DNA microarrays: experimental issues, data analysis, and application to bacterial systems.
DNA microarrays are currently used to study the transcriptional response of many organisms to genetic and environmental perturbations. Although there is much room for improvement of this technology, its potential has been clearly demonstrated in the past 5 years. The general consensus is that the bottleneck is now located in the processing and analysis of transcriptome data and its use for purposes other than the quantification of changes in gene expression levels. In this article we discuss technological aspects of DNA microarrays, statistical and biological issues pertinent to the design of microarray experiments, and statistical tools for microarray data analysis. A review on applications of DNA microarrays in the study of bacterial systems is presented. Special attention is given to studies in the following areas: (1) bacterial response to environmental changes; (2) gene identification, genome organization, and transcriptional regulation; and (3) genetic and metabolic engineering. Soon, the use of DNA microarray technologies in conjunction with other genome/system-wide analyses (e.g., proteomics, metabolomics, fluxomics, phenomics, etc.) will provide a better assessment of genotype-phenotype relationships in bacteria, which serve as a basis for understanding similar processes in more complex organisms.
Dharmadi
Yandi
Y
Department of Chemical Engineering and Food Science & Human Nutrition, Iowa State University, 1035 Sweeney Hall, Ames, Iowa 50011, USA.
Gonzalez
Ramon
R
D000465:Algorithms; D018407:Bacterial Physiological Phenomena; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D004269:DNA, Bacterial / Q000032:analysis*; D003627:Data Interpretation, Statistical; D020869:Gene Expression Profiling / Q000379:methods*; D015964:Gene Expression Regulation, Bacterial / Q000502:physiology*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012107:Research Design; D017422:Sequence Analysis, DNA / Q000379:methods; D015398:Signal Transduction / Q000502:physiology*; D049490:Systems Biology / Q000379:methods; D014157:Transcription Factors / Q000378:metabolism
D001426:Bacterial Proteins; D004269:DNA, Bacterial; D014157:Transcription Factors