Computational protocol: Systems-level understanding of ethanol-induced stresses and adaptation in E. coli

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Protocol publication

[…] The three NEA datasets have a total of seven treatment-versus-control pairs ( and ). The EA dataset has five evolved-versus-the-parental-strain pairs. Differential gene-expression analyses were conducted between each treatment or evolved sample and the matching control sample. For the NEA pairs, gene-expression data were analyzed using the R packages GEOquery and affy. A differentially expressed gene (DEG) between each pair of samples is defined as having a fold change in expression >1.2 or <1/1.2 for up-regulation or down-regulation in Wilcoxon signed- rank test (pā€‰<ā€‰0.05), respectively. For the EA datasets, differential expression analyses were performed between the parental strain and each of the six evolved strains, each collected at five time points during the adaptive evolution in ethanol (). For the EA samples, we used more stringent criteria for determining DEGs since there was only one control, i.e., the parental strain, versus six evolved strains: the six evolved strains must all have greater (or less) expression levels than the parent strain, and the mean difference is greater than 20% compared to the expression level in the parent strain.A pathway enrichment analysis was conducted separately over the up- and down-regulated genes using DAVID against the Gene Ontology database. […]

Pipeline specifications

Software tools GEOquery, affy
Application Transcription analysis
Organisms Bacteria, Escherichia coli
Chemicals Ethanol, Oxygen, Superoxides