Entropy-based analysis of chip-sequencing data

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

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 peakfinding algorithm to locate the local peak(s) within each region. Wehave applied this method to analyze chromosomal binding patterns of Lrp, a global transcriptional regulator of amino acid metabolism in Escherichia coli.

Original languageEnglish (US)
Title of host publication2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009
DOIs
StatePublished - Oct 2 2009
Event2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009 - Minneapolis, MN, United States
Duration: May 17 2009May 21 2009

Publication series

Name2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009

Other

Other2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009
Country/TerritoryUnited States
CityMinneapolis, MN
Period5/17/095/21/09

Keywords

  • Chip sequencing
  • DNA binding sites
  • Relative entropy
  • Transcription factor

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