Hierarchical modular organization map of subroutines comprising the genetic program in E. coli. Each color represents a module, while hierarchical TFs are shown in red. Black arrows indicate the regulatory interactions between hierarchical TFs. For the sake of clarity, RpoD interactions are not shown, and the megamodule is shown as a single yellow node at the bottom. However, according to our data, RpoD affects the transcription of all hierarchical TFs, except RpoE, while RpoD, RpoH, and LexA (a modular TF) could affect RpoD expression. Red rounded-corner rectangles bound hierarchical layers. The presence of five global chains of command is noted: host/free-life sensor and type 1 fimbriae (Lrp); replication, recombination, pili, and extracytoplasmic elements (Fis, Fur, H-NS, FlhDC); respiration forms (NarL); starvation stress (ArcA, RpoS); and heat shock (RpoH). Lrp appears disconnected from other hierarchical TFs because, to date, it is only known that RpoD, Lrp, and GadE (a modular TF) modulate its expression.