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河北医学  2020, Vol. 26 Issue (6): 925-931    DOI: 10.3969/j.issn.1006-6233.2020.06.010
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食管鳞状细胞癌相关miRNA的生物信息学分析
曹诗茹, 李琰, 周荣秒, 黄茜, 霍向然, 王娜
河北医科大学第四医院分子生物学研究室, 河北 石家庄 050011
Bioinformatic Analysis on Related MiRNA of Esophageal Quamous Cell Carcinoma
CAO Shiru, LI Yan, ZHOU Rongmiao, et al
The Fourth Hospital of Hebei Medical University, Hebei Shijiazhuang 050011, China
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摘要 目的:应用生物信息学方法,分析食管鳞状细胞癌miRNA表达谱,筛选差异miRNA并预测其靶基因,分析其生物学功能。 方法:下载GEO数据库食管鳞状细胞癌miRNA表达谱芯片数据GSE114110,应用GEO2R软件对数据进行处理分析,筛选差异表达miRNA;应用GEO数据库食管鳞状细胞癌miRNA表达谱芯片数据GSE97049、GSE59973、GSE55856、GSE43732对所筛选出的差异表达miRNA进行验证;应用miRNet预测其靶基因;采用DAVID进行生物功能富集分析;通过String、Cytoscape构建靶基因的蛋白-蛋白互作网络并筛选Hub基因,进一步构建miRNA-Hub gene网络;利用starBase在线分析工具分析Hub基因的表达情况。 结果:分析GSE114110芯片数据共筛选出159个DE-miRNAs,在食管癌组织中表达上调的86个,下调的73个。预测上调幅度前三名和下调幅度前三名miRNA的靶基因1700个,它们参与癌症通路、黏着斑、p53信号通路等。在PPI网络中,靶基因连通度最高的前十名为Hub基因,如MAPK1等。通过构建miRNA-Hub gene网络,我们发现大部分Hub基因都可能被hsa-miR-196a-5p和hsa-miR-1调控。hsa-miR-1调控的7个靶基因CDC42、POLR2K、PIK3CA、POLR2I、HIST2H2AC、FN1、VEGFA的表达在ESCC组织中较正常组织明显上调, hsa-miR-1与靶基因之间存在着负相关关系。因此,显著上调的7个基因可能是下调hsa-miR-1的靶点。 结论:通过生物信息学方法分析食管鳞癌组织和正常上皮组织的差异DE-miRNAs表达,最终筛选出2个差异显著的miRNA和7个关键的Hub基因为进一步研究食管鳞癌的分子标志物和分子机制提供指导。
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关键词 食管鳞状细胞癌microRNA生物信息学分析GSE114110    
AbstractObjective: To screen the differentially expressed miRNAs(DE-miRNAs) associated with the esophageal squamous cell carcinoma (ESCC) and to analyze their biological functions by using various bioinformatics analysis tools. Methods: The expression profiles of GSE114110 were downloaded from the Gene Expression Omnibus (GEO) database; GEO2R tool was used to analyze the data and to screen DE-miRNAs; The miRNA expression profiles of esophageal squamous cell carcinoma (GSE97049, GSE59973, GSE55856 and GSE43732 )were used to verify the selected DE-miRNAs; the potential target genes were predicted by miRNet ; DAVID was introduced to perform functional annotation and pathway enrichment analysis for these potential targets of DE-miRNAs; String and Cytoscape were used to construct protein-protein interaction (PPI) network and identify the key Hub genes, and further to construct miRNA-Hub gene network; the expression of Hub genes were verified by the starBase analysis tool. Results: A total of 159 DE-miRNAs were screened out, including 86 upregulated miRNAs and 73 downregulated miRNAs in ESCC tissues compared with normal esophageal epithelia. 1700 target genes of the top three upregulated and downregulated miRNAs were predicted, and they were involved in ESCC-related pathways, such as pathway in cancer, focal adhesion and p53 signaling pathway. In the PPI network, the top 10 hub nodes with higher degrees were identified as hub genes, such as MAPK1. Through constructing the miRNA-hub gene network, we found that most of hub genes could be potentially modulated by hsa-miR-196a-5p and hsa-miR-1. The expression of target gene (CDC42,POLR2K,PIK3CA,POLR2I,HIST2H2AC,FN1,VEGFA) of hsa-miR-1 was significantly upregulated in ESCC tissue than normal tissue. There is an inverse relationship between miRNA expression and target gene expression. Thus, these significantly upregulated genes including CDC42,POLR2K,PIK3CA,POLR2I,HIST2H2AC,FN1 and VEGFA may be the most potential targets for the downregulated hsa-miR-1 in theory. Conclusion: Through bioinformatics analysis of the differentially expressed miRNAs between esophageal squamous cell carcinoma tissues and normal epithelial tissues, two DE-miRNAs and seven key hub genes were finally screened to provide theoretical guidance for further research on molecular marker screening and molecular mechanisms of ESCC.
Key wordsEsophageal squamous cell carcinoma    MicroRNA    Bioinformatics analysis    GSE114110
    
基金资助:河北省杰出青年科学基金,(编号:H2015206471)
通讯作者: 王 娜   
引用本文:   
曹诗茹, 李琰, 周荣秒, 黄茜, 霍向然, 王娜. 食管鳞状细胞癌相关miRNA的生物信息学分析[J]. 河北医学, 2020, 26(6): 925-931.
CAO Shiru, LI Yan, ZHOU Rongmiao, et al. Bioinformatic Analysis on Related MiRNA of Esophageal Quamous Cell Carcinoma. HeBei Med, 2020, 26(6): 925-931.
链接本文:  
http://www.hbyxzzs.cn/CN/10.3969/j.issn.1006-6233.2020.06.010     或     http://www.hbyxzzs.cn/CN/Y2020/V26/I6/925
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