下一代测序中ChIP-seq数据的处理与分析

doi:10.3724/SP.J.1005.2012.00773

遗传 ›› 2012, Vol. 34 ›› Issue (6): 773-783.doi: 10.3724/SP.J.1005.2012.00773

下一代测序中ChIP-seq数据的处理与分析

高山¹, 张宁¹, 李勃², 徐硕³, 叶彦波⁴, 阮吉寿¹

1. 南开大学数学学院, 天津 300071 2. 重庆大学生物工程学院, 重庆400044 3. 中国科学技术信息研究所, 北京100038 4. 中国科学院武汉病毒研究所, 武汉 430071;

收稿日期:2011-10-10 修回日期:2011-12-04 出版日期:2012-06-20 发布日期:2012-06-25
通讯作者: 阮吉寿 E-mail:jsruan@nankai.edu.cn
基金资助:
国家自然科学基金项目(编号：31050110432, 68075049)资助

Processing and analysis of ChIP-seq data

GAO Shan¹, ZHANG Ning¹, LI Bo², XU Shuo³, YE Yan-Bo⁴, RUAN Ji-Shou¹

1. College of Mathematics, Nankai University, Tianjin 300071, China 2. College of Bioengineering, Chongqing University, Chongqing 400044, China 3. Institute of Scientific and Technical Information of China, Beijing 100038, China 4. Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China

Received:2011-10-10 Revised:2011-12-04 Online:2012-06-20 Published:2012-06-25

摘要/Abstract

摘要： 将染色质免疫共沉淀技术(ChIP)与下一代高通量测序技术相结合的染色质免疫共沉淀测序(ChIP-seq), 已成为功能基因组学、特别是基因表达调控领域研究的关键技术。ChIP-seq实验带来的海量数据向生物信息学研究人员提出了新的挑战。由于此领域数据处理技术的发展大大滞后于实验技术进步, 有必要系统地介绍和回顾ChIP-seq数据处理的各个方面, 以便更多研究人员进入此领域设计或改进相应的算法。文章结合实例详细介绍了ChIP-seq数据整个流程, 并重点讨论了其中的主要问题和关键环节, 为这一研究领域的科研人员提供一个快速而深入的认识。

关键词: 下一代测序, ChIP-seq, 数据处理, 转录调控, 表观遗传学

Abstract: The next-generation sequencing coupled with chromatin immunoprecipitation (ChIP-seq) is becoming a key technology for the study of transcriptional regulation in the context of functional genomics. Due to the overwhelming amount of data generated from ChIP-seq experiments, the ChIP-seq data processing brings many new challenges in the field of bioinformatics. Considering the development of data processing skills largely behind that of the ChIP-seq experiment techniques, it is urgent to give a review on the ChIP-seq data processing for more and more oncoming researchers to build or improve algorithms. This paper provides a brief overview of the ChIP-seq data processing, highlighting the main prob-lems and methods in detail, to allow scientists to understand rapidly and deeply.

Key words: next generation sequencing, ChIP-seq, data process, transcription regulation, epigenetics

高山，张宁，李勃，徐硕，叶彦波，阮吉寿. 下一代测序中ChIP-seq数据的处理与分析[J]. 遗传, 2012, 34(6): 773-783.

GAO Shan, ZHANG Ning, LI Bo, XU Shuo, YE Yan-Bo, RUAN Ji-Shou. Processing and analysis of ChIP-seq data[J]. HEREDITAS, 2012, 34(6): 773-783.

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下一代测序中ChIP-seq数据的处理与分析

Processing and analysis of ChIP-seq data

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