A Highly Efficient and Effective Motif Discovery Method for ChIP-Seq/ChIP-Chip Data using Positional Information

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A Highly Efficient and Effective Motif Discovery Method for ChIP-Seq/ChIP-Chip Data using Positional Information

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title A Highly Efficient and Effective Motif Discovery Method for ChIP-Seq/ChIP-Chip Data using Positional Information
contributor.author Ma, Xiaotu
contributor.author Kulkarni, Ashwinikumar
contributor.author Zhang, Zhihua
contributor.author Xuan, Zhenyu
contributor.author Serfling, Robert J. (Robert Joseph)
contributor.author Zhang, Michael Q.
contributor.utdAuthor Zhang, Michael Q.
contributor.ISNI 0000 0001 1707 1372 (Zhang, MQ)
contributor.LCNA 99086074‏ ‎(Zhang, MQ)
description.abstract Identification of DNA motifs from ChIP-seq/ChIP-chip [chromatin immunoprecipitation (ChIP)] data is a powerful method for understanding the transcriptional regulatory network. However, most established methods are designed for small sample sizes and are inefficient for ChIP data. Here we propose a new k-mer occurrence model to reflect the fact that functional DNA k-mers often cluster around ChIP peak summits. With this model, we introduced a new measure to discover functional k-mers. Using simulation, we demonstrated that our method is more robust against noises in ChIP data than available methods. A novel word clustering method is also implemented to group similar k-mers into position weight matrices (PWMs). Our method was applied to a diverse set of ChIP experiments to demonstrate its high sensitivity and specificity. Importantly, our method is much faster than several other methods for large sample sizes. Thus, we have developed an efficient and effective motif discovery method for ChIP experiments.
identifier.issn 0305-1048
identifier.uri http://hdl.handle.net/10735.1/3155
identifier.bibliographicCitation Ma, Xiaotu, Ashwinikumar Kulkarni, Zhihua Zhang, Zhenyu Xuan, et al. 2012. "A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information." Nucleic Acids Research 40(7): e50.
identifier.volume 40
identifier.issue 7
identifier.startpage 50
subject DNA-protein interactions
subject Genome-Wide Association Study
subject Chromatin Immunoprecipitation
date.created 2012-01-06
date.issued 2012-01-06
relation.uri http://dx.doi.org/10.1093/nar/gkr1135
rights CC BY-NC 3.0 (Attribution-NonCommercial)
rights © 2012 The Authors.
rights.uri http://creativecommons.org/licenses/by-nc/3.0/
source Nucleic Acids Research

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CC BY-NC 3.0 (Attribution-NonCommercial) Except where otherwise noted, this item's license is described as CC BY-NC 3.0 (Attribution-NonCommercial)