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 57

15 diseases · 27 shared-gene connections
15 Diseases
246 Unique genes
0.068 Avg. similarity score
Hyperlipoproteinemia Most-connected disease (9 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 ⇵
Hyperlipoproteinemia 9 9 40
Hypertriglyceridemia 7 7 28
Lipoprotein lipase deficiency 7 7 30
Hyperlipidemia 5 5 141
Apolipoprotein a5 deficiency 4 4 1
Dyslipidemias 4 4 18
Arteriosclerosis 3 3 41
Hypercholesterolemia 3 3 46
hypercholesterolemia, familial, 1 3 3 1
Growth restriction, hypoplastic kidneys, alopecia, and distinctive facies 2 2 1
congenital disorder of glycosylation, type iit 2 2 1
hypercholesterolemia, familial, 4 2 2 1
Anovulation 1 1 1
Corneal injury 1 1 1
Infantile hypertriglyceridemia with hepatosteatosis 1 1 2

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

Gene ⇵ Member diseases ⇵ Linked diseases
LDLR 7 / 15 Arteriosclerosis, Dyslipidemias, Hypercholesterolemia, hypercholesterolemia, familial, 1 and 3 more
APOB 6 / 15 Arteriosclerosis, Hypercholesterolemia, Hyperlipidemia, Hyperlipoproteinemia and 2 more
LPL 6 / 15 Dyslipidemias, Hypercholesterolemia, Hyperlipidemia, Hyperlipoproteinemia and 2 more
APOA5 5 / 15 Apolipoprotein a5 deficiency, Hyperlipidemia, Hyperlipoproteinemia, Hypertriglyceridemia and 1 more
APOE 5 / 15 Arteriosclerosis, Hypercholesterolemia, Hyperlipidemia, Hyperlipoproteinemia and 1 more
CETP 4 / 15 Hyperlipidemia, Hyperlipoproteinemia, Hypertriglyceridemia, Lipoprotein lipase deficiency
PCSK9 4 / 15 Hypercholesterolemia, Hyperlipidemia, Hyperlipoproteinemia, Lipoprotein lipase deficiency
PPARA 4 / 15 Dyslipidemias, Hyperlipidemia, Hyperlipoproteinemia, Hypertriglyceridemia
ZPR1 4 / 15 Growth restriction, hypoplastic kidneys, alopecia, and distinctive facies, Hyperlipidemia, Hypertriglyceridemia, Lipoprotein lipase deficiency
ABCA1 3 / 15 Hypercholesterolemia, Hyperlipidemia, Hyperlipoproteinemia
ABCG8 3 / 15 Arteriosclerosis, Hyperlipidemia, Hyperlipoproteinemia
ADRB2 3 / 15 Hypercholesterolemia, Hyperlipidemia, Hyperlipoproteinemia
APOC3 3 / 15 Hypercholesterolemia, Hyperlipidemia, Hyperlipoproteinemia
GALNT2 3 / 15 congenital disorder of glycosylation, type iit, Hyperlipidemia, Lipoprotein lipase deficiency
GCKR 3 / 15 Hyperlipidemia, Hypertriglyceridemia, Lipoprotein lipase deficiency
HMGCR 3 / 15 Hypercholesterolemia, Hyperlipidemia, Hyperlipoproteinemia
LDLRAP1 3 / 15 Hypercholesterolemia, hypercholesterolemia, familial, 4, Hyperlipoproteinemia
LEPR 3 / 15 Dyslipidemias, Hyperlipidemia, Hyperlipoproteinemia
LIPC 3 / 15 Hypercholesterolemia, Hyperlipidemia, Hyperlipoproteinemia
NEIL1 3 / 15 Dyslipidemias, Hyperlipidemia, Hyperlipoproteinemia
