Abstract
The combinatorial control of gene regulatory switches involves both
transcription factor (TF) complexes and associated epigenetic modifications
to the chromatin template. The novel high-throughput technologies,
such as Chromatin ImmunoPrecipitation ChIP-chip, have enabled genome-wide
in vivo identification of TF target regulatory regions and related
epigenetic modifications, which led to the view of highly dynamic
TF-DNA interactions in activated or repressed promoters. Consequently,
modeling and elucidating the combinatorial interaction of TFs and
corresponding cis-regulatory modules in target promoters is of paramount
interest. An estimated 5% of the genes in mammalian genomes code
for TF proteins, and computational modeling of cis-regulatory logic
would rapidly increase the pace of experimental confirmation of TF
target promoters at the bench. The purpose of this chapter is to
discuss the use of different bioinformatics tools for predicting
the target genes of TFs of interest in mammalian genomes, and the
application of these methods in the analysis of ChIP-chip experimental
data. The author describes most commonly used databases and prediction
programs that are available on the World Wide Web and demonstrate
the use of some of these programs by an example. A list of these
programs is provided along with their web Uniform Resource Locator
(URLs) and guidelines for successful application are suggested.
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