Document Type

Article

Publication Date

1-1-2022

Publication Title

Computational and structural biotechnology journal

Keywords

JGM, Compendia, Machine learning, Microbiology, Transcriptomics

JAX Source

Comput Struct Biotechnol J . 2022 Aug 10:20:4315-4324.

Volume

20

First Page

4315

Last Page

4324

ISSN

2001-0370

PMID

36016717

DOI

10.1016/j.csbj.2022.08.012

Grant

This work was supported by grants from the Gordon and Betty Moore Foundation (GBMF4552 to CSG) and Cystic Fibrosis Founda- tion (HOGAN19GO to DAH and GREENE21GO to CSG).

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.

Comments

This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

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