Uses and pitfalls of microarrays for studying transcriptional regulation

Microarrays provide a powerful new tool for understanding the regulation of gene expression in bacteria. Many recent publications have used microarrays for identifying regulon members and stimulons that describe the complex organismal responses to environmental perturbations. The use of bioinformatics to identify DNA binding sites of transcription factors greatly facilitates the interpretation of these experiments. Understanding the transcriptome of an organism includes identifying all transcripts and mapping their 5′ and 3′ ends. High-density oligonucleotide arrays have enabled the identification of many new transcripts, including small RNAs and antisense RNAs.