食管腺癌DNA拷贝变化相关基因的生物信息学分析

doi:10.3969/j.issn.1004-616x.2015.04.005

癌变·畸变·突变 ›› 2015, Vol. 27 ›› Issue (4): 278-283.doi: 10.3969/j.issn.1004-616x.2015.04.005

食管腺癌DNA拷贝变化相关基因的生物信息学分析

杜则澎, 邱晓阳, 林旋豪, 詹晓芬, 王媛媛, 王少洪, 沈金辉

汕头市中心医院病理科, 广东汕头 515041

收稿日期:2015-05-15 修回日期:2015-06-27 出版日期:2015-07-30 发布日期:2015-07-30
作者简介:杜则澎,E-mail:zepdu@126.com。
基金资助:
广东省自然科学基金项目(2014A030310390)

Bioinformatics analysis of copy number variants related genes in esophageal adenocarcinoma

DU Zepeng, QIU Xiaoyang, LIN Xuanhao, ZHAN Xiaofen, WANG Yuanyuan, WANG Shaohong, SHEN Jinhui

Department of Pathology, Shantou Central Hospital, Shantou 515041, Guangdong, China

Received:2015-05-15 Revised:2015-06-27 Online:2015-07-30 Published:2015-07-30

摘要/Abstract

摘要： 目的: 探讨食管腺癌DNA拷贝变化相关基因所涉及的功能、信号通路,蛋白-蛋白相互作用及表达相关性。方法:从3篇利用全基因组关联分析(GWAS)技术大规模分析食管腺癌临床样本的文献,收集120个食管腺癌DNA拷贝变化相关基因,进行生物信息学分析,包括基因功能富集分析,蛋白-蛋白相互作用网络的构建,表达谱聚类及表达相关性。结果:基于基因本体论的功能富集分析显示食管腺癌DNA拷贝变化相关基因最显著的功能是转录调控。信号通路富集分析富集基因数量最多的KEGG信号通路为“Pathway in cancer”。DNA拷贝变化相关基因的蛋白-蛋白相互作用网络含3 356个蛋白节点和63 474条边。该网络具有无尺度特点。利用公共的食管腺癌表达谱分析显示食管腺癌DNA拷贝变化相关基因表达谱聚类几乎能够将食管腺癌组织与正常食管组织完全区分,而且DNA拷贝变化相关基因之间在该表达谱中有显著的表达相关性。结论:本研究利用生物信息学方法,对食管腺癌DNA拷贝变化相关基因进行深入的分析,为将来实验验证这些基因在食管腺癌发生发展中的生物学功能奠定基础。

关键词: 食管腺癌, DNA拷贝变化相关基因, 功能富集, 表达相关性

Abstract: OBJECTIVE: To understand the potential functions,signaling pathways and expression correlation of copy number variants related genes in esophageal adenocarcinoma. METHODS: From three references applying genome-wide association studies to analyze large scale clinical sample of esophageal adenocarcinoma,120 copy number variants related genes were collected for bioinformatics analysis,including gene function enrichment,construction of protein-protein interaction network,clustering of expression profile and expression correlation. RESULTS: The result of functional enrichment based on Gene Ontology showed that the most significant function of copy number variants related genes in esophageal adenocarcinoma is the “regulation of transcription”. Pathway enrichment result found the pathway involved largest number of genes is “Pathway in cancer”. Protein-protein interaction network for copy number variants related genes contained 3 356 nodes and 63 474 edges. The network characterized scale-free. Using a public esophageal adenocarcinoma expression profile,the clustering of these genes can almost distinguish esophageal adenocarcinoma and normal esophageal tissue. These genes also showed significant expression correlation in esophageal adenocarcinoma. CONCLUSION: The bioinformatics analyses of copy number variants related genes in esophageal adenocarcinoma provided for a solid foundation for future experimental validation of these genes in the development of esophageal adenocarcinoma.

Key words: esophageal adenocarcinoma, copy number variants related genes, function enrichment, expression correlation

中图分类号:

Q811.4

杜则澎, 邱晓阳, 林旋豪, 詹晓芬, 王媛媛, 王少洪, 沈金辉. 食管腺癌DNA拷贝变化相关基因的生物信息学分析[J]. 癌变·畸变·突变, 2015, 27(4): 278-283.

DU Zepeng, QIU Xiaoyang, LIN Xuanhao, ZHAN Xiaofen, WANG Yuanyuan, WANG Shaohong, SHEN Jinhui. Bioinformatics analysis of copy number variants related genes in esophageal adenocarcinoma[J]. Carcinogenesis, Teratogenesis & Mutagenesis, 2015, 27(4): 278-283.

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食管腺癌DNA拷贝变化相关基因的生物信息学分析

Bioinformatics analysis of copy number variants related genes in esophageal adenocarcinoma

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