Genomic tools for analyzing transcriptional regulatory networks

Abstract

In this chapter, we described how genomic tools can be used to construct and analyze transcription networks. We focus on the ChIP-chip technique as this genomic tool has proven to be a powerful method for identifying the genomic targets of transcription factors. We discuss bioinformatics methods that can be used to analyze ChIP-chip data and discover the DNA motifs bound by a transcription factor. Finally, we describe bioinformatics tools, such as Athena, that can be used to visualize and analyze transcription factor binding sites. We have shown that integrating the analysis of transcription factor binding data with information about gene function or expression can be a powerful tool for deciphering transcriptional networks.