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 254

7 diseases · 11 shared-gene connections
7 Diseases
166 Unique genes
0.054 Avg. similarity score
Hypertriglyceridemia Most-connected disease (5 links)
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Disease Searched: Infantile hypertriglyceridemia with hepatosteatosis 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 ⇵
Hypertriglyceridemia 5 5 28
Lipoprotein lipase deficiency 5 5 30
Hyperlipidemia 4 4 141
Apolipoprotein a5 deficiency 3 3 1
Growth restriction, hypoplastic kidneys, alopecia, and distinctive facies 2 2 1
congenital disorder of glycosylation, type iit 2 2 1
Infantile hypertriglyceridemia with hepatosteatosis 1 1 2

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

Gene ⇵ Member diseases ⇵ Linked diseases
APOA5 4 / 7 Apolipoprotein a5 deficiency, Hyperlipidemia, Hypertriglyceridemia, Lipoprotein lipase deficiency
ZPR1 4 / 7 Growth restriction, hypoplastic kidneys, alopecia, and distinctive facies, Hyperlipidemia, Hypertriglyceridemia, Lipoprotein lipase deficiency
APOB 3 / 7 Hyperlipidemia, Hypertriglyceridemia, Lipoprotein lipase deficiency
CETP 3 / 7 Hyperlipidemia, Hypertriglyceridemia, Lipoprotein lipase deficiency
GALNT2 3 / 7 congenital disorder of glycosylation, type iit, Hyperlipidemia, Lipoprotein lipase deficiency
GCKR 3 / 7 Hyperlipidemia, Hypertriglyceridemia, Lipoprotein lipase deficiency
LPL 3 / 7 Hyperlipidemia, Hypertriglyceridemia, Lipoprotein lipase deficiency
TDRD15 3 / 7 Hyperlipidemia, Hypertriglyceridemia, Lipoprotein lipase deficiency
ANGPTL4 2 / 7 Hyperlipidemia, Hypertriglyceridemia
APOC1 2 / 7 Hyperlipidemia, Lipoprotein lipase deficiency
APOE 2 / 7 Hyperlipidemia, Lipoprotein lipase deficiency
CELSR2 2 / 7 Hyperlipidemia, Lipoprotein lipase deficiency
CREB3L3 2 / 7 Hypertriglyceridemia, Infantile hypertriglyceridemia with hepatosteatosis
DOCK7 2 / 7 Hyperlipidemia, Lipoprotein lipase deficiency
FADS1 2 / 7 Hyperlipidemia, Lipoprotein lipase deficiency
FADS2 2 / 7 Hyperlipidemia, Lipoprotein lipase deficiency
GPD1 2 / 7 Hypertriglyceridemia, Infantile hypertriglyceridemia with hepatosteatosis
HAVCR1 2 / 7 Hyperlipidemia, Hypertriglyceridemia
LDLR 2 / 7 Hyperlipidemia, Lipoprotein lipase deficiency
MLXIPL 2 / 7 Hyperlipidemia, Lipoprotein lipase deficiency
NAT2 2 / 7 Hyperlipidemia, Lipoprotein lipase deficiency
NYAP2 2 / 7 Hyperlipidemia, Lipoprotein lipase deficiency
PCSK9 2 / 7 Hyperlipidemia, Lipoprotein lipase deficiency
PLTP 2 / 7 Hyperlipidemia, Hypertriglyceridemia
PPARA 2 / 7 Hyperlipidemia, Hypertriglyceridemia
PSD3 2 / 7 Hyperlipidemia, Lipoprotein lipase deficiency
SMARCA4 2 / 7 Hyperlipidemia, Lipoprotein lipase deficiency
VEGFA 2 / 7 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
ABCG8, ANGPTL4, APOB, APOC1, APOE, CYP7A1, LDLR, LIPC, LPA, LPL, PCSK9, PLTP
 KEGG 18 / 51 25.5× 2.50e-21 2.22e-18 ✓ sig.
Chylomicron remodeling
APOA5, APOB, APOE, LPL, APOC2, APOC3
 Reactome 6 / 9 48.2× 5.17e-10 6.50e-8 ✓ sig.
