The set of regulatory interactions between genes, mediated by transcription factors, forms a species’ transcriptional
regulatory network (TRN). By comparing this network with measured gene expression data, one can identify functional
properties of the TRN and gain general insight into transcriptional control. We define the subnet of a node as the subgraph
consisting of all nodes topologically downstream of the node, including itself. Using a large set of microarray expression
data of the bacterium Escherichia coli, we find that the gene expression in different subnets exhibits a structured pattern in
response to environmental changes and genotypic mutation. Subnets with fewer changes in their expression pattern have a
higher fraction of feed-forward loop motifs and a lower fraction of small RNA targets within them. Our study implies that the
TRN consists of several scales of regulatory organization: (1) subnets with more varying gene expression controlled by both
transcription factors and post-transcriptional RNA regulation and (2) subnets with less varying gene expression having more
feed-forward loops and less post-transcriptional RNA regulation.