A computational study of bacterial gene regulation and adaptation ...

Chapter 1: Global regulators of bacterial transcription initiationpolish summarisation. The authors of M3D have shown that for their data, this method worksbest (Faith et al. 2007). Differential expression between mid-log and stationary phase wascomputed using the limma package and p-values were adjusted using FDR.1.3.4. Mapping ChIP-chip intensities to genesFor the ChIP-chip data for Fis, IHF and H-NS, which were obtained on tiling arrays, intensityfor each probe was assigned to the mid-point coordinate of the probe. Each gene was assignedto all probes whose mid-point fell within 200 bp upstream of the transcription start sitesannotated in RegulonDB.1.3.5. Standard statistical testsStandard statistical tests used in this study are (1) Wilcoxon-Mann-Whitney test forcomparing distributions; (2) Fisher exact test for categorical data; and (3) Pearson correlationcoefficient. All p-values are reported for the appropriate one-tailed test. These computationswere performed using the R statistical package (http://www.r-project.org).31