Schematic representation of the involved processes and biological elements in the integrative metabolic-regulatory <i>E. coli</i> network.

Gene regulatory processes primarily comprise genes (yellow circles) and several proteins (monomers (brown triangles) as well as complexes (gray triangles)), mainly transcription factors. In contrast, metabolic processes are predominantly defined by small molecules (blue squares) and the catalyzing biochemical reactions (green hexagons). The interactions between regulatory and metabolic processes can be mainly characterized by proteins (also modified proteins (purple triangles)) serving as enzymes and regulators, respectively. The symbols are also explained in Fig 2. While regulatory links are represented as dashed lines, the encoding and reaction-associated links are shown as solid lines. Note that this scheme does not cover all aspects of the biological categories and their classification (see Methods for details).