  A gene expression compendium is a heterogeneous collection of gene expression
experiments assembled from data collected for diverse purposes. The widely
varied experimental conditions and genetic backgrounds across samples creates a
tremendous opportunity for gaining a systems level understanding of the
transcriptional responses that influence phenotypes. Variety in experimental
design is particularly important for studying microbes, where the
transcriptional responses integrate many signals and demonstrate plasticity
across strains including response to what nutrients are available and what
microbes are present. Advances in high-throughput measurement technology have
made it feasible to construct compendia for many microbes. In this review we
discuss how these compendia are constructed and analyzed to reveal
transcriptional patterns.
