加权基因共表达网络分析方法挖掘TCGA数据库中与肝癌分期相关的关键基因  

Mining hub genes related to liver cancer stage in TCGA database with weighted correlation network analysis method

作　　者：李树强[1] 赵文嫣[1] 刘宝林[1] Li Shuqiang;Zhao Wenyan;Liu Baolin(Department of General Surgery,Shengjing Hospital of China Medical University,Shenyang 110004,China)

机构地区：[1]中国医科大学附属盛京医院普通外科,沈阳110004

出　　处：《中国医师进修杂志》2019年第11期974-977,共4页Chinese Journal of Postgraduates of Medicine

摘　　要：目的原发性肝癌是一类高发病率、高病死率的消化道恶性肿瘤.早期诊断困难,且术后高复发率和高转移率,预后差,因此从基因水平更好地了解肝癌的发生、发展,为以后基因治疗或靶向药物治疗提供理论基础显得尤为重要.方法使用TCGA数据库获取肝癌基因转录组数据信息及临床表型信息,利用R语言里edgeR软件包将该转录组数据进行标准化,设定log FC绝对值>1,FDR<0.01的基因为表达差异基因,然后使用加权基因共表达网络分析(WGCNA)方法分析肝癌分期与差异表达基因的关系,寻找关键基因.结果得到与肿瘤分期相关的关键基因4个(TPX2、HJURP、KIAA1524、SGO2).通过绘制Kaplan-Meier生存曲线发现,它们的表达水平与患者生存时间显著相关,高水平表达为独立预后不良因素.结论应用WGCNA的方法,对TCGA数据库信息进行挖掘,发现与肿瘤分期相关的关键基因.其中TPX2、HJURP、KIAA1524与肝癌的关系已有文献报道,但SGO2尚未报道,本研究将为肝癌的后续研究提供重要的理论依据.Objective Primary liver cancer is a kind of gastrointestinal malignant tumor with high morbidity and mortality.Early diagnosis is difficult,with postoperative high recurrence rate and high metastasis rate,poor prognosis,so it is particularly important to better understand the occurrence and development of liver cancer from the gene level,so as to provide theoretical basis for gene therapy or targeted drug therapy in the future.Methods TCGA database for liver cancer gene transcriptome data information and clinical phenotype information was downloaded,and R language edgeR package was used to standardize the transcriptome data.The log FC>1,FDR<0.01 gene was set to be expressing differences gene,and then the weighted correlation network analysis(WGCNA)methods was used to analyze the relationship between liver cancer stage(stage)and the differentially expressed genes to look for hub genes.Results Four hub genes related to tumor staging were identified(TPX2,HJURP,KIAA1524,SGO2).Kaplan-meier survival curve was drawn and it was found that their expression level was significantly correlated with patient survival time,and high expression level was an independent prognostic factor.Conclusions WGCNA method is used to mine the TCGA database information and find the hub genes related to tumor staging.The relationship between TPX2,HJURP,KIAA1524 and liver cancer has been reported in the literature,except SGO2.This study will provide important theoretical basis for the follow-up study of liver cancer.

关 键 词：肝肿瘤 数据库 加权基因共表达网络分析 数据挖掘 

分 类 号：R73[医药卫生—肿瘤]