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

6 diseases · 8 shared-gene connections
6 Diseases
696 Unique genes
0.187 Avg. similarity score
Liver cirrhosis 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 ⇵
Liver cirrhosis 4 4 264
Biliary cholangitis 3 3 147
Biliary cirrhosis 3 3 128
Inner ear disease 2 2 1
Liver disease 2 2 157
Nonalcoholic fatty liver disease 2 2 316

Top shared genes (genes linked to 2+ member diseases ‐ top 100 shown, download for all)

Gene ⇵ Member diseases ⇵ Linked diseases
ABCB4 5 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis, Liver disease and 1 more
ABCC2 4 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis, Nonalcoholic fatty liver disease
CD3D 4 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis, Liver disease
HLA-DQA1 4 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis, Nonalcoholic fatty liver disease
NFE2L2 4 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis, Nonalcoholic fatty liver disease
NFKB1 4 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis, Liver disease
NOS2 4 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis, Liver disease
TGFB1 4 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis, Nonalcoholic fatty liver disease
ABCG2 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
AHR 3 / 6 Liver cirrhosis, Liver disease, Nonalcoholic fatty liver disease
ALB 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
ALDH2 3 / 6 Liver cirrhosis, Liver disease, Nonalcoholic fatty liver disease
APOC1 3 / 6 Liver cirrhosis, Liver disease, Nonalcoholic fatty liver disease
APOE 3 / 6 Liver cirrhosis, Liver disease, Nonalcoholic fatty liver disease
ATG5 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
CCL5 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
CD80 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
CDH5 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
CENPB 3 / 6 Biliary cholangitis, Biliary cirrhosis, Inner ear disease
CLEC16A 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
CXCL10 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
CXCL9 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
CXCR5 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
CYGB 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
CYP1A2 3 / 6 Liver cirrhosis, Liver disease, Nonalcoholic fatty liver disease
CYP2E1 3 / 6 Liver cirrhosis, Liver disease, Nonalcoholic fatty liver disease
DENND1B 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
ENTPD2 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
EXOC3L4 3 / 6 Biliary cholangitis, Biliary cirrhosis, Nonalcoholic fatty liver disease
GSTT1 3 / 6 Liver cirrhosis, Liver disease, Nonalcoholic fatty liver disease
HFE 3 / 6 Liver cirrhosis, Liver disease, Nonalcoholic fatty liver disease
HIF1A 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
HLA-DPB1 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
HLA-DQB1 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
IFNL4 3 / 6 Liver cirrhosis, Liver disease, Nonalcoholic fatty liver disease
IGFBP1 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
IL12A 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
IL12B 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
IL7R 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
KEAP1 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
KHDRBS3 3 / 6 Liver cirrhosis, Liver disease, Nonalcoholic fatty liver disease
KLHL8 3 / 6 Liver cirrhosis, Liver disease, Nonalcoholic fatty liver disease
KRT7 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
LOX 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
LOXL2 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
MAPK14 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
MMEL1 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
MTARC1 3 / 6 Liver cirrhosis, Liver disease, Nonalcoholic fatty liver disease
