下一代测序中ChIP_seq数据的处理与分析_高山.docVIP

下一代测序中ChIP_seq数据的处理与分析_高山 HEREDITAS (Beijing) 2012年6月, 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 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; 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 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; 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. Keywords: next generation sequencing; ChIP-seq; data process; transcription regulation; epigenetics