NOS3 3 / 15 Arteriosclerosis, Hyperlipidemia, Hyperlipoproteinemia
PLTP 3 / 15 Dyslipidemias, Hyperlipidemia, Hypertriglyceridemia
PON1 3 / 15 Arteriosclerosis, Hypercholesterolemia, Hyperlipoproteinemia
TDRD15 3 / 15 Hyperlipidemia, Hypertriglyceridemia, Lipoprotein lipase deficiency
ABCB1 2 / 15 Hyperlipidemia, Hyperlipoproteinemia
ABCG5 2 / 15 Arteriosclerosis, Hypercholesterolemia
ADRB3 2 / 15 Hyperlipidemia, Hyperlipoproteinemia
ALDH3A1 2 / 15 Arteriosclerosis, Corneal injury
ANGPTL4 2 / 15 Hyperlipidemia, Hypertriglyceridemia
APC 2 / 15 Hyperlipidemia, Hyperlipoproteinemia
APOA2 2 / 15 Hypercholesterolemia, Hyperlipoproteinemia
APOA4 2 / 15 Hypercholesterolemia, Hyperlipoproteinemia
APOC1 2 / 15 Hyperlipidemia, Lipoprotein lipase deficiency
APOC2 2 / 15 Hyperlipidemia, Hyperlipoproteinemia
CCL2 2 / 15 Hyperlipidemia, Hyperlipoproteinemia
CELSR2 2 / 15 Hyperlipidemia, Lipoprotein lipase deficiency
CREB3L3 2 / 15 Hypertriglyceridemia, Infantile hypertriglyceridemia with hepatosteatosis
CYP7A1 2 / 15 Hypercholesterolemia, Hyperlipidemia
DOCK7 2 / 15 Hyperlipidemia, Lipoprotein lipase deficiency
EPHX2 2 / 15 Hypercholesterolemia, Hyperlipoproteinemia
FADS1 2 / 15 Hyperlipidemia, Lipoprotein lipase deficiency
FADS2 2 / 15 Hyperlipidemia, Lipoprotein lipase deficiency
GCG 2 / 15 Hyperlipidemia, Hyperlipoproteinemia
GHR 2 / 15 Hypercholesterolemia, Hyperlipoproteinemia
GNB3 2 / 15 Hyperlipidemia, Hyperlipoproteinemia
GPD1 2 / 15 Hypertriglyceridemia, Infantile hypertriglyceridemia with hepatosteatosis
HAVCR1 2 / 15 Hyperlipidemia, Hypertriglyceridemia
HSPA1B 2 / 15 Hyperlipidemia, Hyperlipoproteinemia
ICAM1 2 / 15 Arteriosclerosis, Hypercholesterolemia
IRS1 2 / 15 Hyperlipidemia, Hyperlipoproteinemia
LMX1B 2 / 15 Hyperlipidemia, Hyperlipoproteinemia
LPA 2 / 15 Hypercholesterolemia, Hyperlipidemia
MLXIPL 2 / 15 Hyperlipidemia, Lipoprotein lipase deficiency
NAT2 2 / 15 Hyperlipidemia, Lipoprotein lipase deficiency
NR5A2 2 / 15 Anovulation, Dyslipidemias
NYAP2 2 / 15 Hyperlipidemia, Lipoprotein lipase deficiency
PDE1C 2 / 15 Hypercholesterolemia, Hyperlipoproteinemia
PON2 2 / 15 Hypercholesterolemia, Hyperlipoproteinemia
PPARGC1B 2 / 15 Hyperlipidemia, Hyperlipoproteinemia
PPP1R17 2 / 15 Hypercholesterolemia, Hyperlipoproteinemia
PSD3 2 / 15 Hyperlipidemia, Lipoprotein lipase deficiency
SMARCA4 2 / 15 Hyperlipidemia, Lipoprotein lipase deficiency
TOMM40 2 / 15 Dyslipidemias, Hyperlipidemia
VCAM1 2 / 15 Arteriosclerosis, Hypercholesterolemia
VEGFA 2 / 15 Hyperlipidemia, Lipoprotein lipase 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 ⇵
Cholesterol metabolism
ABCG5, ABCG8, APOB, APOE, LCAT, LDLR, LPL, PLTP, LDLRAP1, PCSK9, ANGPTL4, APOC1
 KEGG 24 / 51 23.0× 1.35e-27 3.24e-24 ✓ sig.
