ABSTRACT
This chapter aims to discover network motifs in transcription networks and discusses their function and explores the number of appearances of patterns in real and random networks. The numbers of subgraphs in randomized networks can be computed analytically or by computer simulations. Since the Escherichia coli network has about equal numbers of positive and negative arrows, one might expect all 8 types of feedforward loops (FFLs) to appear with about equal frequency. In transcription networks, evolutionary selection may have placed the coherent type-1 FFL (C1-FFL) in diverse systems in the cell that require such a protection function. Indeed, the environment of cells is often highly fluctuating, and sometimes stimuli can be present for brief pulses that should not elicit a response. The C1-FFL can offer a filtering function that is advantageous in these types of fluctuating environments. The C1-FFL acts as a persistence detector, filtering out brief pulses of input.
