基于生物信息学方法识别肾透明细胞癌发病机制相关基因  

Identification of renal clear cell carcinoma related genes based on bioinformatics

作　　者：潘宏鑫 陈述 李长福[1] 李海波[1] PAN Hong-xin;CHEN Shu;LI Chang-fu;LI Hai-bo(Department of Urology,The Third Affiliated Hospital of Harbin Medical University,Harbin 150001,China)

机构地区：[1]哈尔滨医科大学附属第三医院泌尿外科

出　　处：《哈尔滨医科大学学报》2019年第5期485-488,共4页Journal of Harbin Medical University

摘　　要：目的识别引起肾透明细胞癌(renal clear cell carcinoma,ccRCC)发病的关键基因和其生物学过程。方法分别从GEO和TCGA数据库中下载相关数据,应用R软件中的limma和EdgeR包筛选出在癌症样本和正样本中差异表达的基因(differentially expressed genes,DEGs)。然后,利用STRING数据库构建蛋白质互作(protein-protein interaction,PPI)网络,并基于网络进行模块挖掘和功能注释。结果共筛选出4 667个DEGs,构建了包含519个DEGs(节点),2 394对互作(边)的PPI网络。挖掘到的得分最高的三个模块注释到了G蛋白偶联受体信号通路、信号转导、防御反应、炎症应答、细胞迁移调控、细胞增殖与分化和神经活性配体-受体相互作用等在ccRCC的发展中有重要作用的生物学过程中。识别出与ccRCC发生发展密切相关的关键基因CA9、CDKN2A、MET、HLA-C、VEGFA、LDHA和TERT等。结论本研究筛选出的几个关键基因和功能通路可能在ccRCC的发展中起关键作用。Objective To identify the crucial genes and biological processes of renal clear cell carcinoma(ccRCC) and provide more evidence for the study of its pathogenesis. Methods The gene expression profile data and RNA-seq data of ccRCC were downloaded from GEO and TCGA databases, respectively. And the differentially expressed genes(DEGs) were screened using the limma and EdgeR packages in the R software. Then, the protein-protein interaction(PPI) network was constructed by STRING database, and the module mining and function annotation were carried out based on the network. Results A total of 4 667 DEGs were screened and the constructed PPI network contained 519 DEGs(nodes), 2 394 pairs of interaction(edges). The three modules with the highest scores were annotated to the G protein-coupled receptor signaling pathway, signal transduction, defense response, inflammatory response, cell migration regulation, cell differentiation and other GO terms related to the development of ccRCC. CA9, CDKN2 A, MET, HLA-C, HFA, LDHA and CDA were also identified as key genes of ccRCC. Conclusion The crucial genes and functional pathways screened by our method may play a key role in the development of ccRCC and of great significance to further study the biomarkers of ccRCC molecular targeted therapy.

关 键 词：ccRCC DEGs 模块挖掘 功能富集 

分 类 号：R776.1[医药卫生—眼科]