Figure 9.

(a) The deletion of transcription factor X may affect gene Z, because X controls the expression of Z (direct effect). It is also possible that the deletion of transcription factor X affects gene Z indirectly, via a direct effect on transcription factor Y. (b) The single input motif as defined by Shen-Orr et al. for a Escherichia coli network and Lee et al. for the ChIP network. (c–f) All cases where a single connection in the mutant network corresponds to two connections in the ChIP network. (c) and (d) resemble the single input motif, with an additional top layer of regulation, whereas (e) and (f) correspond to more complex combinations of network motifs. dashed green, connections in the mutant network; solid red, connections in the ChIP network.