基于NCBI基因表达综合数据库筛查胃癌关键基因和信号通路的分析

doi:10.3969/j.issn.1673-8640.2018.03.013

摘要/Abstract

摘要： 目的利用生物信息学方法筛选胃癌相关的关键基因以及参与的信号通路,初步探索胃癌发生、发展的相关指标。方法以美国国立生物技术信息中心（NCBI）基因表达综合数据库（GEO）的胃癌相关芯片数据,利用GEO2R分析平台筛选出胃癌组织和对照组织表达有显著差异的基因。对这些差异基因进行基因本体（GO）生物过程分析和京都基因与基因组百科全书（KEGG）通路分析。利用卡普兰—迈尔—绘图仪（KM-Plotter）分析关键基因对胃癌患者生存时间的影响。结果在3个胃癌数据集中共筛选出1 480个差异基因,其中上调基因879个,下调基因601个。对表达有差异的基因进行信号通路和生物功能分析,鉴定发现主要集中于细胞色素P450家族、葡萄糖醛酸转移酶家族等基因簇。进一步分析这些关键基因,新发现ALDH3A1、NEUROD1等基因与胃癌的发生、发展密切相关。根据这些关键基因表达水平的高低对胃癌患者进行分组,2个组患者生存时间差异有统计学意义（P<0.05）。结论建立的整合基因组学分析方法筛选出了新的胃癌发生、发展关键基因,该方法为胃癌研究提供了有价值的信息,为进一步的功能研究提供了依据。

关键词: 基因表达综合数据库, 生物信息学分析, 信号通路, 胃癌

Abstract:

Objective To identify the key gastric cancer-related genes and signaling pathway,and to analyze the parameters in the development of gastric cancer. Methods The gastric cancer-related data from the National Center for Biotechnology Information （NCBI）Gene Expression Omnibus （GEO） were downloaded. The genes of gastric cancer tissue and control tissue were screened by GEO2R analysis platform. The Gene Ontology （GO） and the Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway were performed. The influence of key genes on the survival of patients with gastric cancer was analyzed by Kaplan Meirer Plotter（KM-Plotter）. Results Based on 3 large-scale human gastric cancer datasets,1 480 differenced genes,including 879 up-regulated genes and 601 down-regulated genes, were identified. Through the analysis of GO and KEGG pathway,the differenced genes mainly enriched on cytochrome P450 family,glcuronyl transferase family and other gene clusters. Furthermore,ALDH3A1 and NEUROD1 were deemed the most important genes being related to the progression of gastric cancer. According to the expression of the important genes,there was statistical significance for survival time between high and low expression（P<0.05）. Conclusions This study demonstrates the value of using genetic data from large-scale datasets for key gastric cancer-related genes,which provides a reference for future research.

Key words: Gene Expression Omnibus, Bioinformatics analysis, Signaling pathway, Gastric cancer

中图分类号:

R446.1

张鹏, 罗琴, 汪婷婷, 袁向亮, 沈立松. 基于NCBI基因表达综合数据库筛查胃癌关键基因和信号通路的分析[J]. 检验医学, 2018, 33(3): 242-247.

ZHANG Peng, LUO Qin, WANG Tingting, YUAN Xiangliang, SHEN Lisong. Key gastric cancer-related genes and signaling pathway based on NCBI Gene Expression Omnibus[J]. Laboratory Medicine, 2018, 33(3): 242-247.

图/表 4

参考文献 17

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分类	主要基因
细胞色素P450家族	CYP2C18、CYP2C9、CYP3A4、CYP3A5、CYP2C19
葡萄糖醛酸转移酶家族	UGT1A5、UGT1A3、UGT1A8、UGT1A9、UGT2B15
胶原蛋白家族	COL10A1、COL12A1、COL1A1、COL11A1、COL1A2、COL8A1、COL4A1
醛酮还原酶家族	AKR1、AKR1C2、AKR1C1、AKR1B10、AKR7A3
醇脱氢酶家族	ADH1A 、ADH1B、ADH7
谷胱甘肽S-转移酶家族	GSTA1、GSTA3
衰老相关上皮膜蛋白家族	CLDN1、CLDN3、CLDN4、CLDN7、CLDN18
血小板反应素	THBS1、THBS2
其他基因	MMP3、IL-8、PTGS2、PLA2G2A、SST、SSTR、NEUROD1、ALDH3A1、CA2、TFF1 、 TFF2、GKN2、BGN、KCNJ15、KCNJ16、SERPINH1、SPARC、TIMP1、PRSS1、PRSS3

分类	主要基因
细胞色素P450家族	CYP2C18、CYP2C9、CYP3A4、CYP3A5、CYP2C19
葡萄糖醛酸转移酶家族	UGT1A5、UGT1A3、UGT1A8、UGT1A9、UGT2B15
胶原蛋白家族	COL10A1、COL12A1、COL1A1、COL11A1、COL1A2、COL8A1、COL4A1
醛酮还原酶家族	AKR1、AKR1C2、AKR1C1、AKR1B10、AKR7A3
醇脱氢酶家族	ADH1A 、ADH1B、ADH7
谷胱甘肽S-转移酶家族	GSTA1、GSTA3
衰老相关上皮膜蛋白家族	CLDN1、CLDN3、CLDN4、CLDN7、CLDN18
血小板反应素	THBS1、THBS2
其他基因	MMP3、IL-8、PTGS2、PLA2G2A、SST、SSTR、NEUROD1、ALDH3A1、CA2、TFF1 、 TFF2、GKN2、BGN、KCNJ15、KCNJ16、SERPINH1、SPARC、TIMP1、PRSS1、PRSS3

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