Using genome-wide expression compendia to study microorganisms

TL;DR

This paper discusses how large, diverse collections of gene expression data from microbes can be used to understand their transcriptional responses and phenotypes at a systems level.

Contribution

It reviews methods for constructing and analyzing microbial gene expression compendia to uncover transcriptional patterns and biological insights.

Findings

Compendia reveal transcriptional responses to environmental signals.

Analysis of compendia can identify strain-specific gene regulation.

High-throughput data enables comprehensive microbial systems biology studies.

Abstract

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.