Significance versus correlation of gene expression and plasmid supercoiling values for all genes over all experiments. For each gene we computed the correlation coefficient between its gene expression ratios (base 2 logarithm) over all experiments with the superhelical density (σ) of a reporter plasmid, as measured by gel electrophoresis. These values are plotted against the p-value, which represents the chance that the difference in expression between relaxation and control experiments could have arisen randomly. (a) Scatter plot for all genes. There is a general trend in which genes with low p-values showed very high correlation (absolute value) between expression and plasmid supercoiling. The points corresponding to the topoisomerase genes gyrA, gyrB, topA and topB are indicated. (b) Expanded portion of (a) highlighting those genes classified as significant (p < 0.05). Genes with very low p-values show high positive or negative correlation between expression and plasmid supercoiling.
Peter et al. Genome Biology 2004 5:R87 doi:10.1186/gb-2004-5-11-r87