ABSTRACT
This chapter argues that transcription networks contain recurring network motifs that perform specific functions. It examines two of these motifs in detail, negative autoregulation and the feedforward loop (FFL). The chapter discusses how the network motifs fit together to build the global structure of transcription networks. Temporal order may be generated by the action of a master coordinating regulator even if the network pattern is not strictly a Single-Input Module, as long as all regulators except one have a constant activity during the interval of interest. In addition to the multi-output FFL, there is a second four-node network motif, the bi-fan. Transcription networks, such as those of Escherichia coli and yeast, show several large dense overlaping regulons, each controlling tens to hundreds of genes. The FFLs in the network are combined in a way that utilizes their delay and pulse-generating features to generate a three-wave temporal program of gene expression.
