Networks of transcription factors

Transcription factors are responsible for both tissue-specific gene expression and the regulation of gene activity in response to specific stimuli. Analysis of whole genome gene expression data and studies on the specificities of transcription factor binding to genomic DNA sequences are common ways of inferring transcriptional regulatory networks. The interplay between different levels of regulation occurs when a series of transcription factors triggers a gene cascade that controls the whole regulatory program for cells under associated phenotypes. In this chapter, we discuss the role that transcription factors and other related molecules have on the intricate series of processes leading to genome-wide transcriptional regulatory programs. Experimental, computational, and modeling approaches to this problem are presented, and some general methods and algorithms are described in greater detail. Finally, we present an overview section on how to incorporate epigenomic and other regulatory processes in the context of networks of transcription factors.