利用转录组测序数据分析胃癌长链非编码RNA的研究

Analysis of long non-coding RNAs in gastric cancer using RNA-Seq data

目的检测长链非编码RNA(lncRNA)在胃癌中的表达,并初步分析其功能。方法 34对胃癌及癌旁正常组织的转录组测序数据从癌症基因组图谱计划(TCGA)网站下载获得。用Subread和feature Counts分析数据,获得mRNA和lncRNA的表达值。用edgeR分析获得差异表达lncRNA和与差异表达lncRNA共表达的mRNA,并作基因本体论(GO)和京都基因与基因组百科全书(KEGG)分析。结果在胃癌组织和癌旁正常组织中差异表达的lncRNA有1345个,其中在胃癌组织中表达上调758个,下调587个。共表达分析显示,1045个编码基因与lncRNA表达相关。与差异表达lncRNA共表达的mRNA涉及的GO生物学过程包括有丝分裂期、细胞分裂、DNA复制等,涉及的KEGG通路包括细胞周期、细胞粘附分子等。结论 lncRNA在胃癌和癌旁正常组织中的表达有显著差异,提示其在胃癌的发生、发展中起重要作用。

Objective To detect the expression of long non-coding RNAs（lncRNAs） in gastric cancer and analyze its function.Methods RNA-Seq data of 34 paired gastric cancer and normal adjacent tissues were downloaded from the website of the Cancer Genome Atlas（TCGA）.Subread and feature Counts were used to analyze the data.The expression of mRNAs and lncRNAs was obtained.EdgeR was utilized to identify the differentially expressed lncRNAs between gastric cancer and normal adjacent tissues.The mRNAs co-expressed with the differentially expressed lncRNAs were identified and subjected to Gene Ontology（GO） and Kyoto Encyclopedia of Genes and Genomes（KEGG） analysis.Results One thousand three hundred and forty-five lncRNAs were differentially expressed between gastric cancer and normal adjacent tissues.Among these lncRNAs,758 lncRNAs were up-regulated and 587 lncRNAs were down-regulated in gastric cancer.Coexpression analysis showed that 1045 coding genes were correlated with lncRNAs.The GO biological process terms associated with co-expressed mRNAs included mitotic nuclear division,cell division,DNA replication,etc.The KEGG pathways involved cell cycle,cell adhesion molecules,etc.Conclusion The expression of lncRNAs in gastric cancer changes significantly compared with normal adjacent tissues,suggesting lncRNAs may play important roles in development and progression of gastric cancer.