Functional Transcriptomics for Bacterial Gene Detectives


Perez-Sepulveda, Blanca M and Hinton, Jay CD ORCID: 0000-0003-2671-6026 (2018) Functional Transcriptomics for Bacterial Gene Detectives. MICROBIOLOGY SPECTRUM, 6 (5).

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Abstract

Developments in transcriptomic technology and the availability of whole-genome-level expression profiles for many bacterial model organisms have accelerated the assignment of gene function. However, the deluge of transcriptomic data is making the analysis of gene expression a challenging task for biologists. Online resources for global bacterial gene expression analysis are not available for the majority of published data sets, impeding access and hindering data exploration. Here, we show the value of preexisting transcriptomic data sets for hypothesis generation. We describe the use of accessible online resources, such as SalComMac and SalComRegulon, to visualize and analyze expression profiles of coding genes and small RNAs. This approach arms a new generation of "gene detectives" with powerful new tools for understanding the transcriptional networks of <i>Salmonella</i>, a bacterium that has become an important model organism for the study of gene regulation. To demonstrate the value of integrating different online platforms, and to show the simplicity of the approach, we used well-characterized small RNAs that respond to envelope stress, oxidative stress, osmotic stress, or iron limitation as examples. We hope to provide impetus for the development of more online resources to allow the scientific community to work intuitively with transcriptomic data.

Item Type: Article
Uncontrolled Keywords: Salmonella, Iron, Gene Expression Profiling, Stress, Psychological, Computational Biology, Gene Expression Regulation, Bacterial, Oxidative Stress, Genes, Bacterial, Osmotic Pressure, Databases, Genetic, Online Systems, Gene Regulatory Networks, Transcriptome
Depositing User: Symplectic Admin
Date Deposited: 30 Sep 2019 09:38
Last Modified: 24 Jan 2024 13:13
DOI: 10.1128/microbiolspec.RWR-0033-2018
Open Access URL: http://asmscience.org/content/journal/microbiolspe...
Related URLs:
URI: https://livrepository.liverpool.ac.uk/id/eprint/3051346

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