MTHFR 3 / 6 Liver cirrhosis, Liver disease, Nonalcoholic fatty liver disease
NOS3 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
NSA2 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
PNPLA3 3 / 6 Liver cirrhosis, Liver disease, Nonalcoholic fatty liver disease
RELA 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
SERPINA1 3 / 6 Liver cirrhosis, Liver disease, Nonalcoholic fatty liver disease
SERPINA2 3 / 6 Liver cirrhosis, Liver disease, Nonalcoholic fatty liver disease
SLC4A2 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
SLC51A 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
SLC51B 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
SPIB 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
ST8SIA1 3 / 6 Liver cirrhosis, Liver disease, Nonalcoholic fatty liver disease
STAT4 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
TM6SF2 3 / 6 Liver cirrhosis, Liver disease, Nonalcoholic fatty liver disease
TNF 3 / 6 Liver cirrhosis, Liver disease, Nonalcoholic fatty liver disease
TNFRSF1A 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
TRIB1 3 / 6 Liver cirrhosis, Liver disease, Nonalcoholic fatty liver disease
TYK2 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
UBD 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
UGT3A1 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver disease
VDR 3 / 6 Biliary cholangitis, Biliary cirrhosis, Liver cirrhosis
ABCB11 2 / 6 Liver cirrhosis, Liver disease
ACE 2 / 6 Liver cirrhosis, Nonalcoholic fatty liver disease
ACTA2 2 / 6 Liver cirrhosis, Liver disease
AKNA 2 / 6 Liver disease, Nonalcoholic fatty liver disease
ALAD 2 / 6 Liver cirrhosis, Liver disease
ALDH1A1 2 / 6 Liver disease, Nonalcoholic fatty liver disease
ANP32B 2 / 6 Biliary cholangitis, Biliary cirrhosis
ARID3A 2 / 6 Biliary cholangitis, Biliary cirrhosis
ARL14 2 / 6 Biliary cholangitis, Biliary cirrhosis
ATP7B 2 / 6 Liver cirrhosis, Liver disease
ATXN2 2 / 6 Biliary cholangitis, Biliary cirrhosis
BCL2 2 / 6 Liver cirrhosis, Nonalcoholic fatty liver disease
C1ORF53 2 / 6 Biliary cholangitis, Biliary cirrhosis
CA1 2 / 6 Biliary cholangitis, Biliary cirrhosis
CA2 2 / 6 Biliary cholangitis, Biliary cirrhosis
CACNA1S 2 / 6 Biliary cholangitis, Biliary cirrhosis
CACNA2D1 2 / 6 Liver cirrhosis, Nonalcoholic fatty liver disease
CAPSL 2 / 6 Biliary cholangitis, Biliary cirrhosis
CAT 2 / 6 Liver cirrhosis, Nonalcoholic fatty liver disease
CCDC88B 2 / 6 Biliary cholangitis, Biliary cirrhosis
CCL2 2 / 6 Liver cirrhosis, Liver disease
CCL20 2 / 6 Biliary cholangitis, Biliary cirrhosis
CCR2 2 / 6 Liver disease, Nonalcoholic fatty liver disease
CCR6 2 / 6 Biliary cholangitis, Biliary cirrhosis
CD14 2 / 6 Liver cirrhosis, Nonalcoholic fatty liver disease
CD226 2 / 6 Biliary cholangitis, Biliary cirrhosis
CD58 2 / 6 Biliary cholangitis, Biliary cirrhosis
CDC37 2 / 6 Biliary cholangitis, Biliary cirrhosis
CDH2 2 / 6 Liver cirrhosis, Nonalcoholic fatty liver disease
CEP43 2 / 6 Biliary cholangitis, Biliary cirrhosis
CFAP263 2 / 6 Biliary cholangitis, Biliary cirrhosis
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
HIF1A, IL12A, IL12B, NOS2, TGFB1, TYK2, IL4R, CCL2, COL1A2, FGF2, FOXO3, HGF
 Reactome 38 / 108 6.1× 1.68e-20 1.38e-17 ✓ sig.
Interleukin-10 signaling
CCL5, CD80, CXCL10, IL12A, IL12B, TNFRSF1A, TYK2, CCL20, CCL2, ICAM1, IL10, IL6
 Reactome 26 / 47 9.5× 1.74e-20 1.42e-17 ✓ sig.
AGE-RAGE signaling pathway in diabetic complications
MAPK14, NFKB1, NOS3, RELA, TGFB1, PRKCB, AGT, CCL2, COL1A1, COL1A2, COL3A1, F3
 KEGG 36 / 101 6.2× 1.05e-19 7.92e-17 ✓ sig.
Pathways in cancer
HIF1A, IL12A, IL12B, IL7R, KEAP1, NFE2L2, NFKB1, NOS2, RELA, STAT4, TGFB1, ETS1
 KEGG 87 / 533 2.8× 3.53e-19 2.55e-16 ✓ sig.
Inflammatory bowel disease
HLA-DQA1, IL12A, IL12B, NFKB1, RELA, STAT4, TGFB1, HLA-DPB1, HLA-DQB1, HLA-DRA, IL12RB2, IL21R
 KEGG 27 / 66 7.1× 7.01e-17 3.25e-14 ✓ sig.
