Representation and statistics of the E. coli transcriptional regulatory network. a. Graphical representation of the network. Blue diamonds represent transcription factors (TF), while the red circles denote the regulated operons. The links are color-coded according to their function: blue-activator, green-repressor, brown-activator or repressor effect. The number of the two types of elementary links, i.e., the autoregulatory loops and the directed links, is listed at the bottom of the panel. b. The top panel depicts graphical representations of (1) coherent type 1 feed-forward motif (FF), (2) incoherent type 4 FF, (3) coherent bi-fan motif (BF), and (4) incoherent BF (see Ref.  for nomenclature). The red links indicate repressors, while all other links denote activator links. Detailed statistics of the nodes (middle panel) and the two statistically significant motifs (bottom panel) found in the network. TF, transcription-factor; TF/gene, transcription-factor encoded as a single gene; TF/operon, transcription-factor encoded as part of an operon; BF/ mixed denotes those bi-fan motifs in which one node receives coherent input signals while the other node receives incoherent input signals.
Dobrin et al. BMC Bioinformatics 2004 5:10 doi:10.1186/1471-2105-5-10