Array platforms and bioinformatics tools for the analysis of plant transcriptome in response to abiotic stress

Current microarray technologies allow high-density in situ synthesis of oligonucleotides or ex situ spotting of target molecules (cDNA) for conducting genome-wide comparative gene expression profiling studies. The avalanche of available microarray gene expression data from model plant species covering cell-related, tissue-specific, and developmental events, as well as perturbations to a variety of environmental stimuli has triggered many activities regarding the development of adequate bioinformatics tools for the analysis of these complex data sets. In this chapter we summarize the technical issues of different microarray technologies, discuss the availability of bioinformatics tools, and present approaches to extract biologically meaningful knowledge. For case studies of abiotic stress transcriptome analysis we highlight the unprecedented opportunities provided by these high-throughput technologies to understand networks of regulatory and metabolic pathway responses of plant cells to the application of abiotic stress stimuli.