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. 2016 Jan 17;44(4):1514–1524. doi: 10.1093/nar/gkw007

Figure 2.

Figure 2.

Difference of TCDS in genes sensitive to high negative supercoiling (hyp) and DNA relaxation (rel) in Escherichia coli. The z-score of the difference of the median of TCDS in hyp and rel genes (medianTCDS(hyp)-medianTCDS(rel)) is plotted on the z-axis. z-scores are based on the TCDS bias between hyp and rel genes relative to the bias for random gene sets. The z-score is coded in color and height. A z-score larger than 2 or smaller than −2, indicating a significant deviation from randomness, is color-coded in red and blue respectively. Hence, a blue color indicates a significantly more negative TCDS at promoters preferring high negative supercoiling than at promoters preferring relaxation. The opposite holds for a red color. The time axis indicates the 43 different time steps spanning from inoculation (0) over exponential phase (≤120) to stationary phase (≥360) The TCDS axis shows the TCDS decay parameter of the mathematical model. The longer the TCDS range the slower the decay with distance. At the indicated range the TCDS reaches 1% of its initial strength. The blue cleft spans to ∼15 kb and has its minimum (highest significance) around 10 kb.