TY - GEN
T1 - Entropy-based analysis of chip-sequencing data
AU - Zare, Hossein
AU - Kaveh, Mostafa
AU - Khodursky, Arkady B.
PY - 2009/10/2
Y1 - 2009/10/2
N2 - 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.
AB - 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.
KW - Chip sequencing
KW - DNA binding sites
KW - Relative entropy
KW - Transcription factor
UR - http://www.scopus.com/inward/record.url?scp=70349506993&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=70349506993&partnerID=8YFLogxK
U2 - 10.1109/GENSIPS.2009.5174339
DO - 10.1109/GENSIPS.2009.5174339
M3 - Conference contribution
AN - SCOPUS:70349506993
SN - 9781424447619
T3 - 2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009
BT - 2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009
T2 - 2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009
Y2 - 17 May 2009 through 21 May 2009
ER -