On motifs and functional modules in complex networks

Although the emergence of motifs certainly reflects functional constraints and design principles underlying complex networks, our studies on digital circuits and a transcriptional regulatory network indicate that motifs are not ¿basic¿ functional building blocks as many claimed before, since most motif instances do not represent independent units that are functionally separable from the rest of the network. We also argue that the over-representation of motifs arises not because motifs are fundamental network fragments, but as a result of (1) predesigned basic functional modules consisting of motif-clusters, and (2) cross-module connections involving buses in the circuits and global regulators in the transcriptional regulatory network.