Smolen, Paul, Douglas A. Baxter, and John H. Byrne. “Mathematical modeling of gene networks.” Neuron 26, no. 3 (2000): 567-580.
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The expression of clusters of genes can be regulated by stimulus-induced activation of signal transduction pathways that modulate the activity of transcription factors (TFs). TFs regulate transcription by binding to stretches of DNA known as responsive elements (reviewed by Karin, 1994). Many genes are regulated by multiple TFs. Furthermore, genes coding for TFs are often activated or repressed by their own products as well as by other TFs. A large number—on the order of thousands—of such interactions together constitute the total array of genetic regulation in neurons and other cells. The term “gene network” can be used to refer to clusters of genes that satisfy two conditions. The expression of the genes in the cluster is affected in concert by specific stimuli, such as exposure to a hormone or neurotransmitter. Also, the protein products of some members of the cluster act as TFs to regulate the expression of other members.