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  A physical model for tiling array analysis.

Chung, H.-R., Kostka, D., & Vingron, M. (2007). A physical model for tiling array analysis. Bioinformatics, 23(13), i80-i86. doi:10.1093/bioinformatics/btm167.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-81AF-C Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-81B0-6
Genre: Journal Article
Alternative Title : Bioinformatics

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 Creators:
Chung, Ho-Ryun1, Author              
Kostka, Dennis2, Author
Vingron, Martin3, Author              
Affiliations:
1Computational Epigenetics (Ho-Ryun Chung), Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479658              
2Max Planck Society, ou_persistent13              
3Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479639              

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 Abstract: Motivation: Chromatin immunoprecipitation (ChIP) is a powerful experimental approach to identify in vivo binding sites of sequence-specific transcription factors (TFs). These experiments are designed to specifically enrich DNA fragments that are bound to the TF. Tiling arrays have become more and more popular for the identification of these DNA fragments. However, many studies showed that only a fraction of the identified DNA fragments contains bona fide binding sites for the TF, suggesting that indirect binding mechanisms play a very important role. We explored the possibility that the lack of binding sites can also be explained by problems in identifying ChIP-enriched DNA fragments from the measured intensities. Results: We derived a physical model that explains some (but not all) variation of the measured probe intensities of Affymetrix tilling arrays. We used the physical model to estimate the probe-specific behavior and corrected for it. Subsequently, we developed a method to identify ChIP-enriched DNA fragments. We termed it physical model for tiling array analysis (PMT). We applied PMT to the data of ChIP-chip experiments interrogating chromosome 21 and 22 of the human genome for binding of the TFs MYC, SP1 and P53. Almost all regions recovered by PMT showed evidence for sequence-specific binding of the TFs.

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Language(s): eng - English
 Dates: 2007-07-01
 Publication Status: Published in print
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Title: Bioinformatics
  Alternative Title : Bioinformatics
Source Genre: Journal
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Pages: - Volume / Issue: 23 (13) Sequence Number: - Start / End Page: i80 - i86 Identifier: ISSN: 1367-4803