基于生物信息学筛选活动性结核差异基因和验证  

Bioinformatics-based screening of differential genes for active tuberculosis and validation

作　　者：马庆庆[1] 龚亚东[1] 刘木波 韩晓静 陈云华 唐竹 MA Qingqing;GONG Yadong;LIU Mubo;HAN Xiaojing;CHEN Yunhua;TANG Zhu(Central Laboratory,Guizhou Aerospace Hospital,Zunyi,Guizhou 563000,China)

机构地区：[1]贵州航天医院中心实验室,贵州遵义563000

出　　处：《现代医药卫生》2022年第3期400-405,共6页Journal of Modern Medicine & Health

基　　金：贵州省遵义市科学技术基金资助项目(遵市科合社字〔2018〕30号;遵市科合支撑NS〔2019〕6号;遵市科人才〔2021〕8号)。

摘　　要：目的基于生物信息学方法探究结核病患者基因表达差异和生物学过程改变,为结核病的诊治提供依据。方法2021年3月搜索美国国立生物技术信息中心的基因表达数据库中结核病相关基因芯片,下载GSE29536与GSE42834芯片数据。使用GEO2R与bioinformatics在线分析差异基因。利用R语言包进行基因本体功能分析与京都基因与基因组百科全书(KEGG)通路富集。利用STRING数据库分析蛋白相互作用,应用Cytoscape软件分析关键(hub)基因。结果获得差异基因166个,包括114个上调基因和52个下调基因;主要富集在防御病毒、免疫反应、先天免疫反应等生物过程;介导蛋白质结合、腺苷三磷酸结合等分子功能;富集在细胞质、胞质溶胶、质膜等组成部分及线粒体等细胞组分。KEGG通路主要富集在甲型流行性感冒、单纯疱疹、麻疹等信号通路。信号传导及转录活化因子1(STAT1)、ISG15、OAS1表达上调,差异均有统计学意义(P<0.05)。结论STAT1、CXCL10、干扰素调节因子7、ISG15、IFIH1、IFIT1、IFIT3、GBP1、OAS1、OAS2为结核病患者最相关特征基因,免疫反应、防御病毒等信号通路与结核病密切相关,STAT1、ISG15、OAS1表达上调,为后续研究提供了重要思路。Objective To explore the differences in gene expression and altered biological processes in patients with tuberculosis based on bioinformatics methods,and to provide a basis for the diagnosis and treatment of tuberculosis.Methods The National Center for Biotechnology Information′s Gene Expression Database was searched in March 2021 for tuberculosis-related gene microarrays,and GSE29536 and GSE42834 microarray data were downloaded.Differential genes were analyzed online using GEO2R and bioinformatics.R language package was used to conduct gene ontology functional analysis and kyoto encyclopedia of genomes(KEGG)pathway enrichment.Protein interactions were analyzed using the STRING database,and key(hub)genes were analyzed using the Cytoscape software.Results A total of 166 differential genes were obtained,including 114 up-regulated genes and 52 down-regulated genes.They were mainly enriched in biological processes such as defense against viruses,immune response and innate immune response,mediated molecular functions such as protein binding and adenosine triphosphate binding,and they were enriched in cytoplasm,cytosol,plasma membrane and cell components such as mitochondria.The KEGG pathway was mainly enriched in signalling pathways such as influenza A,herpes simplex and measles.Signal transducer and activator of transcription 1(STAT1),ISG15 and OAS1 expression were up-regulated,with statistically significant differences(P<0.05).Conclusion STAT1,CXCL10,interferon regulatory factor 7,ISG15,IFIH1,IFIT1,IFIT3,GBP1,OAS1 and OAS2 are the most relevant characteristic genes in TB patients.Signaling pathways such as immune response and defense against viruses are closely related to TB.Upregulation of STAT1,ISG15 and OAS1 expression provides important ideas for subsequent studies.

关 键 词：结核 计算生物学 差异基因 验证 

分 类 号：R52[医药卫生—内科学]