COPD相关差异表达基因筛选、生物学功能分析及其编码蛋白互作网络分析

Screening, bioinformatics analysis and protein-protein interaction network of COPD-related differentially expressed genes

目的分析慢性阻塞性肺病(COPD)患者肺组织中差异表达基因及其编码蛋白的互作关系,筛选出COPD相关的关键基因。方法从NCBI公共数据平台GEO数据库下载COPD表达谱数据集GSE57148,采用R软件及其扩展包对表达谱数据进行处理和分析,获得差异表达基因,并通过STRING、Cytoscape等对差异表达基因进行生物学功能分析及编码蛋白互作分析。结果一共获得117个基因为差异表达基因,其中发生上调的基因有63 个,发生下调的基因有54个;信号通路分析发现这些基因主要富集于细胞外基质形成、胶原纤维化形成和氧化激活通路等。蛋白网络互作分析发现VWF、FGG、IGF1、F5、RPS15、RPS12、SEC61B、THBS1、F13A1为差异表达基因中的Hub基因。结论COPD肺组织中共有117个基因差异性表达,上调表达基因63个,下调基因54个;这些差异性表达基因主要参与细胞外基质改变、纤维化和氧化还原活性等信号通路;VWF、FGG、IGF1、F5、RPS15、RPS12、 SEC61B、THBS1和F13A1为Hub基因,可能在COPD的疾病进程中发挥了关键作用。

Objective To analyze the differentially expressed genes (DEGs) and protein-protein interaction network in lung tissues of chronic obstructive pulmonary disease (COPD), and to screen out the COPD-related Rey genes. Methods Gene expression data of COPD GSE57148 was downloaded from GEO database. The expression data were processed and analyzed by R software and its extension packages to obtain DGEs, and the biological function analysis and protein-protein interaction analysis were performed by STRING and Cytoscape. Results A total of 117 significantly differentially expressed genes were found, including 63 up-regulated genes and 54 down-regulated genes. These DEGs were mainly enriched in extracellular matrix organization ( GO:0030198 ), collagen fibril organization ( GO:0030199) and oxidoreductase activity (GO:0016676). Subsequently, 9 genes including VWF, FGG, IGF1, F5, RPS15, RPS12, SEC61B, THBS1, and F13A1 , were identified from DEGs by the complex protein-protein interaction network, which were taken as the Hub genes. Conclusions There are 117 DEGs in COPD lung samples, including 63 up-regulated genes and 54 down-regulated genes, and these DEGs are mainly involved in extracellular matrix organization, collagen fibril organization and oxidoreductase activity. VWF, FGG, IGF1, F5, RPS15, RPS12, SEC61B, THBS1, and F13A1 are the Hub genes, which play a importont rol in the progression of COPD.