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 366

5 diseases · 8 shared-gene connections
5 Diseases
111 Unique genes
0.142 Avg. similarity score
Cognition disorder Most-connected disease (4 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 ⇵
Cognition disorder 4 4 54
Delirium, dementia, and cognitive disorders 4 4 56
Bile acid malabsorption 3 3 3
Diabetes complications 3 3 12
Brain disease 2 2 42

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

Gene ⇵ Member diseases ⇵ Linked diseases
SLC10A2 4 / 5 Bile acid malabsorption, Cognition disorder, Delirium, dementia, and cognitive disorders, Diabetes complications
SLC51B 4 / 5 Bile acid malabsorption, Cognition disorder, Delirium, dementia, and cognitive disorders, Diabetes complications
ABCC4 3 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders, Diabetes complications
APP 3 / 5 Brain disease, Cognition disorder, Delirium, dementia, and cognitive disorders
CDK5R1 3 / 5 Brain disease, Cognition disorder, Delirium, dementia, and cognitive disorders
NR0B2 3 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders, Diabetes complications
OTC 3 / 5 Brain disease, Cognition disorder, Delirium, dementia, and cognitive disorders
SLC1A1 3 / 5 Brain disease, Cognition disorder, Delirium, dementia, and cognitive disorders
SLC51A 3 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders, Diabetes complications
TSC1 3 / 5 Brain disease, Cognition disorder, Delirium, dementia, and cognitive disorders
AFF4 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
AGT 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
APOE 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
BCHE 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
CAPN2 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
CNR1 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
COMT 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
CRH 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
DRD2 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
DRD3 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
EIF2S1 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
EPO 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
FGF14 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
FMR1 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
FOSB 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
GSK3B 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
HTR2A 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
IGF2 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
LAMB2 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
LEPR 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
MAOA 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
MAPT 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
MET 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
OXTR 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
PHLDA1 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
PINK1 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
PSEN1 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
PTGS2 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
SETD7 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
SLC4A10 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
SLC6A4 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
SMAD4 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
VIP 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
WDR48 2 / 5 Cognition disorder, Delirium, dementia, and cognitive disorders
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 ⇵
PI3K-Akt signaling pathway
IFNB1, LAMC3, PPP2R2B, TSC1, TSC2, EPO, GSK3B, IGF2, LAMB2, MET, VEGFA, BDNF
 KEGG 15 / 361 4.5× 1.09e-6 5.27e-5 ✓ sig.
Cocaine addiction
CDK5R1, TH, DRD2, FOSB, MAOA, BDNF
 KEGG 6 / 49 13.2× 5.51e-6 2.05e-4 ✓ sig.
Hormone signaling
AGT, CRH, DRD2, DRD3, EPO, IGF2, LEPR, OXTR, SMAD4, VIP, INS
 KEGG 11 / 219 5.4× 5.52e-6 2.06e-4 ✓ sig.
Human papillomavirus infection
IFNB1, IRF3, LAMC3, PPP2R2B, TBK1, TICAM1, TSC1, TSC2, GSK3B, LAMB2, PSEN1, PTGS2
