Design of a Combinatorial DNA Microarray for Protein-DNA Interaction Studies

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dc.contributor.author Mintseris, Julian en_US
dc.contributor.author Eisen, Michael B en_US
dc.date.accessioned 2012-01-11T21:09:33Z
dc.date.available 2012-01-11T21:09:33Z
dc.date.copyright 2006 en_US
dc.date.issued 2006-10-3 en_US
dc.identifier.citation Mintseris, Julian, Michael B Eisen. "Design of a combinatorial DNA microarray for protein-DNA interaction studies" BMC Bioinformatics 7:429. (2006) en_US
dc.identifier.issn 1471-2105 en_US
dc.identifier.uri http://hdl.handle.net/2144/3193
dc.description.abstract BACKGROUND. Discovery of precise specificity of transcription factors is an important step on the way to understanding the complex mechanisms of gene regulation in eukaryotes. Recently, double-stranded protein-binding microarrays were developed as a potentially scalable approach to tackle transcription factor binding site identification. RESULTS. Here we present an algorithmic approach to experimental design of a microarray that allows for testing full specificity of a transcription factor binding to all possible DNA binding sites of a given length, with optimally efficient use of the array. This design is universal, works for any factor that binds a sequence motif and is not species-specific. Furthermore, simulation results show that data produced with the designed arrays is easier to analyze and would result in more precise identification of binding sites. CONCLUSION. In this study, we present a design of a double stranded DNA microarray for protein-DNA interaction studies and show that our algorithm allows optimally efficient use of the arrays for this purpose. We believe such a design will prove useful for transcription factor binding site identification and other biological problems. en_US
dc.description.sponsorship Department of Energy Computational Science Graduate Fellowship en_US
dc.language.iso en en_US
dc.publisher BioMed Central en_US
dc.rights Copyright 2006 Mintseris and Eisen; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. en_US
dc.rights.uri http://creativecommons.org/licenses/by/2.0 en_US
dc.title Design of a Combinatorial DNA Microarray for Protein-DNA Interaction Studies en_US
dc.type article en_US
dc.identifier.doi 10.1186/1471-2105-7-429 en_US
dc.identifier.pubmedid 17018151 en_US
dc.identifier.pmcid 1635571 en_US

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