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Comprehensive bioinformation analysis of methylated and differentially expressed genes in esophageal squamous cell carcinoma
Molecular Omics ( IF 3.0 ) Pub Date : 2019-01-24 , DOI: 10.1039/c8mo00218e Hao Peng 1, 2, 3, 4, 5 , Shasha Wang 1, 2, 3, 4, 5 , Lijuan Pang 1, 2, 3, 4, 5 , Lan Yang 1, 2, 3, 4, 5 , Yunzhao Chen 6, 7, 8, 9, 10 , Xiao-bin Cui 1, 2, 3, 4, 5
Molecular Omics ( IF 3.0 ) Pub Date : 2019-01-24 , DOI: 10.1039/c8mo00218e Hao Peng 1, 2, 3, 4, 5 , Shasha Wang 1, 2, 3, 4, 5 , Lijuan Pang 1, 2, 3, 4, 5 , Lan Yang 1, 2, 3, 4, 5 , Yunzhao Chen 6, 7, 8, 9, 10 , Xiao-bin Cui 1, 2, 3, 4, 5
Affiliation
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Differentially methylated genes (DMGs) play a crucial role in the etiology and pathogenesis of esophageal squamous cell carcinoma (ESCC). This study aimed to ascertain aberrant DMGs and pathways by comprehensive bioinformatics analysis. We downloaded the gene expression microarray of GSE51287 from the Gene Expression Omnibus (GEO). Aberrant DMGs were obtained using the GEO2R tool. Gene ontology (GO) analysis and Kyoto Encyclopedia of Gene and Genome pathway enrichment analyses were performed on selected genes by using the Database for Annotation Visualization and Integrated Discovery. A protein–protein interaction (PPI) network was constructed with the Retrieval of Interacting Genes (STRING) and visualized in Cytoscape. Then, the modules in the PPI networks were analyzed with Molecular Complex Detection, and the hub genes derived from the PPI networks were verified by using the Cancer Genome Atlas. A total of 271 DMGs, including 173 hypermethylated genes, were enriched in the biological processes of peptidyl-tyrosine phosphorylation, positive regulation of transcription from RNA polymerase II promoters, and autophosphorylation. Pathway analysis enrichment revealed cancer, PI3K-Akt, and Ras signaling pathways, and 98 hypomethylated genes were enriched in the biological processes of the immune response, extracellular matrix disassembly, and macrophage differentiation. Pathway enrichment showed rheumatoid arthritis, cytokine–cytokine receptor interaction, and toxoplasmosis. Furthermore, bioinformatics analysis indicated feasible aberrant DMGs and pathways in ESCC. The results provided valuable information on the pathogenesis of ESCC. The significant DMGs may provide novel insights into their potential predictive and prognostic value as methylation-based biomarkers for the precise diagnosis and treatment of ESCC.
中文翻译：
食管鳞状细胞癌甲基化和差异表达基因的综合生物信息分析
差异甲基化基因（DMG）在食管鳞状细胞癌（ESCC）的病因和发病机理中起着至关重要的作用。这项研究旨在通过全面的生物信息学分析来确定异常的DMG和途径。我们从Gene Expression Omnibus（GEO）下载了GSE51287的基因表达微阵列。异常DMG是使用GEO2R工具获得的。通过使用注释可视化和综合发现数据库，对选定的基因进行了基因本体论（GO）分析和《京都议定书》百科全书，并进行了基因组和基因组途径富集分析。通过检索相互作用基因（STRING）构建了蛋白质-蛋白质相互作用（PPI）网络，并在Cytoscape中可视化。然后，使用分子复合物检测对PPI网络中的模块进行分析，并使用《癌症基因组图谱》对源自PPI网络的中枢基因进行了验证。总计271个DMG（包括173个高甲基化的基因）在肽基酪氨酸磷酸化，RNA聚合酶II启动子的转录正调控和自磷酸化的生物学过程中富集了。途径分析的丰富性揭示了癌症，PI3K-Akt和Ras信号通路，在免疫反应，细胞外基质分解和巨噬细胞分化的生物学过程中，有98个低甲基化的基因得以丰富。途径富集显示类风湿性关节炎，细胞因子-细胞因子受体相互作用和弓形体病。此外，生物信息学分析表明ESCC中可行的异常DMG和途径。结果为ESCC的发病机理提供了有价值的信息。
更新日期：2019-02-13
中文翻译：
食管鳞状细胞癌甲基化和差异表达基因的综合生物信息分析
差异甲基化基因（DMG）在食管鳞状细胞癌（ESCC）的病因和发病机理中起着至关重要的作用。这项研究旨在通过全面的生物信息学分析来确定异常的DMG和途径。我们从Gene Expression Omnibus（GEO）下载了GSE51287的基因表达微阵列。异常DMG是使用GEO2R工具获得的。通过使用注释可视化和综合发现数据库，对选定的基因进行了基因本体论（GO）分析和《京都议定书》百科全书，并进行了基因组和基因组途径富集分析。通过检索相互作用基因（STRING）构建了蛋白质-蛋白质相互作用（PPI）网络，并在Cytoscape中可视化。然后，使用分子复合物检测对PPI网络中的模块进行分析，并使用《癌症基因组图谱》对源自PPI网络的中枢基因进行了验证。总计271个DMG（包括173个高甲基化的基因）在肽基酪氨酸磷酸化，RNA聚合酶II启动子的转录正调控和自磷酸化的生物学过程中富集了。途径分析的丰富性揭示了癌症，PI3K-Akt和Ras信号通路，在免疫反应，细胞外基质分解和巨噬细胞分化的生物学过程中，有98个低甲基化的基因得以丰富。途径富集显示类风湿性关节炎，细胞因子-细胞因子受体相互作用和弓形体病。此外，生物信息学分析表明ESCC中可行的异常DMG和途径。结果为ESCC的发病机理提供了有价值的信息。
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