 KEGG 13 / 333 4.2× 1.18e-5 3.84e-4 ✓ sig.
Dopaminergic synapse
PPP2R2B, TH, COMT, DRD2, DRD3, GSK3B, MAOA, CACNA1C
 KEGG 8 / 132 6.6× 2.94e-5 8.20e-4 ✓ sig.
Herpes simplex virus 1 infection
IFNB1, IFNG, IRF3, TBK1, TICAM1, TSC1, TSC2, EIF2S1, NECTIN2
 KEGG 9 / 182 5.4× 4.63e-5 1.20e-3 ✓ sig.
Kaposi sarcoma-associated herpesvirus infection
IFNB1, IRF3, TBK1, TICAM1, GSK3B, PTGS2, HIF1A, VEGFA, FGF2
 KEGG 9 / 196 5.0× 8.23e-5 1.92e-3 ✓ sig.
Enzymatic degradation of Dopamine by monoamine oxidase
COMT, MAOA
 Reactome 2 / 2 108× 8.47e-5 1.96e-3 ✓ sig.
Metabolism of serotonin
MAOA, ALDH2
 Reactome 2 / 2 108× 8.47e-5 1.96e-3 ✓ sig.
HDL remodeling
ALB, APOE, APOC3
 Reactome 3 / 10 32.5× 8.80e-5 2.02e-3 ✓ sig.
Serotonergic synapse
APP, HTR2A, MAOA, PTGS2, SLC6A4, CACNA1C, CYP2D6
 KEGG 7 / 115 6.6× 9.19e-5 2.09e-3 ✓ sig.
Malaria
IFNG, TGFB1, MET, CR1, CSF3
 KEGG 5 / 50 10.8× 9.37e-5 2.13e-3 ✓ sig.
Hepatitis C
IFNB1, IFNG, IRF3, PPP2R2B, TBK1, TICAM1, EIF2S1, GSK3B
 KEGG 8 / 159 5.4× 1.10e-4 2.43e-3 ✓ sig.
Pathways in cancer
IFNG, LAMC3, TGFB1, AGT, EPO, GSK3B, IGF2, LAMB2, MET, PTGS2, SMAD4, HIF1A
 KEGG 15 / 533 3.0× 1.11e-4 2.44e-3 ✓ sig.
Regulation of gene expression by Hypoxia-inducible Factor
EPO, HIF1A, VEGFA
 Reactome 3 / 11 29.5× 1.20e-4 2.60e-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 ⇵
negative regulation of gene expression
APP, IFNG, TBK1, TGFB1, AGT, APOE, CRH, GSK3B, MAPT, NR0B2, PINK1, PSEN1
 GO:0010629 18 / 339 8.9× 1.49e-12 6.58e-10 ✓ sig.
response to ethanol
TGFB1, TH, CRH, DRD2, DRD3, FOSB, NR0B2, SETD7, CSF3, FGF2
 GO:0045471 10 / 110 15.3× 1.03e-9 2.30e-7 ✓ sig.
memory
APP, SLC1A1, TH, COMT, HTR2A, MAPT, PSEN1, SLC6A4, TAFA2
 GO:0007613 9 / 87 17.4× 2.31e-9 4.69e-7 ✓ sig.
positive regulation of glycolytic process
APP, IFNG, HTR2A, PSEN1, HIF1A, INS
 GO:0045821 6 / 24 42.1× 4.73e-9 8.87e-7 ✓ sig.
positive regulation of amyloid fibril formation
APP, APOE, PSEN1, CLU
 GO:1905908 4 / 5 135× 5.87e-9 1.08e-6 ✓ sig.
learning or memory
APP, SLC1A1, COMT, CRH, DRD3, MAPT, PSEN1, PICALM
 GO:0007611 8 / 72 18.7× 1.05e-8 1.78e-6 ✓ sig.
synaptic transmission, dopaminergic
TH, COMT, CRH, DRD2, DRD3
 GO:0001963 5 / 15 56.1× 1.93e-8 3.03e-6 ✓ sig.
behavioral response to cocaine
DRD2, DRD3, FOSB, HTR2A, SLC6A4
 GO:0048148 5 / 17 49.5× 3.95e-8 5.55e-6 ✓ sig.
positive regulation of gene expression
APP, IFNG, TGFB1, TICAM1, CRH, GSK3B, NR0B2, PSEN1, SLC6A4, SMAD4, CLU, HIF1A
 GO:0010628 16 / 504 5.3× 4.77e-8 6.53e-6 ✓ sig.
intracellular copper ion homeostasis
APP, CP, SCO1, SCO2, MT2A
 GO:0006878 5 / 18 46.8× 5.44e-8 7.27e-6 ✓ sig.
positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
APP, TBK1, TGFB1, AGT, GSK3B, IGF2, PINK1, VEGFA, CSF3, FGF2, INS
 GO:0051897 11 / 217 8.5× 6.88e-8 8.87e-6 ✓ sig.
response to hypoxia
TGFB1, TH, CAPN2, COMT, DRD2, EPO, SLC6A4, SMAD4, HIF1A, VEGFA
 GO:0001666 10 / 176 9.6× 9.65e-8 1.17e-5 ✓ sig.
positive regulation of cell population proliferation
CXCR2, IFNG, STAMBP, TGFB1, CRH, EPO, HTR2A, IGF2, LEPR, VIP, CR1, HDAC4
 GO:0008284 16 / 532 5.1× 1.00e-7 1.21e-5 ✓ sig.
positive regulation of nitric oxide biosynthetic process
APP, IFNG, TICAM1, APOE, PTGS2, CLU
 GO:0045429 6 / 42 24.1× 1.69e-7 1.88e-5 ✓ sig.
regulation of amyloid-beta clearance
APP, APOE, CLU
 GO:1900221 3 / 3 168× 2.04e-7 2.21e-5 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Cognition disorder Delirium, dementia, and cognitive disorders 0.657 44 2.12e-108 2.91e-106 ✓ sig.
Cognition disorder Diabetes complications 0.081 5 3.41e-10 3.43e-9 ✓ sig.
Delirium, dementia, and cognitive disorders Diabetes complications 0.078 5 4.12e-10 4.10e-9 ✓ sig.
Brain disease Cognition disorder 0.054 5 3.38e-7 2.29e-6 ✓ sig.
Brain disease Delirium, dementia, and cognitive disorders 0.053 5 4.07e-7 2.70e-6 ✓ sig.
Bile acid malabsorption Diabetes complications 0.143 2 1.67e-6 9.97e-6 ✓ sig.
Bile acid malabsorption Cognition disorder 0.036 2 3.61e-5 1.76e-4 ✓ sig.
Bile acid malabsorption Delirium, dementia, and cognitive disorders 0.034 2 3.89e-5 1.88e-4 ✓ sig.