当前位置: X-MOL 学术BioMed Res. Int. › 论文详情
Our official English website, www.x-mol.net, welcomes your feedback! (Note: you will need to create a separate account there.)
Identification of Functional Genes in Pterygium Based on Bioinformatics Analysis
BioMed Research International ( IF 3.246 ) Pub Date : 2020-11-23 , DOI: 10.1155/2020/2383516
Yuting Xu 1 , Chen Qiao 2 , Siying He 3 , Chen Lu 4 , Shiqi Dong 1 , Xiying Wu 1 , Ming Yan 1 , Fang Zheng 2
Affiliation  

Purpose. The competing endogenous RNA (ceRNA) network regulatory has been investigated in the occurrence and development of many diseases. This research aimed at identifying the key RNAs of ceRNA network in pterygium and exploring the underlying molecular mechanism. Methods. Differentially expressed long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and mRNAs were obtained from the Gene Expression Omnibus (GEO) database and analyzed with the R programming language. LncRNA and miRNA expressions were extracted and pooled by the GEO database and compared with those in published literature. The lncRNA-miRNA-mRNA network was constructed of selected lncRNAs, miRNAs, and mRNAs. Metascape was used to perform Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses on mRNAs of the ceRNA network and to perform Protein-Protein Interaction (PPI) Network analysis on the String website to find candidate hub genes. The Comparative Toxicogenomic Database (CTD) was used to find hub genes closely related to pterygium. The differential expressions of hub genes were verified using the reverse transcription-real-time fluorescent quantitative PCR (RT-qPCR). Result. There were 8 lncRNAs, 12 miRNAs, and 94 mRNAs filtered to construct the primary ceRNA network. A key lncRNA LIN00472 ranking the top 1 node degree was selected to reconstruct the LIN00472 network. The GO and KEGG pathway enrichment showed the mRNAs in ceRNA networks mainly involved in homophilic cell adhesion via plasma membrane adhesion molecules, developmental growth, regulation of neuron projection development, cell maturation, synapse assembly, central nervous system neuron differentiation, and PID FOXM1 PATHWAY. According to the Protein-Protein Interaction Network (PPI) analysis on mRNAs in LINC00472 network, 10 candidate hub genes were identified according to node degree ranking. Using the CTD database, we identified 8 hub genes closely related to pterygium; RT-qPCR verified 6 of them were highly expressed in pterygium. Conclusion. Our research found LINC00472 might regulate 8 hub miRNAs (miR-29b-3p, miR-183-5p, miR-138-5p, miR-211-5p, miR-221-3p, miR-218-5p, miR-642a-5p, miR-5000-3p) and 6 hub genes (CDH2, MYC, CCNB1, RELN, ERBB4, RB1) in the ceRNA network through mainly PID FOXM1 PATHWAY and play an important role in the development of pterygium.

中文翻译:

基于生物信息学分析的翼状胬肉功能基因鉴定

目的。竞争性内源性 RNA (ceRNA) 网络调控已在许多疾病的发生和发展中进行了研究。本研究旨在鉴定翼状胬肉中ceRNA网络的关键RNA,并探索其潜在的分子机制。方法. 从 Gene Expression Omnibus (GEO) 数据库中获得差异表达的长链非编码 RNA (lncRNA)、microRNA (miRNA) 和 mRNA,并使用 R 编程语言进行分析。LncRNA 和 miRNA 表达由 GEO 数据库提取和汇集,并与已发表文献中的表达进行比较。lncRNA-miRNA-mRNA 网络由选定的 lncRNA、miRNA 和 mRNA 构成。Metascape 用于对 ceRNA 网络的 mRNA 进行基因本体论 (GO) 和京都基因和基因组百科全书 (KEGG) 分析,并在 String 网站上进行蛋白质-蛋白质相互作用 (PPI) 网络分析以寻找候选中心基因。比较毒物基因组数据库(CTD)用于寻找与翼状胬肉密切相关的中心基因。结果. 有 8 个 lncRNA、12 个 miRNA 和 94 个 mRNA 被过滤以构建初级 ceRNA 网络。选取一个节点度排名前 1 的关键 lncRNA LIN00472 来重构 LIN00472 网络。GO和KEGG通路富集显示,ceRNA网络中的mRNA主要通过质膜粘附分子参与同嗜性细胞粘附、发育生长、调节神经元投射发育、细胞成熟、突触组装、中枢神经系统神经元分化和PID FOXM1 PATHWAY。根据LINC00472网络中mRNA的蛋白质-蛋白质相互作用网络(PPI)分析,根据节点度排序确定了10个候选hub基因。使用CTD数据库,我们确定了8个与翼状胬肉密切相关的枢纽基因;RT-qPCR证实其中6个在翼状胬肉中高表达。结论。我们的研究发现 LINC00472 可能调节 8 个中枢 miRNA(miR-29b-3p、miR-183-5p、miR-138-5p、miR-211-5p、miR-221-3p、miR-218-5p、miR-642a- 5p、miR-5000-3p)和6个中枢基因(CDH2、MYC、CCNB1、RELN、ERBB4、RB1)在ceRNA网络中主要通过PID FOXM1 PATHWAY,在翼状胬肉的发生发展中发挥重要作用。
更新日期:2020-11-23
down
wechat
bug