Chylomicron remodeling
APOB, APOE, LPL, APOA5, APOA1, APOA2, APOC3, APOC2, GPIHBP1
 Reactome 9 / 9 48.8× 5.49e-16 2.24e-13 ✓ sig.
Lipid and atherosclerosis
APOB, HSPD1, ICAM1, IL1B, LDLR, MMP1, MMP3, MMP9, NFKBIA, NOS3, TLR4, TNFSF10
 KEGG 26 / 216 5.9× 2.78e-13 6.55e-11 ✓ sig.
Chylomicron assembly
APOB, APOE, APOA1, APOA2, APOC3, MTTP, APOC2
 Reactome 7 / 9 38.0× 4.83e-11 7.48e-9 ✓ sig.
HDL remodeling
APOE, LCAT, PLTP, CETP, APOA1, APOC3, APOC2
 Reactome 7 / 10 34.2× 1.58e-10 2.19e-8 ✓ sig.
Interleukin-4 and Interleukin-13 signaling
ALOX5, F13A1, ICAM1, IL10, IL1B, MMP1, MMP2, MMP3, MMP9, PTGS2, VCAM1, VEGFA
 Reactome 16 / 108 7.2× 5.61e-10 6.71e-8 ✓ sig.
Chylomicron clearance
APOB, APOE, LDLR, LDLRAP1, LIPC
 Reactome 5 / 5 48.8× 3.46e-9 3.40e-7 ✓ sig.
Fat digestion and absorption
ABCG5, ABCG8, APOB, PLA2G12B, ABCA1, APOA1, APOA4, MTTP, NPC1L1, SCARB1
 KEGG 10 / 43 11.4× 1.15e-8 9.82e-7 ✓ sig.
PPAR signaling pathway
MMP1, LPL, PLTP, PPARA, PPARG, APOA5, ANGPTL4, CYP7A1, FADS2, APOA1, APOA2, APOC3
 KEGG 12 / 76 7.7× 4.06e-8 2.96e-6 ✓ sig.
Rheumatoid arthritis
ICAM1, IL1B, MMP1, MMP3, TLR4, TCIRG1, TNFRSF11A, HLA-DQA1, HLA-DRA, HLA-DRB1, VEGFA, CCL2
 KEGG 13 / 95 6.7× 6.40e-8 4.44e-6 ✓ sig.
AGE-RAGE signaling pathway in diabetic complications
ICAM1, IL1B, MMP2, NOS3, VCAM1, VEGFA, COL3A1, EDN1, NOX1, SELE, CCL2, JAK2
 KEGG 13 / 101 6.3× 1.34e-7 8.44e-6 ✓ sig.
Fluid shear stress and atherosclerosis
GSTA4, ICAM1, IL1B, MMP2, MMP9, NOS3, VCAM1, VEGFA, EDN1, NCF1, NOX1, SELE
 KEGG 15 / 141 5.2× 1.89e-7 1.14e-5 ✓ sig.
Type I diabetes mellitus
HSPD1, IL1B, HLA-C, HLA-DQA1, HLA-DRA, HLA-DRB1, HLA-DQB1, FASLG, INS
 KEGG 9 / 44 10.0× 2.08e-7 1.24e-5 ✓ sig.
Bile secretion
ABCG5, ABCG8, LDLR, CYP7A1, HMGCR, BAAT, EPHX1, SLC10A1, ABCB1, SCARB1, UGT2B15, UGT2B17
 KEGG 12 / 90 6.5× 2.78e-7 1.60e-5 ✓ sig.