HDL remodeling
APOE, PLTP, CETP, APOC2, APOC3
 Reactome 5 / 10 36.2× 1.13e-7 7.79e-6 ✓ sig.
Chylomicron clearance
APOB, APOE, LDLR, LIPC
 Reactome 4 / 5 57.9× 1.74e-7 1.13e-5 ✓ sig.
NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux
ABCG8, APOC1, APOE, PLTP, CETP, ABCA1, APOC2
 Reactome 7 / 37 13.7× 6.17e-7 3.41e-5 ✓ sig.
Type I diabetes mellitus
HLA-C, HLA-DQA1, HLA-DRA, HLA-DRB1, HLA-DQB1, FASLG, INS
 KEGG 7 / 44 11.5× 2.12e-6 9.95e-5 ✓ sig.
Chylomicron assembly
APOB, APOE, APOC2, APOC3
 Reactome 4 / 9 32.2× 4.20e-6 1.77e-4 ✓ sig.
Autoimmune thyroid disease
HLA-C, HLA-DQA1, HLA-DRA, HLA-DRB1, HLA-DQB1, FASLG, IFNA2
 KEGG 7 / 54 9.4× 8.71e-6 3.18e-4 ✓ sig.
PPAR signaling pathway
APOA5, ANGPTL4, CYP7A1, LPL, PLTP, FADS2, PPARA, APOC3
 KEGG 8 / 76 7.6× 9.55e-6 3.41e-4 ✓ sig.
Assembly of active LPL and LIPC lipase complexes
ANGPTL4, LIPC, LPL, LMF1
 Reactome 4 / 11 26.3× 1.08e-5 3.78e-4 ✓ sig.
Allograft rejection
HLA-C, HLA-DQA1, HLA-DRA, HLA-DRB1, HLA-DQB1, FASLG
 KEGG 6 / 39 11.1× 1.42e-5 4.74e-4 ✓ sig.
Toxoplasmosis
HLA-DQA1, HLA-DRA, HLA-DRB1, LDLR, HLA-DQB1, HSPA1B, JAK2, AKT1, LAMC1
 KEGG 9 / 112 5.8× 2.41e-5 7.38e-4 ✓ sig.
Fat digestion and absorption
ABCG8, APOB, PLA2G12B, ABCA1, NPC1L1, SCARB1
 KEGG 6 / 43 10.1× 2.54e-5 7.71e-4 ✓ sig.
Graft-versus-host disease
HLA-C, HLA-DQA1, HLA-DRA, HLA-DRB1, HLA-DQB1, FASLG
 KEGG 6 / 45 9.6× 3.32e-5 9.56e-4 ✓ sig.
Bile secretion
ABCG8, CYP7A1, HMGCR, LDLR, ABCB1, SCARB1, UGT2B15, UGT2B17
 KEGG 8 / 90 6.4× 3.33e-5 9.59e-4 ✓ 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 ⇵
triglyceride homeostasis
APOA5, ABCG8, ANGPTL4, APOC1, APOE, GCKR, LIPC, LPL, MLXIPL, CETP, PLA2G12B, APOC2
 GO:0070328 15 / 38 44.4× 1.15e-21 2.33e-18 ✓ sig.
cholesterol homeostasis
APOA5, ABCG8, APOB, APOE, CYP7A1, LDLR, LIPC, LPL, PCSK9, CETP, PLA2G12B, ABCA1
 GO:0042632 17 / 112 17.1× 1.51e-16 1.38e-13 ✓ sig.
lipoprotein metabolic process
APOA5, APOB, APOC1, APOE, LDLR, PCSK9, ABCA1, NPC1L1, PPARA, APOC3
 GO:0042157 10 / 26 43.3× 1.09e-14 7.21e-12 ✓ sig.
chylomicron remnant clearance
APOC1, APOE, LIPC, APOC2, APOC3, LMF1
 GO:0034382 6 / 6 113× 4.49e-13 2.19e-10 ✓ sig.
cholesterol metabolic process
APOA5, APOB, APOC1, APOE, CYP7A1, HMGCR, LDLR, LIPC, PCSK9, CETP, ABCA1, INSIG2
 GO:0008203 14 / 107 14.7× 6.52e-13 3.09e-10 ✓ sig.
