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Table 3 Results of statistically overrepresented biological processes and molecular function in set of differentially methylated genes

From: DNA methylation microarrays identify epigenetically regulated lipid related genes in obese patients with hypercholesterolemia

Description p-value Corr
p-value
N Hypermethylated Hypomethylated
a. Gene Ontology_Biological Processes
Lipid metabolic process 6.0610E−33 1.0849E−29 47 ABCG1 ACADM ACP6 ACSL6 AHRR CAV1 CPT1A ELOVL3 ELOVL5 ELOVL6 FDFT1 FDPS GPX1 GPX4 HDLBP NR1H2 LDLR LRP1 LRP5 PCSK9 PMVK RXRA SREBF1 SQLE ABCB4 ACOT1 ACOT7 ACSF2 AGPAT2 AMN CRAT CYP1B1 CYP27B1 CYP51A1 DHCR7 FASN IL6ST INSIG1 LIPA LPL LRP8 MLYCD MCAT PPARD PPARG SLC27A1 STARD3
 Regulation of lipid biosynthetic process 1.8237E−6 3.4005E−5 6 ABCG1 ACSL6 NR1H2 DHCR7 FGF19 SLC27A1
 Negative regulation of lipid biosynthetic process 6.2381E−3 2.5581E−2 2   FGF19 SLC27A1
 Fatty acid metabolic process 9.26E−17 2.37E−14 19 ACADM ACSL6 CPT1A ELOVL3 ELOVL5 ELOVL6 PPARA ACOT1 ACOT7 ACSF2 AMN CRAT FASN LIPA LPL MCAT MLYCD PPARD SLC27A1
 Cholesterol metabolic process 6.73E−19 6.02E−16 16 ABCG1 FDFT1 FDPS HDLBP LDLR PCSK9 PMVK RXRA SREBF1 SQLE CYP51A1 DHCR7 LIPA PPARD SREBF2 STARD3
 Triglyceride metabolic process 1.02E−08 4.81E−07 7 ACSL6 CAV1 CPT1A PCSK9 IL6ST LIPA LPL
 Cholesterol biosynthetic process 5.57E−07 1.49E−05 5 FDFT1 FDPS PMVK CYP51A1 DHCR7
 Regulation of cholesterol storage 8.89E−09 4.42E−07 5 ABCG1 NR1H2 PPARA LPL PPARG
 Cholesterol transport 2.01E−07 6.09E−06 6 ABCA5 ABCG1 ABCG4 CAV1 LDLR LIPA
 Cholesterol efflux 1.00E−05 1.50E−04 4 ABCA5 ABCG1 ABCG4 CAV1  
 Reverse cholesterol transport 5.57E−03 2.37E−02 2 ABCA5 ABCG1  
 Regulation of cholesterol transport 4.57E−04 3.38E−03 3 NR1H2 LRP1 PPARG
 Negative regulation of cholesterol storage 2.72E−08 1.08E−06 4 ABCG1 NR1H2 PPARA PPARG
 Fatty acid biosynthetic process 1.60E−06 3.12E−05 7 ELOVL3 ELOVL5 ELOVL6 FASN LPL MLYCD MCAT
Fatty acid transport 2.46E−08 1.05E−06 6 ACSL6 PPARA PPARD PPARG SLC25A20 SLC27A1
 Fatty acid beta-oxidation 1.22E−06 2.63E−05 5 ACADM CPT1A AMN CRAT PPARD
 Regulation of fatty acid oxidation 2.39E−06 4.32E−05 5 CPT1A PPARA MLYCD PPARG SLC25A20
 Long-chain fatty acid metabolic process 1.90E−03 1.04E−02 2 ACSL6 ACOT1
 Regulation of macrophage derived foam cell differentiation 1.52E−08 6.63E−07 6 ABCA5 ABCG1 NR1H2 PPARA LPL PPARG
 Low-density lipoprotein receptor metabolic process 4.37E−05 5.00E−04 2 PCSK9 PPARG
 Plasma lipoprotein particle remodeling 3.99E−04 3.11E−03 3 ABCA5 ABCG1 LPL
 High-density lipoprotein particle remodeling 3.77E−03 1.75E−02 2 ABCA5 ABCG1  
 Regulation of steroid metabolic process 3.09E−03 1.52E−02 3 ABCG1 FGF19 DHCR7
 Glucose homeostasis 1.17E−06 2.58E−05 5 FOXO3 NCOR2 TCF4 TCF7L2 PPARG
 Response to glucose stimulus 6.04E−05 6.47E−04 4 EP300 TCF7L2 TCF4 PPARD
 Regulation of insulin secretion 4.82E−04 3.50E−03 3 CPT1A TCF4 TCF7L2  
 Carbohydrate homeostasis 1.17E−06 2.58E−05 5 FOXO3 NCOR2 TCF4 TCF7L2 PPARG
 Regulation of response to stress 5.02E−05 5.65E−04 10 AP2A2 AP2S1 AP2M1 CAV1 GPX4 FGF19 IL6ST IRAK1 PPARG PRKACA
 Negative regulation of apoptosis 3.59E−03 1.70E−02 8 ANGPTL4 NKX2-6 SIN3A PCSK6 TCF4 TCF7L2 FGFR1 IRAK1
b. Gene Ontology_Molecular Function
 Lipid binding 2.19E−08 3.54E−06 15 ABCG1 AP2A2 AP2M1 CAV1 HDLBP PPARA RXRA S1PR4 ACOT7 ITPR1 LIPA LPL PPARD PPARG STARD3
 Receptor binding 1.99E−06 1.16E−04 19 ANGPTL4 CAV1 EP300 LRP1 IL6ST IL13 NCOA2 NCOR2 NR1H2 PCSK9 RXRA TCF4 TCF7L2 TGFB1I1 CD8A FGF19 IRAK1 LPL PPARG
 Transporter activity 1.44E−03 1.01E−02 16 ABCC1 ABCC9 ABCG1 AMN AP2A2 AP2S1 AP2M1 APC2 KCNJ6 LRP1 SLC27A1 ABCB4 FASN ITPR1 SLC25A20 STARD3
 Transcription factor binding 1.26E−08 3.54E−06 17 CTCF GATA4 EP300 LRP1 MED21 NCOA2 NCOR2 NR1H2 RXRA SIN3A TCF4 TCF7L2 TGFB1I1 NFYC MED7 PPARD PPARG
 Transcription cofactor activity 1.14E−05 4.22E−04 11 CTCF EP300 LRP1 MED21 NCOR2 NCOA2 RXRA SIN3A TGFB1I1 NFYC MED7
 Lipoprotein binding 1.21E−03 9.26E−03 3 LDLR LRP1 LRP8
  1. Analyses performed using BiNGO plugin in Cytoscape software. (a) Shows involvement of genes in biological processes and (b) in molecular function