基于TCGA数据库的胆囊癌关键基因及预后基因的挖掘与分析<sup>★</sup>

doi:10.3969/j.issn.2095-1264.2023.02.09

首页 > 过刊浏览>2023年第2期 >187-193. DOI:10.3969/j.issn.2095-1264.2023.02.09

基于TCGA数据库的胆囊癌关键基因及预后基因的挖掘与分析★
DOI:
                        10.3969/j.issn.2095-1264.2023.02.09
                    
作者:
                        
                        
                    
作者单位:中南大学湘雅医学院附属株洲医院 肝胆胰脾外科，湖南 株洲，412007
作者简介:徐涛，男，副主任医师，研究方向：肝胆胰疾病。
通讯作者:赵志坚，男，硕士，主任医师，研究方向：肝胆胰疾病。
中图分类号:R735.8
基金项目:★湖南省科技计划项目经费资助（2016SK4006）；株洲市科技局计划项目（20215506）。

Explore and analyze the hub genes and prognostic genes of gallbladder cancer based on TCGA database^★

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Affiliation:

Department of Hepatobiliary and Pancreatosplenic Surgery, the Affiliated Zhuzhou Hospital of Xiangya School of Medicine, Central South University, Zhuzhou, 412007, Hunan, China

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摘要:

目的通过TCGA数据库深入挖掘胆囊癌发生的关键基因，寻找胆囊癌的预后基因。方法从癌症基因组图谱（TCGA）数据库中下载胆囊癌及癌旁正常组织转录组数据，采用R软件中的edgeR包对数据进行差异表达分析，将获取的差异表达基因进行GO和KEGG富集分析，并通过STRING在线生物信息学工具构建蛋白质-蛋白质相互作用（PPI）网络，通过Cytoscape软件进行关键基因筛选，利用R软件中的survival包对关键基因进行生存预后分析。结果共获取胆囊癌差异表达基因1 766个，其中上调基因1 172个，下调基因594个。差异基因主要富集于环氧酶P450途径、细胞器膜、四烯酸环氧酶活性和代谢途径。构建PPI网络，获取10个关键基因，分别是BUB1、BUB1B、CDK1、UBE2C、KIF2C、AURKB、CDC20、KIF23、CCNB2和KIF20A。生存分析显示，KIF23与胆囊癌的预后显著相关。结论基于TCGA数据库挖掘出10个胆囊癌关键基因，有助于深入了解胆囊癌的发生发展过程，KIF23有可能成为胆囊癌潜在的治疗靶点及预后标志物。

Abstract:

Objective To explore the hub genes of gallbladder cancer occurrence through TCGA database, and to search for prognostic genes of gallbladder cancer.Methods Download the transcriptome data of gallbladder cancer and normal tissues from the Cancer Genome Atlas (TCGA) database. Use the edgeR package in R software to analyze the differential expression of the data and obtain the differentially expressed genes for GO and KEGG enrichment analysis, and construct protein-protein interaction (PPI) network through STRING online bioinformatics tools. Cytoscape software was applied for the screening of hub genes, and the survival package in R software was applied for the survival prognosis analysis of these hub genes.Results A total of 1 766 differentially expressed genes in the gallbladder were obtained, including 1 172 up-regulated genes and 594 down-regulated genes. The differentially expressed genes were mainly enriched in cyclooxygenase P450 pathway, organelle membrane, arachidonic acid cyclooxygenase activity and metabolic pathway. The PPI network obtained 10 hub genes, namely BUB1, BUB1B, CDK1, UBE2C, KIF2C, AURKB, CDC20, KIF23, CCNB2, and KIF20A. Survival analysis showed that KIF23 was significantly associated with the prognosis of gallbladder cancer.Conclusion The 10 hub genes of gallbladder cancer mined on the base of TCGA database will help to understand the development process of gallbladder cancer. KIF23 may become a potential therapeutic target and prognostic marker for gallbladder cancer.