Figure 2.

Expression profiles of relaxation-induced and repressed genes. The figure shows a cluster diagram ordered according to the p-value of each gene (from 0.000125 to 0.05). Each row represents a gene and each column an experiment. Therefore, each of the entries of the array shows the expression level for a gene in a given experiment. (a) Relaxation-repressed genes; (b) relaxation-induced genes. The set of experiments labeled 1 to 14, to the left of the vertical mark in (a and b), represents the control set in which plasmid supercoiling did not change. Experiments to the right of the vertical mark, labeled from 15 to 35, are experiments in which the chromosome is relaxed. As experiments were done in a time-dependent fashion, red color means that gene expression is higher at time points after relaxation of the chromosomes, while green means the opposite. Black indicates no change in expression during the experiment. Columns 1-5, gene expression measured after addition of 15 μg/ml norfloxacin to a norfloxacin-resistant strain at times t = 2, 5, 10, 20 or 30 min; columns 19-27, gene expression measured after addition of 15 μg/ml norfloxacin to an isogenic wild-type strain at times t = 2, 3, 4, 5, 7, 10, 15, 20 or 30 min; columns 6-10, gene expression at times t = 2, 5, 10, 20 or 30 min after addition of 50 μg/ml norfloxacin to a norfloxacin-resistant strain; columns 28-32, gene expression at these times after addition of the same concentration of norfloxacin to an isogenic wild-type strain; columns 15-18, gene expression at times t = 2, 5, 10 or 20 min after temperature shift in a temperature-sensitive mutant strain; columns 11-14, gene expression at times t = 2, 5, 10 or 20 min after temperature shift in an isogenic wild-type strain; columns 33-35, gene expression at fixed time t = 5 min and varying concentrations of novobiocin (Novo) = 20, 50 or 200 μg/ml on a wild-type strain. A total of 200 genes are repressed in response to DNA relaxation, while 106 genes are induced. The top row is a model expression profile of the supercoiling of the reporter plasmid in each experiment (Table 1). p-values and correlation coefficients with plasmid supercoiling levels for the top 10% of genes in each class are listed. The complete expression data for each gene can be found in Additional data file 2.