下一代测序中ChIP-seq数据的处理与分析.pdfVIP

HEREDITAS (Beijing) 2012 6 , 34(6): 773―783 ISSN 0253-9772 技术与方法 DOI: 10.3724/SP.J.1005.2012.00773 下一代测序中ChIP-seq 数据的处理与分析 1 1 2 3 4 1 高山 , 张宁 , 李勃 , 徐硕 , 叶彦波 , 阮吉寿 1. , 300071; 2. , 400044; 3. , 100038; 4. , 430071; 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。 下一代测序; ChIP-seq; 数据处理; 转录调控; 表观遗传学 Processing and analysis of ChIP-seq data 1 1 2 3 4 1 GAO Shan , ZHANG Ning , LI Bo , XU Shuo , YE Yan-Bo , RUAN Ji-Shou 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; 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 processin