Properties of the reconstructed σ-factor network in Escherichia coli. (a) Extensive overlapping between σ-factor binding sites. For each σ-factor, σ70, σ38, σ54, σ32, σ28, σ24, and σ19, we identified 1,643, 903, 180, 312, 65, 51, and 7 binding regions, respectively. The number of binding regions overlapping between any two σ-factors is shown. For instance, 805 binding regions that were bound by both σ70 and σ38 were identified. (b) Number of promoters bound by multiple σ-factors showed a complex overlap between different σ-factors, indicating complicated alternative σ-factor usage. (c) A regulatory network between σ-factors in E. coli, in which σ70 and σ38 regulate expression of most of the seven σ-factors; σ70 and σ24 auto-regulate themselves. (d) Reconstruction of a three-layered network of σ-factors, transcription units (TUs), and genes. This network shows that many transcription start sites (TSSs) are shared by multiple σ-factors, suggesting possible competition between σ-factors for promoter binding. (e) Examples of thrLABC and hypBCDE-fhlA transcription units that are differently regulated by multiple σ-factors, and result in different TUs containing different sets of genes. For instance, TU001 is regulated by σ70 and contains four genes, thrLABC, while TU0005 is regulated by σ38 and had only two genes, thrB and thrC.