title: [Design and realization of a microarray data analysis platform].
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.
  
  
  CONCLUSIONS
  The platform we have constructed integrates comprehensive resources, and with a user-friendly interface, allows direct result visualization to facilitate microarray data analysis.
authors.affiliation: Institude of Bioinformatics, School of Preclinical Medicine, Southern Medical University, Guangzhou 510515, China. heather_sun@126.com
authors.forename: Xian-He
authors.initials: XH
authors.lastname: Sun
authors.forename: Yun-Bo
authors.initials: YB
authors.lastname: Guo
authors.forename: Na
authors.initials: N
authors.lastname: Liu
authors.forename: Li
authors.initials: L
authors.lastname: Ma
authors.forename: Qin-Kai
authors.initials: QK
authors.lastname: Deng
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods; D020022:Genetic Predisposition to Disease; D006801:Humans; D008264:Macrophages / Q000378:metabolism / Q000382:microbiology; D009169:Mycobacterium tuberculosis / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D012984:Software; D014376:Tuberculosis / Q000235:genetics / Q000276:immunology; D014584:User-Computer Interface