南方医科大学学报2011，Vol.31Issue(4)：610-614,5.
微阵列数据处理平台设计与实现
Design and realization of a microarray data analysis platform
摘要
Abstract
Objective To design a platform for microarray data analysis and processing in the browser/server mode running in Linux operating system. Methods Based on the Apache HTTP server, the platform, programmed with Perl language, integrated R language and Bioconductor packages for processing and analysis of the input data of oligonucleotide arrays and two-color spotted arrays. Users were allowed to submit data and parameter configurations to the platform via the web page, and the results of analysis were also returned via the web page. Results With an easy operation and high performance, the platform fulfilled the functions of processing, quality assessment, biological annotation and statistical analysis of the data from oligonucleotide arrays and two-color spotted arrays. Using the platform, we analyzed the gene expression profiles in Mtb-stimulated macrophages of three clinical phenotypes, namely latent TB (LTB), pulmonary (PTB) and meningeal (TBM), and obtained valuable clues for identifying tuberculosis susceptibility genes. We also analyzed the effect of INH treatment on Mycobacterium tuberculosis gene expression in various dormancy models, such as hypoxia and KatG mutant, and found that a set of genes responded to INH treatment during exponential growth but not in dormancy, and that the overall number of differentially regulated genes was reduced in the cells in low metabolic state. Conclusion The platform we have constructed integrates comprehensive resources, and with a user-friendly interface, allows direct result visualization to facilitate microarray data analysis.关键词
微阵列/生物信息学/寡核苷酸微阵列/双色点样微阵列/R语言/Bioconductor/结核分支杆菌/结核性脑膜炎/异烟肼Key words
microarray/ bioinformatics/ oligonucleotide arrays/ two-color spotted arrays/ R language/ bioconductor/ Mycobacterium tuberculosis/ tuberculous meningitis/ isoniazid分类
生物科学引用本文复制引用
孙显赫,郭云波,刘娜,马骊,邓亲恺..微阵列数据处理平台设计与实现[J].南方医科大学学报,2011,31(4):610-614,5.基金项目
国家重大科技专项资助(2008ZX10003013-02) （2008ZX10003013-02）
