pscan-chip - 1.1-3 main

Regulation of transcription is one of the main check points of gene
expression regulation and plays a key role in fundamental processes like
cellular differentiation and dynamic molecular responses to stimuli The
transcriptional activity of genes is finely regulated by the interaction
of sequence elements on the DNA (transcription factor binding sites or
TFBSs) and particular proteins called Transcription Factors (TFs).
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TFBSs are usually clustered in specific regulatory genomic regions
called promoters and enhancers. TFs usually recognize TFBSs in a loose
sequence specific fashion but there is no computational way to determine
if any given sequence motif on the DNA is actually bound in-vivo by a
TF, even when the motif is an istance of the sequences typically bound
by the TF itself.
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Tools like Pscan and PscanChIP analyse a set of regulatory sequences
to detect motif enrichment. The rationale is that if a given TFBS is
present in a "surpisingly high" number of istances then there is a good
chance that the TF that recognize that motif is a common regulator of
the input sequences, thus they use redundancy as an information source.
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While Pscan (of the pscan-tfbs package) is tailored to work on promoters,
that is the regulatory regions upstream of transcription start sites,
PscanChIP is suited to work on more general regulatory genomic regions
like the ones identified through ChIP-Seq experiments.