Allograft rejection
CD80, HLA-DQA1, IL12A, IL12B, HLA-DPB1, HLA-DQB1, HLA-DRA, HLA-B, HLA-DPA1, HLA-DRB1, IFNG, IL10
 KEGG 20 / 39 8.8× 3.40e-15 1.19e-12 ✓ sig.
Type I diabetes mellitus
CD80, HLA-DQA1, IL12A, IL12B, HLA-DPB1, HLA-DQB1, HLA-DRA, HLA-B, HLA-DPA1, HLA-DRB1, IFNG, TNF
 KEGG 21 / 44 8.2× 4.49e-15 1.53e-12 ✓ sig.
Leishmaniasis
HLA-DQA1, IL12A, IL12B, MAPK14, NFKB1, NOS2, RELA, TGFB1, HLA-DPB1, HLA-DQB1, HLA-DRA, PRKCB
 KEGG 27 / 78 6.0× 9.87e-15 3.09e-12 ✓ sig.
Influenza A
CCL5, CXCL10, HLA-DQA1, IL12A, IL12B, NFKB1, RELA, TNFRSF1A, TYK2, HLA-DPB1, HLA-DQB1, HLA-DRA
 KEGG 40 / 173 4.0× 2.26e-14 6.53e-12 ✓ sig.
Cytokine-cytokine receptor interaction
CCL5, CXCL10, CXCL9, CXCR5, IL12A, IL12B, IL7R, TGFB1, TNFRSF1A, CCL20, CCR6, IL12RB2
 KEGG 54 / 298 3.1× 3.80e-14 1.04e-11 ✓ sig.
Th17 cell differentiation
CD3D, HIF1A, HLA-DQA1, MAPK14, NFKB1, RELA, TGFB1, TYK2, HLA-DPB1, HLA-DQB1, HLA-DRA, IL21R
 KEGG 31 / 109 4.9× 4.94e-14 1.32e-11 ✓ sig.
Fluid shear stress and atherosclerosis
CDH5, KEAP1, MAPK14, NFE2L2, NFKB1, NOS3, RELA, TNFRSF1A, PDGFB, CCL2, CTNNB1, CYBA
 KEGG 35 / 141 4.3× 1.03e-13 2.62e-11 ✓ sig.
Toxoplasmosis
HLA-DQA1, IL12A, IL12B, MAPK14, NFKB1, NOS2, RELA, TGFB1, TNFRSF1A, TYK2, HLA-DPB1, HLA-DQB1
 KEGG 31 / 112 4.8× 1.12e-13 2.83e-11 ✓ sig.
Graft-versus-host disease
CD80, HLA-DQA1, HLA-DPB1, HLA-DQB1, HLA-DRA, HLA-B, HLA-DPA1, HLA-DRB1, IFNG, IL6, KIR3DS1, TNF
 KEGG 20 / 45 7.7× 1.12e-13 2.83e-11 ✓ sig.
MAPK signaling pathway
MAPK14, NFKB1, RELA, TGFB1, TNFRSF1A, CACNA1S, PDGFB, PRKCB, RPS6KA4, CACNA2D1, MAPKAPK5, ARRB1
 KEGG 52 / 299 3.0× 6.22e-13 1.41e-10 ✓ 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 ⇵
immune response
CCL5, CD80, CTLA4, CXCL10, CXCL9, CXCR5, HLA-DQA1, IL12A, IL7R, STAT4, TYK2, CCL20
 GO:0006955 77 / 543 3.8× 1.87e-24 5.44e-21 ✓ sig.
cytokine-mediated signaling pathway
IL7R, RELA, STAT4, TNFRSF1A, TYK2, IL12RB2, IL16, IL1RL2, IL20RA, IL21R, IL22RA2, IL4R
 GO:0019221 36 / 145 6.7× 4.88e-20 8.04e-17 ✓ sig.
positive regulation of MAPK cascade
TGFB1, FCRL3, PDGFB, CDH2, JCAD, ADRA1A, CTNNB1, DRD4, F2R, FGF19, FGF2, FGF7
 GO:0043410 43 / 224 5.2× 4.59e-19 6.48e-16 ✓ sig.
response to xenobiotic stimulus
LOX, NFE2L2, RELA, TGFB1, ATG5, DNMT3A, ADRA1A, AHR, ALAD, CDH1, COL1A1, CTNNB1
 GO:0009410 42 / 248 4.5× 1.40e-16 1.29e-13 ✓ sig.
