4, HDAC5, NOTCH1, NOTCH3
 Reactome 5 / 28 23.6× 1.91e-6 7.29e-5 ✓ sig.
Cytokine-cytokine receptor interaction
BMPR2, ACVRL1, GDF2, CCL1, CCL2, CD40LG, CXCL8, LEPR, TNF, BMP10, BMPR1A, BMPR1B
 KEGG 12 / 298 5.3× 2.39e-6 8.78e-5 ✓ sig.
Allograft rejection
CD40LG, TNF, HLA-DPA1, HLA-DPB1, HLA-B
 KEGG 5 / 39 16.9× 1.05e-5 3.03e-4 ✓ sig.
Interleukin-4 and Interleukin-13 signaling
ALOX5, CCL2, CXCL8, FOXO1, HIF1A, TNF, PIM1
 Reactome 7 / 108 8.6× 1.70e-5 4.56e-4 ✓ sig.
Hormone signaling
SMAD9, CALCA, LEPR, NPPB, PRKG1, BMPR1A, BMPR1B, SMAD1, SMAD4
 KEGG 9 / 219 5.4× 4.06e-5 9.25e-4 ✓ sig.
FOXO-mediated transcription of cell cycle genes
CAV1, FOXO1, SMAD4
 Reactome 3 / 11 36.0× 6.65e-5 1.37e-3 ✓ sig.
Apelin signaling pathway
HDAC4, HDAC5, NOS3, RYR1, KLF2, NOTCH3, SMAD4
 KEGG 7 / 140 6.6× 9.01e-5 1.75e-3 ✓ sig.
Asthma
CD40LG, TNF, HLA-DPA1, HLA-DPB1
 KEGG 4 / 32 16.5× 9.43e-5 1.81e-3 ✓ sig.
Calcium signaling pathway
EDNRB, HTR2B, NFATC2, NOS3, TGFA, RYR1, KDR, PDE1A, PDGFD
 KEGG 9 / 254 4.7× 1.27e-4 2.29e-3 ✓ sig.
Renin secretion
ACE, EDN1, KCNMA1, AQP1, PDE1A
 KEGG 5 / 69 9.6× 1.71e-4 2.91e-3 ✓ sig.
Th17 cell differentiation
HIF1A, NFATC2, AHR, HLA-DPA1, HLA-DPB1, SMAD4
 KEGG 6 / 109 7.3× 1.74e-4 2.94e-3 ✓ 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 ⇵
vasodilation
ACE, CALCA, EDNRB, KCNMA1, NOS3, NPPB, PRKG1, SOD2, TNF, CPS1, KLF2
 GO:0042311 11 / 50 45.2× 6.26e-16 5.30e-13 ✓ sig.
angiogenesis
ACVRL1, CAV1, GDF2, SOX17, TBX4, ENG, CCL2, CXCL8, HIF1A, LEPR, NOS3, SLC31A1
 GO:0001525 16 / 284 11.6× 4.98e-13 2.48e-10 ✓ sig.
positive regulation of gene expression
BMPR2, CAV1, GDF2, HDAC1, SOX17, CCL2, CXCL8, HIF1A, NFATC2, NOS3, SLC6A4, TNF
 GO:0010628 19 / 504 7.7× 3.31e-12 1.41e-9 ✓ sig.
BMP signaling pathway
BMPR2, ACVRL1, GDF2, SMAD9, ENG, BMP10, BMPR1A, BMPR1B, SMAD1, SMAD4
 GO:0030509 10 / 88 23.3× 1.49e-11 5.48e-9 ✓ sig.
response to xenobiotic stimulus
HDAC5, KCNK3, ABCA3, CA9, EDN1, HTR2B, LOX, NFATC2, SLC6A4, SOD2, TNF, CPS1
 GO:0009410 14 / 248 11.6× 1.57e-11 5.73e-9 ✓ sig.
response to hypoxia
CAV1, ENG, CA9, EDN1, HIF1A, KCNA5, KCNMA1, SLC6A4, SOD2, TNF, RYR1, SMAD4
 GO:0001666 12 / 176 14.0× 5.53e-11 1.80e-8 ✓ sig.
