Preliminary modules in the reduced transcriptional regulatory network of E. coli. All the operons in the top three layers (Fig. 1b) and operons which are regulated only by them were removed to reduce the network. The weakly connected components of the reduced network were calculated and shown in different colors. Only WCCs which contain at least three nodes were considered as preliminary modules. The small WCCs which contain only two nodes were grouped at upper regulation level. The three largest WCCs were split into two preliminary modules by investigating their connectivity.