Motif clusters and superclusters. a. The 42 detected feed-forward loops join together forming six homologous motif clusters, and one isolated motif. b. The 209 bi-fan motifs coalesce into two homologous motif clusters, and one isolated motif. In (a,b) motifs which share links are shown in blue, otherwise they are colored in red. The purple cross represents nodes that were originally provided in Reference 3. c. The feed-forward- and bi-fan motif clusters together form a heterologous motif superstructure. The vertex coordinates are shown as in (b). The feed-forward motif clusters are colored as in (a). The thick lines mark the links involved in feed-forward motifs, while curved thick lines are those shared among links of feed-forward and bi-fan motifs. As in a, the flagella motor cluster (2) and the aerobic/ anaerobic switch clusters (1) are indicated. d. The connected giant component of the complete E. coli transcriptional regulatory network contains all components of the motif superstructures, colored as in (c). In panel e, we plot the cumulative connectivity distribution, P(k), for the original network (shown in Fig. 1a), and for the networks from panels 3a-d, respectively. The solid black line has an exponent γ = -1.5, and provides the best fit for the original network (black circles). The clustering distribution, C(k), as a function of connectivity for the same networks is shown in panel f. The solid black line has slope τ = -1, and is the best fit for all networks. The clustering coefficient of a node is a measure of its near-neighbors connectivity, and thus for the BF motifs this value is zero.