Entropy-based analysis of ChIP-Sequencing data

ChIP-Sequencing (ChIP-Seq) is an advanced emerging technology to detect protein-DNA associations and to identify transcription factor binding sites. This technology, which is an alternative to the ChIP-on-chip technique, provides several advantages including data with higher resolution and quality. In this paper we present a framework for the analysis of ChIP-Seq data in order to identify targets of a transcription factor and its binding sites. The introduced method employs the relative entropy measure to identify candidate binding regions with high affinity in the genome and then applies a peak-finding algorithm to locate the local peak(s) within each region. We have applied this method to analyze chromosomal binding patterns of Lrp, a global transcriptional regulator of amino acid metabolism in Escherichia coli.