A Systems Biology Approach To Disentangle the Direct and Indirect Effects of Global Transcription Factors on Gene Expression in Escherichia coli
Authors:
Open Access
- 13 April 2023
- journal article
- research article
- Published by American Society for Microbiology in Microbiology Spectrum
- Vol. 11 (2) , e0210122
Abstract
Understanding the pleiotropic effects of global TFs on gene expression and their relevance underlying a specific response in a particular environment has been challenging. Here, we distinguish the TF-driven direct effects and growth rate-mediated indirect effects on gene expression using single- and double-deletion mutants of FNR, ArcA, and IHF regulators under anaerobic glucose fermentation.Keywords
All Related Versions
Funding Information
- Department of Biotechnology, Ministry of Science and Technology, India (BT/PF13713/BBE/117/83/2015)
- Department of Science and Technology, Ministry of Science and Technology, India (SB/S3/CE/080/2015)
This publication has 75 references indexed in Scilit:
- Dissecting specific and global transcriptional regulation of bacterial gene expressionMolecular Systems Biology, 2013
- Shared control of gene expression in bacteria by transcription factors and global physiology of the cellMolecular Systems Biology, 2013
- FIMO: scanning for occurrences of a given motifBioinformatics, 2011
- Growth Rate-Dependent Global Effects on Gene Expression in BacteriaCell, 2009
- edgeR: a Bioconductor package for differential expression analysis of digital gene expression dataBioinformatics, 2009
- The Sequence Alignment/Map format and SAMtoolsBioinformatics, 2009
- Fast and accurate short read alignment with Burrows–Wheeler transformBioinformatics, 2009
- AmiGO: online access to ontology and annotation dataBioinformatics, 2008
- Functional organisation of Escherichia coli transcriptional regulatory networkJournal of Molecular Biology, 2008
- Integrating high-throughput and computational data elucidates bacterial networksNature, 2004