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主管单位 工业和信息化部 主办单位 哈尔滨工业大学 主编 任南琪 国际刊号ISSN 1672-5565 国内刊号CN 23-1513/Q

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引用本文:李林芝,谢君,朱乃硕.HBV感染者肝细胞样本的关键基因和信号通路的生物信息学挖掘[J].生物信息学,2018,16(4):214-221.
LI Linzhi,XIE Jun,ZHU Naishuo.Identification of key genes and signaling pathways in HBV infected liver cell samples[J].Chinese Journal of Bioinformatics,2018,16(4):214-221.
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HBV感染者肝细胞样本的关键基因和信号通路的生物信息学挖掘
李林芝,谢君,朱乃硕
(遗传工程国家重点实验室 分子免疫学实验室(复旦大学 生命科学学院),上海 200438)
摘要:
为探究乙型肝炎病毒(Hepatitis B virus,HBV)感染后肝细胞基因表达和信号通路的改变情况,从Gene Expression Omnibus(GEO)数据库中下载了HBV感染者肝细胞样本制作的基因表达谱数据集GSE83148,进行质量检测、数据标准化后筛选出差异表达基因,进一步做GO和KEGG富集分析以及基因网络相互作用分析,筛选关键基因和信号通路。从HBV感染样本中筛选出fold change≥2,p-value<0.05的上调差异表达基因44个,GO分析获得关键基因BAK1和TP63,差异表达基因网络互作获得5个位于枢纽位置的基因:NDUFS1、NDUFS2、COX7B、ATP5B、OPA1。KEGG分析获得关键信号通路有:乙型肝炎信号通路、病毒癌变信号通路、FoxO信号通路、PI3K-Akt信号通路。本研究筛选出的多数基因与线粒体和氧化呼吸链有关,造成这一现象的具体机制还需进一步探究。
关键词:  HBV  差异表达基因  关键基因  关键信号通路
DOI:10.12113/j.issn.1672-5565.201804003
分类号:R711.22
文献标识码:A
基金项目:国家自然科学基金(No. 31370927).
Identification of key genes and signaling pathways in HBV infected liver cell samples
LI Linzhi , XIE Jun, ZHU Naishuo
(Lab of Molecular Immunology, State Key Lab of Genetic Engineering (School of Life Sciences, Fudan University), Shanghai 200438,China)
Abstract:
In order to explore the key genes and signaling pathways in HBV-infected liver cells, we downloaded genes expression profile data GSE83148 from the Gene Expression Omnibus (GEO) database and conducted a series of studies. Differentially expressed genes were screened out after quality testing and data normalization, GO and KEGG enrichment analysis and gene network interaction analysis were further performed to select key genes and signaling pathways. In this study, 44 up-regulated differentially expressed genes that fold change ≥2 and p-value<0.05 were screened out from HBV-infected sampe group. Key genes BAK1 and TP63 were obtained by GO analysis. From GeneMANIA analysis, we obtained five genes located in the hub: NDUFS1, NDUFS2, COX7B, ATP5B, and OPA1. The key signaling pathways obtained by KEGG analysis were as follows: hepatitis B signaling pathway, viral cancerous signaling pathway, FoxO signaling pathway, and PI3K-Akt signaling pathway. Most genes selected in this study are related to mitochondria and oxidative respiratory chain, but the specific mechanisms that cause this phenomenon need further exploration.
Key words:  HBV  Differentially expressed genes  Key genes  Key signaling pathways

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