We apply the methodology to E. coli as it is believed to have the most well understood TRN; therefore it serves as an excellent test case. However, out of roughly 4300 genes and around 300 predicted TFs [1], the current E. coli TRN includes only 984 genes and 144 TFs. Hence, it is clear that we only know a fraction of the network. According to Babu and Teichmann three-quarters of the TFs are two-domain proteins, i.e., DNA-binding domain and regulatory domain (mostly for small molecules), showing the importance of TFs in adapting to environmental conditions [1]. Like most biological interaction networks, the E. coli network seems to follow a power law (scale free) distribution, suggesting that TRNs tend to be connected among high-degree nodes and low-degree ones [2]. Another important property of TRNs is the statistically overrepresented network motifs. Shen-Orr et al. showed that the feed forward motif (two TFs co-regulating one gene and one TF regulating the other) is overrepresented by a factor of 8 in the known E. coli TRN [3]. These studies advance our understanding of design principles in bacterial TRNs. However, they do not have a direct impact on the construction of TRNs.