response to lipopolysaccharide
CXCL10, IL12A, MAPK14, NOS2, NOS3, RELA, HPGD, IL12RB2, TRIB1, ALAD, CNR2, F2R
 GO:0032496 32 / 161 5.3× 5.82e-15 3.94e-12 ✓ sig.
cellular response to lipopolysaccharide
CD80, CXCL10, CXCL9, IL12B, MAPK14, NFKB1, NOS2, RELA, IRF8, CCL2, CD14, IL10
 GO:0071222 34 / 187 4.9× 1.33e-14 8.44e-12 ✓ sig.
positive regulation of cell population proliferation
CXCL10, IL7R, RELA, TGFB1, CEP43, IL12RB2, PDGFB, RAD51B, MLXIPL, BAMBI, CTNNB1, F2
 GO:0008284 60 / 532 3.0× 1.69e-14 1.06e-11 ✓ sig.
response to hypoxia
CYGB, HIF1A, LOXL2, NOS2, TGFB1, ALAD, ARNT, CYBA, HSD11B2, MMP2, MTHFR, NPPA
 GO:0001666 32 / 176 4.9× 8.02e-14 4.49e-11 ✓ sig.
positive regulation of gene expression
CDH5, HIF1A, IL7R, MAPK14, NFE2L2, NOS3, RELA, TGFB1, VDR, DGKQ, ETS1, ITGB8
 GO:0010628 56 / 504 3.0× 2.48e-13 1.29e-10 ✓ sig.
lipid metabolic process
ABCB4, LBR, DGKQ, HPGD, PLCL2, APOC1, APOE, FDFT1, HSD17B13, PNPLA3, ST8SIA1, TM6SF2
 GO:0006629 76 / 840 2.4× 6.00e-13 2.87e-10 ✓ sig.
positive regulation of miRNA transcription
HIF1A, RELA, TGFB1, ETS1, PDGFB, AGT, FGF2, FOXO3, IL10, IL6, MRTFA, SMAD3
 GO:1902895 18 / 56 8.6× 8.64e-13 4.01e-10 ✓ sig.
cellular response to virus
CCL5, CXCL10, HIF1A, IL12A, MAPK14, NFKB1, TGFB1, TYK2, IRF5, POU2AF1, WDFY4, IFNL4
 GO:0098586 22 / 89 6.6× 1.01e-12 4.67e-10 ✓ sig.
positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
CCL5, TGFB1, PDGFB, MERTK, AGT, ARRB2, F2, F2R, FGF2, FLT1, HGF, IGF1
 GO:0051897 34 / 217 4.2× 1.16e-12 5.27e-10 ✓ sig.
inflammatory response
CCL5, CXCL10, CXCL9, NFE2L2, NFKB1, NOS2, RELA, TGFB1, TNFRSF1A, CCL20, IL1RL2, IRF5
 GO:0006954 52 / 467 3.0× 1.69e-12 7.36e-10 ✓ sig.
cell surface receptor signaling pathway via JAK-STAT
IL12B, STAT4, TNFRSF1A, TYK2, IFNL4, CCL2, IFNG, IFNL3, IL6, STAT1, TNF, LEP
 GO:0007259 19 / 67 7.6× 2.51e-12 1.05e-9 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Biliary cholangitis Biliary cirrhosis 0.865 128 2.44e-297 2.68e-294 ✓ sig.
Liver cirrhosis Nonalcoholic fatty liver disease 0.155 78 9.78e-70 7.35e-68 ✓ sig.
Biliary cirrhosis Liver cirrhosis 0.133 46 4.56e-49 2.47e-47 ✓ sig.
Biliary cholangitis Liver cirrhosis 0.126 46 7.88e-46 4.02e-44 ✓ sig.
Liver disease Nonalcoholic fatty liver disease 0.107 46 1.37e-40 6.17e-39 ✓ sig.
Liver cirrhosis Liver disease 0.093 36 1.53e-30 5.00e-29 ✓ sig.
Biliary cirrhosis Inner ear disease 0.008 1 8.31e-3 9.63e-3 ✓ sig.
Biliary cholangitis Inner ear disease 0.007 1 9.55e-3 1.09e-2 ✓ sig.