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Updated: Aug 30, 2025

Gene Expression Profiling of Infecting Microbes Using a Digital Bar-coding Platform
Published on: January 13, 2016
Using genome-wide expression compendia to study microorganisms
Alexandra J Lee1, Taylor Reiter2, Georgia Doing3
1Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, PA, USA.
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.
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