Toxoplasmosis
ALOX5, IL10, LDLR, NFKBIA, TLR4, HLA-DQA1, HLA-DRA, HLA-DRB1, HLA-DQB1, HSPA1B, JAK2, AKT1
 KEGG 13 / 112 5.7× 4.58e-7 2.48e-5 ✓ 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 ⇵
cholesterol homeostasis
NR5A2, ABCG5, ABCG8, APOB, APOE, LCAT, LDLR, LPL, APOA5, LDLRAP1, PCSK9, CYP7A1
 GO:0042632 29 / 112 19.7× 1.18e-29 6.05e-26 ✓ sig.
triglyceride homeostasis
ABCG5, ABCG8, APOE, LPL, APOA5, ANGPTL4, APOC1, GCKR, LIPC, MLXIPL, CETP, PLA2G12B
 GO:0070328 18 / 38 36.0× 2.00e-24 5.78e-21 ✓ sig.
lipoprotein metabolic process
APOB, APOE, LCAT, LDLR, PPARA, APOA5, PCSK9, APOC1, ABCA1, APOA1, APOA2, APOA4
 GO:0042157 15 / 26 43.8× 2.73e-22 6.05e-19 ✓ sig.
cholesterol metabolic process
APOB, APOE, LCAT, LDLR, PON1, LEPR, APOA5, LDLRAP1, PCSK9, APOC1, CYP7A1, HMGCR
 GO:0008203 23 / 107 16.3× 1.06e-21 2.12e-18 ✓ sig.
reverse cholesterol transport
APOE, LCAT, LIPC, CETP, ABCA1, CES1, APOA1, APOA2, APOA4, APOC3, APOC2, SCARB1
 GO:0043691 12 / 17 53.6× 1.21e-19 1.85e-16 ✓ sig.
high-density lipoprotein particle remodeling
APOE, LCAT, LPL, PLTP, APOC1, LIPC, CETP, APOA1, APOA2, APOA4, APOC3, SCARB1
 GO:0034375 12 / 21 43.4× 5.48e-18 6.54e-15 ✓ sig.
cholesterol efflux
ABCG5, ABCG8, APOB, APOE, APOA5, APOC1, ABCA1, APOA1, APOA2, APOA4, APOC3, APOC2
 GO:0033344 13 / 31 31.9× 4.34e-17 4.51e-14 ✓ sig.
cholesterol transport
APOB, LCAT, LDLR, MSR1, LDLRAP1, LIPC, CETP, ABCA1, APOA1, APOA2, NPC1L1, SCARB1
 GO:0030301 12 / 28 32.6× 5.23e-16 4.31e-13 ✓ sig.
lipid metabolic process
AKR1B1, ALDH3A1, ALOX5, APOB, APOE, LCAT, LDLR, PTGS2, LPL, PLTP, PPARA, LDLRAP1
 GO:0006629 45 / 840 4.1× 6.23e-16 5.07e-13 ✓ sig.
very-low-density lipoprotein particle remodeling
APOE, LCAT, LPL, LIPC, APOH, CETP, APOA4, APOC2
 GO:0034372 8 / 8 76.0× 8.05e-16 6.39e-13 ✓ sig.
phospholipid efflux
APOE, APOA5, APOC1, ABCA1, APOA1, APOA2, APOA4, APOC3, APOC2
 GO:0033700 9 / 13 52.6× 7.01e-15 4.65e-12 ✓ sig.
lipid transport
ABCG5, ABCG8, APOB, APOE, LDLR, PLTP, APOA5, APOC1, CERT1, LPA, CETP, SLC10A1
 GO:0006869 21 / 189 8.4× 7.60e-14 4.27e-11 ✓ sig.
triglyceride metabolic process
APOE, LPL, APOA5, PCSK9, APOC1, CETP, APOA2, APOC3, MTTP, INSIG2, LMF1
 GO:0006641 11 / 39 21.4× 1.99e-12 8.55e-10 ✓ sig.
chylomicron remnant clearance
APOE, APOC1, LIPC, APOC3, APOC2, LMF1
 GO:0034382 6 / 6 76.0× 4.90e-12 1.92e-9 ✓ sig.
steroid metabolic process
APOB, APOE, LCAT, LDLR, LDLRAP1, PCSK9, CYP7A1, HMGCR, CETP, ABCA1, SREBF2, APOA1
 GO:0008202 16 / 135 9.0× 2.86e-11 9.34e-9 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Hyperlipidemia Hyperlipoproteinemia 0.182 28 2.52e-49 1.37e-47 ✓ sig.
