Characterization of differentially expressed genes involved in pathways associated with gastric cancer.
Characterization of differentially expressed genes involved in pathways associated with gastric cancer.
复制标题
胃癌相关通路中差异表达基因的表征。
DOI：
10.1371/journal.pone.0125013
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Liu B
中科院分区：
文献类型：
--
作者：
Li H;Yu B;Li J;Su L;Yan M;Zhang J;Li C;Zhu Z;Liu B
为了探索胃癌的基因表达模式，我们共收集了26对来自患者的胃癌和非癌组织进行基因表达芯片分析。采用Limma方法对数据进行分析，如果错误发现率（False Discovery Rate， FDR）值<0.01，p值<0.01，且折叠变化（fold change， FC）值为bb0.2，则认为基因存在显著差异表达。随后，利用基因本体（Gene Ontology， GO）分类分析差异表达基因的主要功能。根据京都基因与基因组百科全书（KEGG）数据库，我们发现了与差异基因显著相关的途径。根据数据库中基因、蛋白和化合物之间的关系，分别构建基因-行为网络和共表达网络。选择2371个mrna和350个lncRNAs作为显著差异表达基因进行进一步分析。GO分类、通路分析和Gene-Act网络显示一致的结果：上调基因参与肿瘤发生、迁移、血管生成和微环境形成，下调基因参与代谢。本研究结果在胃癌的编码rna、lncRNAs、通路及共表达网络等方面提供了一些新的发现，对指导胃癌的进一步研究和靶向治疗具有重要意义。
To explore the patterns of gene expression in gastric cancer, a total of 26 paired gastric cancer and noncancerous tissues from patients were enrolled for gene expression microarray analyses. Limma methods were applied to analyze the data, and genes were considered to be significantly differentially expressed if the False Discovery Rate (FDR) value was < 0.01, P-value was <0.01 and the fold change (FC) was >2. Subsequently, Gene Ontology (GO) categories were used to analyze the main functions of the differentially expressed genes. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, we found pathways significantly associated with the differential genes. Gene-Act network and co-expression network were built respectively based on the relationships among the genes, proteins and compounds in the database. 2371 mRNAs and 350 lncRNAs considered as significantly differentially expressed genes were selected for the further analysis. The GO categories, pathway analyses and the Gene-Act network showed a consistent result that up-regulated genes were responsible for tumorigenesis, migration, angiogenesis and microenvironment formation, while down-regulated genes were involved in metabolism. These results of this study provide some novel findings on coding RNAs, lncRNAs, pathways and the co-expression network in gastric cancer which will be useful to guide further investigation and target therapy for this disease.
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影响因子：
2.9
作者：
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通讯作者：
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影响因子：
4.3
作者：
Cao, Xue-Yuan;Jia, Zhi-Fang;Jiang, Jing
通讯作者：
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