| 引用本文: | 岁品品,邢旭东,王宏,崔颖.基于位置权重矩阵的核小体识别及功能分析[J].生物信息学,2016,14(1):1-6. |
| SUI Pinpin,XING Xudong,WANG Hong,CUI Ying.Nucleosome positioning identification and functional analysis on the position weight matrix[J].Chinese Journal of Bioinformatics,2016,14(1):1-6. |
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| 摘要: |
| 为研究高通量的人类CD4+T细胞的核小体定位模式,使用迭代算法对核小体定位模式进行分类,并利用位置权重矩阵方法分别构建稳定核小体定位序列、动态核小体定位序列和连接区序列模型,通过十倍交叉验证评估模型性能,并与Segal方法与弯曲度方法进行比较,发现位置权重矩阵方法在敏感性、精度和准确性方面都具有一定优越性。同时采用滑窗法在全基因组选取候选序列进行核小体识别,挖掘核小体定位相关基因,并进行基因生物学进程功能富集分析,发现稳定与动态核小体、真实与潜在核小体对应的基因所参与调控的生物学过程各有不同,但也有一些生物学过程为不同类别核小体所共有,例如对细胞内大分子的调控功能。 |
| 关键词: 核小体定位 位置权重矩阵 基因功能富集分析 |
| DOI：10.3969/j.issn.1672-5565.2016.01.01 |
| 分类号:Q523 |
| 文献标识码:A |
| 基金项目:黑龙江省卫生厅科研课题资助(2013129)。 作者简介:岁品品,男,本科生,研究方向:生物信息学；E-mail:1447806377@qq.com. |
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| Nucleosome positioning identification and functional analysis on the position weight matrix |
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SUI Pinpin,XING Xudong,WANG Hong,CUI Ying
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(College of Bioinformatics Science and Technology,Harbin Medical University,Harbin 150081, China)
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| Abstract: |
| This study was based on high throughout nucleosome positioning data of CD4+T cell in human genome to investigate the model of nucleosome positioning and category the nucleosomes.We constructed three the models by using position weight matrix, including stable nucleosome model, dynamic nucleosome model and linker sequences model respectively. Ten-fold cross validation was used to evaluate the performance of the three models, and the assessment results were compared with Segal model and curvature profile method.It was found that the position weight matrix method was superior to the other two methods in terms of sensitivity, precision and accuracy. At the same time the sliding window method is adopted to select candidate sequences in the genome to identify the nucleosomes. Furthermore we mined the related genes of nucleosome positioning and completed enrichment analysis of gene functions and found that different nucleosome positioning modes involved in both a certain similarity and difference in regulation function in biological processes.Whereas there are some biological processes are co-regulated by different nucleosome positioning modes,such as regulation of macromolecule. |
| Key words: Nucleosome Position weight matrix Enrichment analysis of gene function |