Hyperlipidemia Lipoprotein lipase deficiency 0.147 22 1.43e-39 6.26e-38 ✓ sig.
Hypercholesterolemia Hyperlipoproteinemia 0.279 19 1.78e-39 7.74e-38 ✓ sig.
Hyperlipidemia Hypertriglyceridemia 0.069 11 4.80e-16 7.73e-15 ✓ sig.
Hypertriglyceridemia Lipoprotein lipase deficiency 0.135 7 5.77e-14 8.06e-13 ✓ sig.
Hyperlipoproteinemia Lipoprotein lipase deficiency 0.109 7 8.94e-13 1.15e-11 ✓ sig.
Arteriosclerosis Hypercholesterolemia 0.086 7 2.74e-11 3.05e-10 ✓ sig.
Dyslipidemias Hyperlipoproteinemia 0.093 5 7.63e-10 7.39e-9 ✓ sig.
Arteriosclerosis Hyperlipoproteinemia 0.079 6 8.73e-10 8.41e-9 ✓ sig.
Hyperlipoproteinemia Hypertriglyceridemia 0.078 5 8.59e-9 7.32e-8 ✓ sig.
Hypertriglyceridemia Infantile hypertriglyceridemia with hepatosteatosis 0.069 2 3.19e-6 1.81e-5 ✓ sig.
Dyslipidemias Hypertriglyceridemia 0.068 3 4.31e-6 2.40e-5 ✓ sig.
Anovulation Dyslipidemias 0.053 1 1.17e-3 1.88e-3 ✓ sig.
Dyslipidemias hypercholesterolemia, familial, 1 0.053 1 1.17e-3 1.88e-3 ✓ sig.
Apolipoprotein a5 deficiency Hypertriglyceridemia 0.034 1 1.82e-3 2.66e-3 ✓ sig.
Growth restriction, hypoplastic kidneys, alopecia, and distinctive facies Hypertriglyceridemia 0.034 1 1.82e-3 2.66e-3 ✓ sig.
Growth restriction, hypoplastic kidneys, alopecia, and distinctive facies Lipoprotein lipase deficiency 0.032 1 1.95e-3 2.81e-3 ✓ sig.
hypercholesterolemia, familial, 1 Lipoprotein lipase deficiency 0.032 1 1.95e-3 2.81e-3 ✓ sig.
congenital disorder of glycosylation, type iit Lipoprotein lipase deficiency 0.032 1 1.95e-3 2.81e-3 ✓ sig.
Apolipoprotein a5 deficiency Lipoprotein lipase deficiency 0.032 1 1.95e-3 2.81e-3 ✓ sig.
hypercholesterolemia, familial, 1 Hyperlipoproteinemia 0.024 1 2.60e-3 3.50e-3 ✓ sig.
hypercholesterolemia, familial, 4 Hyperlipoproteinemia 0.024 1 2.60e-3 3.50e-3 ✓ sig.
Apolipoprotein a5 deficiency Hyperlipoproteinemia 0.024 1 2.60e-3 3.50e-3 ✓ sig.
Arteriosclerosis Corneal injury 0.024 1 2.66e-3 3.58e-3 ✓ sig.
Hypercholesterolemia hypercholesterolemia, familial, 4 0.021 1 2.99e-3 3.94e-3 ✓ sig.
congenital disorder of glycosylation, type iit Hyperlipidemia 0.007 1 9.16e-3 1.05e-2 ✓ sig.
Apolipoprotein a5 deficiency Hyperlipidemia 0.007 1 9.16e-3 1.05e-2 ✓ sig.