## 9 Temporal Expression Patterns of Regulons and Couplons
Pearson correlations (ordinate) between the temporal expression of FIS regulon, FIS/RpoD couplons and FIS/ASF couplons (FIS/RpoS and FIS/RpoH, as indicated on abscissa). **(C,D)**. The same as in (**A**,**B**), but for H-NS regulon and couplons. **(E,F**), the same as in (**A**,**B**) but for Lrp regulon and couplons. Note the high positive correlation between the temporal expression of NAP regulons and NAP/RpoD couplons but not the NAP/ASF couplons. Plots **A**, **C** and **E**, data from [29]. The expression patterns of _fis_, _lns_ and _lrp_ genes in **A**, **C** and **E** respectively) are indicated by grey dashed lines. fis/+, hns/+ and lrp/+ respectively indicate the FIS, H-NS and Lrp regulons. Numbers in squared brackets indicate the minimum and maximum of the regulon/couplon before normalization to [0;1]. Note, that these numbers are averages of the regulon/couplon genes already normaized individually to [0;1]. Numbers in round brackets indicate the number of genes involved in the respective regulon or couplon. The _Escherichia coli_ CSH50 overnight (16 h) cultures were inoculated at an initial OD600 of 0.1 in rich double yeast-tryptone (dYT) medium and grown in a fermenter under constant pH 7.4 and high aeration (5 L air per min) at 37 \({}^{\circ}\)C for 7 h. Samples for RNA-seq were taken at 1, 2, 3, 5 and 7 h after inoculation and immediately dissolved in ice-cold ethanol-phenol (5% phenol) solution to prevent mRNA degradation. RNA was extracted using the RNeasy Mini kit (Qiagen, Hilden Germany) and treated with Turbo DNase (Life Technologies, Carlsbad USA). Subsequent rRNA depletion was carried out using the MicroB Express kit (Life Technologies) and 0.5 ug of enriched mRNA of each sample were subjected to RNA-seq (Illumina HiSeq 2000). Figure 7: Correlation between the temporal expression of ASF regulons and couplons. (**A**). Growth phase-dependent expression of the RpoS regulon and RpoS/NAP couplons. The colored curves were computed as described in the legend to Figure 6. Abscissa—time in minutes after inoculation of cells in fresh growth medium; ordinate—relative frequency of each class of genes as indicated in the inset. (**B**). Pearson correlations (ordinate) between the temporal expression of RpoS regulon, RpoS/NAP and RpoS/global TF (CRP and Fnr) couplons (as indicated on the abscissa). (**C**,**D**). The same as in (**A**,**B**), but for the RpoN sigma factor. Note the high positive correlation between the temporal expression of both ASF (RpoS and RpoN) regulons and that of NAP/ASF and global TF/ASF couplons. The expression patterns of _rpoS_ and _rpoN_ genes (in **A** and **C**, respectively) are indicated by grey dashed lines. rpoS/+ and rpoN/+ respectively indicate the RpoS and RpoN regulons. Numbers in squared brackets indicate the minimum and maximum of the regulon/couplon before normalization to [0;1]. Note, that these numbers are averages of the regulon couplon genes already normalised individually to [0;1]. Numbers in round brackets indicate the number of genes involved in the respective regulon or couplon The experimental procedure was as described in the legend to Figure 6 (plots **A** and **C**, data from [29]). Figure 8: The temporal regulon/couplon correlation patterns for IHF and global TFs. (**A**). Pearson correlation between the expression of IHF regulon, IHF/RpoD and IHF/ASF couplons. (**B**,**C**), the same as in (**A**), but for CRP and Fnr, respectively Note that the couplon patterns show positive correlation with those of IHF and global TFs irrespective of the involved sigma factor (data from [29]). Figure 9: Correlation between the expression patterns of regulators and their cognate regulons. (**A**). Pearson correlation (ordinate) between the expression of NAP genes and their corresponding regulons. Individual regulators for which the correlations between cognate gene/regulon expression were calculated are indicated on the abscissa. (**B**). Pearson correlation between the expression of sigma factor genes and their corresponding regulons (data from [29]).