Nucleic Acids Research Advance Access originally published online on November 7, 2006
Nucleic Acids Research 2006 34(21):e146; doi:10.1093/nar/gkl803
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Nucleic Acids Research, 2006, Vol. 34, No. 21 e146
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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A comparative analysis of genome-wide chromatin immunoprecipitation data for mammalian transcription factors
Department of Statistics, Harvard University 1 Oxford Street, Cambridge, MA 02138, USA 1 Department of Molecular and Cellular Biology, Harvard University 16 Divinity Avenue, Cambridge, MA 02138, USA 2 Department of Statistics, Stanford University 390 Serra Mall, Stanford, CA 94305, USA
*To whom correspondence should be addressed. Tel: +1 650 725 2915; Fax: +1 650 725 8977; Email: whwong{at}stanford.edu
Received July 13, 2006. Revised September 26, 2006. Accepted September 28, 2006.
Genome-wide location analysis (ChIP-chip, ChIP-PET) is a powerful technique to study mammalian transcriptional regulation. In order to obtain a basic understanding of the location data generated for mammalian transcription factors and potential issues in their analysis, we conducted a comparative study of eight independent ChIP experiments involving six different transcription factors in human and mouse. Our cross-study comparisons, to the best of our knowledge the first to analyze multiple datasets, revealed the importance of carefully chosen genomic controls in the de novo identification of key transcription factor binding motifs, raised issues about the interpretation of ubiquitously occurring sequence motifs, and demonstrated the clustering tendency of protein-binding regions for certain transcription factors.
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