positive regulation of transcription by RNA polymerase II
BMPR2, ACVRL1, GDF2, HDAC1, HDAC4, HDAC5, SMAD9, SOX17, ENG, BRD4, EDN1, FBLN5
 GO:0045944 26 / 1,208 4.4× 6.29e-11 2.02e-8 ✓ sig.
lung development
BMPR2, TBX4, ABCA3, LOX, NOS3, FOXF1, BMPR1A, FBN1, KDR, NOTCH1
 GO:0030324 10 / 108 19.0× 1.18e-10 3.57e-8 ✓ sig.
cellular response to BMP stimulus
BMPR2, ACVRL1, GDF2, SMAD9, BMPR1A, BMPR1B, SMAD4
 GO:0071773 7 / 33 43.6× 1.98e-10 5.64e-8 ✓ sig.
heart development
ACVRL1, SOX17, ENG, EDN1, HTR2B, LOX, PRKG1, SOD2, FOXF1, BMP10, BMPR1A, FBN1
 GO:0007507 13 / 273 9.8× 7.21e-10 1.75e-7 ✓ sig.
positive regulation of SMAD protein signal transduction
BMPR2, ACVRL1, GDF2, ENG, BMP10, BMPR1A, SMAD4
 GO:0060391 7 / 42 34.2× 1.21e-9 2.73e-7 ✓ sig.
regulation of blood pressure
ACVRL1, ACE, CALCA, EDN1, EDNRB, NOS3, NPPB, SOD2
 GO:0008217 8 / 83 19.8× 6.77e-9 1.26e-6 ✓ sig.
cartilage development
GDF2, ATP7A, EDN1, HIF1A, NFATC2, BMPR1A, BMPR1B, SMAD1
 GO:0051216 8 / 89 18.5× 1.18e-8 2.04e-6 ✓ sig.
positive regulation of cartilage development
BMPR2, GDF2, BMP10, BMPR1B, SMAD1
 GO:0061036 5 / 17 60.4× 1.45e-8 2.44e-6 ✓ sig.
vasoconstriction
CAV1, EDN1, EDNRB, HTR2B, SLC6A4
 GO:0042310 5 / 18 57.0× 2.00e-8 3.22e-6 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Pulmonary arterial hypertension Pulmonary hypertension 0.174 16 3.13e-28 5.92e-27 ✓ sig.
Heritable pulmonary arterial hypertension Pulmonary arterial hypertension 0.174 8 2.63e-21 4.01e-20 ✓ sig.
Heritable pulmonary arterial hypertension Pulmonary hypertension 0.127 8 4.12e-20 6.07e-19 ✓ sig.
Heritable pulmonary arterial hypertension Idiopathic pulmonary arterial hypertension 0.333 3 9.05e-11 8.46e-10 ✓ sig.
Idiopathic pulmonary arterial hypertension Pulmonary arterial hypertension 0.065 3 2.29e-8 1.76e-7 ✓ sig.
Pulmonary capillary hemangiomatosis Pulmonary veno-occlusive disease and/or pulmonary capillary hemangiomatosis 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Pulmonary capillary hemangiomatosis Pulmonary venoocclusive disease 2 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Pulmonary veno-occlusive disease and/or pulmonary capillary hemangiomatosis Pulmonary venoocclusive disease 2 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Idiopathic pulmonary arterial hypertension Pulmonary veno-occlusive disease and/or pulmonary capillary hemangiomatosis 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Idiopathic pulmonary arterial hypertension Pulmonary venoocclusive disease 2 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Idiopathic pulmonary arterial hypertension Pulmonary capillary hemangiomatosis 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Heritable pulmonary arterial hypertension Pulmonary capillary hemangiomatosis 0.111 1 5.17e-4 9.13e-4 ✓ sig.
Heritable pulmonary arterial hypertension Pulmonary veno-occlusive disease and/or pulmonary capillary hemangiomatosis 0.111 1 5.17e-4 9.13e-4 ✓ sig.
Heritable pulmonary arterial hypertension Pulmonary venoocclusive disease 2 0.111 1 5.17e-4 9.13e-4 ✓ sig.
Pulmonary arterial hypertension Pulmonary hypertension, primary, autosomal recessive 0.022 1 2.91e-3 3.71e-3 ✓ sig.
Pulmonary hypertension Pulmonary hypertension, primary, autosomal recessive 0.016 1 4.00e-3 4.91e-3 ✓ sig.