基于GEO数据库的2型糖尿病骨骼肌差异表达基因生物信息学分析  

Bioinformatics analysis of differentially expressed genes of skeletal muscles in patients with T2DM based on GEO database

作　　者：刘静[1] 鲁明[2] 李春惠 刘志红[1] LIU Jing;LU Ming;LI Chunhui(Department of Endocrinology,The Second Hospital of Hebei Medical University,Hebei,Shijiazhuang 050000,China;不详)

机构地区：[1]河北医科大学第二医院内分泌科,石家庄市050000 [2]河北医科大学第二医院医务处,石家庄市050000

出　　处：《河北医药》2022年第6期810-814,共5页Hebei Medical Journal

基　　金：河北省医学科学研究重点课题计划(编号:20211154)。

摘　　要：目的通过采用生物信息学的方法筛选2型糖尿病(type 2 diabetes,T2DM)的差异表达基因,并探索与之发生相关的潜在靶点,为T2DM的诊治提供新思路。方法从GEO(gene expression omnibus,GEO)数据库下载GSE29221基因芯片,利用GEO2R在线工具筛选出T2DM患者与健康人群骨骼肌组织的差异表达基因(adj.P<0.01,logFC绝对值>1)。用DAVID在线工具及STRING在线网站对差异表达基因(differentially expressed genes,DEGs)分别进行功能富集分析和蛋白质互作网络分析,并使用Cytoscape 3.8.0软件筛选关键基因。结果经筛选得到116个DEGs,其中上调DEGs 19个,下调DEGs 97个。基因本体分析提示DEGs在生物过程主要富集于细胞外基质组织、细胞外结构组织、细胞基质黏附等;在细胞组成方面主要富集于细胞外基质、细胞外基质成分、内质网等;在分子功能主要富集于细胞外基质结构成分、纤连蛋白结合、整合素结合等。通路分析提示,DEGs主要富集于PI3K-Akt信号通路、糖尿病并发症中的AGE-RAGE信号通路、AMPK信号通路等。利用Cytoscape筛选出10个关键基因,分别是COL1A1、THBS2、TIMP2、CD44、BGN、FBLN1、FMOD、SPARC、THBS1、VEGFA。结论T2DM中的DEGs与疾病的发生发展相关,通过生物信息学分析可以发现2型糖尿病发展过程中新的生物学过程。Objective To screen the differentially expressed genes in patients with type 2 diabetes mellitus(T2DM),and to explore the potential targets related to T2DM,so as to provide new ideas for the prevention and treatment of T2DM.Methods The gene chip GSE29221 was downloaded from gene expression omnibus(GEO)database,and the differentially expressed genes in skeletal muscle tissues in patients with T2DM and healthy subjects were screened by GEO2R online analysis tool(adj.P<0.01,absolute value of logFC>1).DAVID online database and STRING website were used for enrichment analysis and protein-protein interaction(PPI)analysis of differentially expressed genes(DEGs)respectively,and Cytoscape 3.8.0 software was used to construct PPI network diagram and hub genes.Results A total of 116 DEGs were screened,including 19 up-regulated genes and 97 down-regulated genes.Gene ontology analysis showed that DEGs were mainly enriched in extracellular matrix organization,extracellular structure organization,and cell-substrate adhesion in the biological process.In the cell composition,which were mainly concentrated in collagen-containing extracellular matrix,basement membrane,and endoplasmic reticulum;in molecular function,which were mainly enriched in extracellular matrix structural constituent,fibronectin binding,integrity binding.Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed that DEGs were significantly concentrated in PI3K-Akt signaling pathway,and AGE-RAGE signaling pathway in diabetic complications,and AMPK signaling pathway.And the 10 hub genes were screened by using Cytoscape,which were COL1A1,THBS2,TIMP2,CD44,BGN,FBLN1,FMOD,SPARC,THBS1,VEGFA,respectively.Conclusion DEGs in T2DM are closely correlated with the occurrence and development of T2DM,and bioinformatics analysis can find the new biological process in the pathogenesis and development of T2DM.

关 键 词：2型糖尿病 生物信息学分析 GEO数据库 差异表达基因 

分 类 号：R587.1[医药卫生—内分泌]