Fig. 2.

Strongly connected components of the genetic network and synchronization of gene coexpression in the fibers in E. coli. (A, Top) Two-gene connected component of crp-fis. This component controls a rich set of fibers as shown. We also show the symmetry fibration collapsing the graph to the base. We highlight the fiber uxuR-lgoR which sends information to its regulator exuR and forms a 2-Fibonacci fiber $\left|{\phi }_2=1.6180..,\ell =2\right.⟩$, as well as the double-layer composite $\left|add-oxyS\right.⟩=\left|\mathrm{0,1}\right.⟩\oplus \left|\mathrm{1,1}\right.⟩$. (A, Bottom) Coexpression correlation matrix calculated from the Pearson coefficient between the expression levels of each pair of genes in A, Top. Synchronization of the genes in the respective fibers is corroborated as the block structure of the matrix. (B) The core of the E. coli network is the strongly connected component formed by genes involved in the pH system as shown. This component supports two Fibonacci fibers: 3-FF and 4-FF and fibers as shown. Open colored circles indicate genes that are in fibers and also belong to the pH component.