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

dc.contributor.ISNI0000 0001 1707 1372 (Zhang, MQ)
dc.contributor.LCNA99086074‏ ‎(Zhang, MQ)
dc.contributor.authorMa, Xiaotuen_US
dc.contributor.authorKulkarni, Ashwinikumaren_US
dc.contributor.authorZhang, Zhihuaen_US
dc.contributor.authorXuan, Zhenyuen_US
dc.contributor.authorSerfling, Robert J. (Robert Joseph)en_US
dc.contributor.authorZhang, Michael Q.en_US
dc.contributor.utdAuthorZhang, Michael Q.en_US
dc.date.accessioned2014-03-14T19:55:42Z
dc.date.available2014-03-14T19:55:42Z
dc.date.created2012-01-06en_US
dc.date.issued2012-01-06en_US
dc.description.abstractIdentification 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.en_US
dc.identifier.bibliographicCitationMa, 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.en_US
dc.identifier.issn0305-1048en_US
dc.identifier.issue7en_US
dc.identifier.startpage50en_US
dc.identifier.urihttp://hdl.handle.net/10735.1/3155
dc.identifier.volume40en_US
dc.relation.urihttp://dx.doi.org/10.1093/nar/gkr1135
dc.rightsCC BY-NC 3.0 (Attribution-NonCommercial)en_US
dc.rights© 2012 The Authors.en_US
dc.rights.urihttp://creativecommons.org/licenses/by-nc/3.0/en_US
dc.sourceNucleic Acids Research
dc.subjectDNA-protein interactionsen_US
dc.subjectGenome-Wide Association Studyen_US
dc.subjectChromatin Immunoprecipitationen_US
dc.titleA Highly Efficient and Effective Motif Discovery Method for ChIP-Seq/ChIP-Chip Data using Positional Informationen_US
dc.typeTexten_US
dc.type.genreArticleen_US

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