Bioinformatics analysis of aberrantly methylated-differentially expressed genes and pathways in hepatocellular carcinoma

doi:10.3748/wjg.v24.i24.2605

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World Journal of Gastroenterology

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1007-9327

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Baishideng Publishing Group Inc, 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA

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World J Gastroenterol. Jun 28, 2018; 24(24): 2605-2616
Published online Jun 28, 2018. doi: 10.3748/wjg.v24.i24.2605

Table 1 GO enrichment analysis of methylated-differentially expressed genes related with hepatocellular carcinoma

Category		Term	Count	%	P value
Hyper-LGs	GOTERM_BP_FAT	GO:0048545~response to steroid hormone stimulus	18	6.79	1.51E-08
	GOTERM_BP_FAT	GO:0009725~response to hormone stimulus	24	9.06	3.15E-08
	GOTERM_BP_FAT	GO:0007166~cell surface receptor linked signal transduction	60	22.64	1.75E-07
	GOTERM_BP_FAT	GO:0009719~response to endogenous stimulus	24	9.06	1.89E-07
	GOTERM_BP_FAT	GO:0007610~behavior	25	9.43	6.76E-07
	GOTERM_CC_FAT	GO:0044421~extracellular region part	48	18.11	1.97E-11
	GOTERM_CC_FAT	GO:0005886~plasma membrane	107	40.38	9.53E-10
	GOTERM_CC_FAT	GO:0005576~extracellular region	68	25.66	1.10E-08
	GOTERM_CC_FAT	GO:0044459~plasma membrane part	71	26.79	3.27E-08
	GOTERM_CC_FAT	GO:0031226~intrinsic to plasma membrane	47	17.74	1.22E-07
	GOTERM_MF_FAT	GO:0005539~glycosaminoglycan binding	11	4.15	7.78E-05
	GOTERM_MF_FAT	GO:0004714~transmembrane receptor protein tyrosine kinase activity	8	3.02	8.88E-05
	GOTERM_MF_FAT	GO:0001871~pattern binding	11	4.15	1.72E-04
	GOTERM_MF_FAT	GO:0030247~polysaccharide binding	11	4.15	1.72E-04
	GOTERM_MF_FAT	GO:0004713~protein tyrosine kinase activity	11	4.15	3.15E-04

Hypo-HGs	GOTERM_BP_FAT	GO:0006260~DNA replication	10	6.25	6.22E-05
	GOTERM_BP_FAT	GO:0051301~cell division	12	7.50	8.37E-05
	GOTERM_BP_FAT	GO:0051276~chromosome organization	15	9.38	1.41E-04
	GOTERM_BP_FAT	GO:0006259~DNA metabolic process	15	9.38	2.19E-04
	GOTERM_BP_FAT	GO:0007049~cell cycle	19	11.88	2.44E-04
	GOTERM_CC_FAT	GO:0005694~chromosome	14	8.75	3.77E-04
	GOTERM_CC_FAT	GO:0044427~chromosomal part	12	7.50	1.01E-03
	GOTERM_CC_FAT	GO:0000793~condensed chromosome	7	4.38	1.34E-03
	GOTERM_CC_FAT	GO:0000785~chromatin	8	5.00	2.77E-03
	GOTERM_CC_FAT	GO:0044421~extracellular region part	19	11.88	3.60E-03
	GOTERM_MF_FAT	GO:0030414~peptidase inhibitor activity	6	3.75	1.24E-02
	GOTERM_MF_FAT	GO:0016849~phosphorus-oxygen lyase activity	3	1.88	1.65E-02
	GOTERM_MF_FAT	GO:0009975~cyclase activity	3	1.88	1.80E-02
	GOTERM_MF_FAT	GO:0004857~enzyme inhibitor activity	7	4.38	3.53E-02
	GOTERM_MF_FAT	GO:0008092~cytoskeletal protein binding	10	6.25	3.83E-02

Top five terms were listed on the basis of P value if over five terms in the category, Hyper-LGs (hypermethylated, lowly expressed genes), Hypo-HGs (hypomethylated, highly expressed genes).

Citation: Sang L, Wang XM, Xu DY, Zhao WJ. Bioinformatics analysis of aberrantly methylated-differentially expressed genes and pathways in hepatocellular carcinoma. World J Gastroenterol 2018; 24(24): 2605-2616
URL: https://www.wjgnet.com/1007-9327/full/v24/i24/2605.htm
DOI: https://dx.doi.org/10.3748/wjg.v24.i24.2605