cholesterol efflux
APOA5, ABCG8, APOB, APOC1, APOE, ABCA1, APOC2, SCARB1, APOC3
 GO:0033344 9 / 31 32.7× 4.72e-12 1.90e-9 ✓ sig.
high-density lipoprotein particle remodeling
APOC1, APOE, LIPC, LPL, PLTP, CETP, SCARB1, APOC3
 GO:0034375 8 / 21 42.9× 6.04e-12 2.36e-9 ✓ sig.
very-low-density lipoprotein particle remodeling
APOE, LIPC, LPL, APOH, CETP, APOC2
 GO:0034372 6 / 8 84.4× 1.24e-11 4.47e-9 ✓ sig.
lipid metabolic process
ALDH1A2, ANGPTL4, APOB, APOC1, APOE, CYP26A1, CYP7A1, HMGCR, LDLR, LIPC, LPA, LPL
 GO:0006629 31 / 840 4.2× 1.25e-11 4.49e-9 ✓ sig.
triglyceride metabolic process
APOA5, APOC1, APOE, LPL, PCSK9, CETP, INSIG2, APOC3, LMF1
 GO:0006641 9 / 39 26.0× 4.67e-11 1.48e-8 ✓ sig.
reverse cholesterol transport
APOE, LIPC, CETP, ABCA1, APOC2, SCARB1, APOC3
 GO:0043691 7 / 17 46.4× 6.94e-11 2.10e-8 ✓ sig.
lipid transport
APOA5, ABCG8, APOB, APOC1, APOE, CERT1, LDLR, LPA, PLTP, CETP, ABCA6, ABCB1
 GO:0006869 15 / 189 8.9× 1.43e-10 4.01e-8 ✓ sig.
phospholipid efflux
APOA5, APOC1, APOE, ABCA1, APOC2, APOC3
 GO:0033700 6 / 13 52.0× 7.31e-10 1.71e-7 ✓ sig.
steroid metabolic process
APOB, APOE, CYP7A1, HMGCR, LDLR, PCSK9, CETP, ABCA1, INSIG2, NPC1L1, UGT2B15, UGT2B17
 GO:0008202 12 / 135 10.0× 2.91e-9 5.76e-7 ✓ sig.
cholesterol transport
APOB, LDLR, LIPC, CETP, ABCA1, NPC1L1, SCARB1
 GO:0030301 7 / 28 28.1× 3.89e-9 7.43e-7 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Hyperlipidemia Lipoprotein lipase deficiency 0.147 22 1.43e-39 5.91e-38 ✓ sig.
Hyperlipidemia Hypertriglyceridemia 0.069 11 4.80e-16 7.31e-15 ✓ sig.
Hypertriglyceridemia Lipoprotein lipase deficiency 0.135 7 5.77e-14 7.62e-13 ✓ sig.
Hypertriglyceridemia Infantile hypertriglyceridemia with hepatosteatosis 0.069 2 3.19e-6 1.71e-5 ✓ sig.
Apolipoprotein a5 deficiency Hypertriglyceridemia 0.034 1 1.82e-3 2.68e-3 ✓ sig.
Growth restriction, hypoplastic kidneys, alopecia, and distinctive facies Hypertriglyceridemia 0.034 1 1.82e-3 2.68e-3 ✓ sig.
Apolipoprotein a5 deficiency Lipoprotein lipase deficiency 0.032 1 1.95e-3 2.83e-3 ✓ sig.
congenital disorder of glycosylation, type iit Lipoprotein lipase deficiency 0.032 1 1.95e-3 2.83e-3 ✓ sig.
Growth restriction, hypoplastic kidneys, alopecia, and distinctive facies Lipoprotein lipase deficiency 0.032 1 1.95e-3 2.83e-3 ✓ sig.
Apolipoprotein a5 deficiency Hyperlipidemia 0.007 1 9.16e-3 1.05e-2 ✓ sig.
congenital disorder of glycosylation, type iit Hyperlipidemia 0.007 1 9.16e-3 1.05e-2 ✓ sig.