DiNuP: a systematic approach to identify regions of differential nucleosome positioning

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DiNuP: a systematic approach to identify regions of differential nucleosome positioning

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Title: DiNuP: a systematic approach to identify regions of differential nucleosome positioning
Author: Fu, Kai; Tang, Qianzi; Feng, Jianxing; Liu, Xiaole Shirley; Zhang, Yong

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Citation: Fu, Kai, Qianzi Tang, Jianxing Feng, X. Shirley Liu, and Yong Zhang. 2012. DiNuP: a systematic approach to identify regions of differential nucleosome positioning. Bioinformatics 28(15): 1965-1971.
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Abstract: Motivation: With the rapid development of high-throughput sequencing technologies, the genome-wide profiling of nucleosome positioning has become increasingly affordable. Many future studies will investigate the dynamic behaviour of nucleosome positioning in cells that have different states or that are exposed to different conditions. However, a robust method to effectively identify the regions of differential nucleosome positioning (RDNPs) has not been previously available. Results:: We describe a novel computational approach, DiNuP, that compares nucleosome profiles generated by high-throughput sequencing under various conditions. DiNuP provides a statistical P-value for each identified RDNP based on the difference of read distributions. DiNuP also empirically estimates the false discovery rate as a cutoff when two samples have different sequencing depths and differentiate reliable RDNPs from the background noise. Evaluation of DiNuP showed it to be both sensitive and specific for the detection of changes in nucleosome location, occupancy and fuzziness. RDNPs that were identified using publicly available datasets revealed that nucleosome positioning dynamics are closely related to the epigenetic regulation of transcription. Availability and implementation: DiNuP is implemented in Python and is freely available at http://www.tongji.edu.cn/~zhanglab/DiNuP.
Published Version: doi:10.1093/bioinformatics/bts329
Other Sources: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3400967/pdf/
Terms of Use: This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA
Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:10498801
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