Using genome-wide expression compendia to study microorganisms

Alexandra J Lee; Taylor Reiter; Georgia Doing; Julia Oh; Deborah A Hogan; Casey S Greene

doi:10.1016/j.csbj.2022.08.012

Using genome-wide expression compendia to study microorganisms

Comput Struct Biotechnol J. 2022 Aug 10:20:4315-4324. doi: 10.1016/j.csbj.2022.08.012. eCollection 2022.

Authors

Alexandra J Lee¹, Taylor Reiter², Georgia Doing³, Julia Oh³, Deborah A Hogan⁴, Casey S Greene²

Affiliations

¹ Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, PA, USA.
² Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Denver, CO, USA.
³ The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
⁴ Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth, Hanover, NH, 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.

Keywords: Compendia; Machine learning; Microbiology; Transcriptomics.

Publication types

Review

Abstract

Publication types

Grants and funding