Reveal cell type-specific regulatory elements and their characterized histone code classes via a hidden Markov model

doi:10.1186/s12864-018-5274-9

CORC > 数学与系统科学研究院 > 中国科学院数学与系统科学研究院 > 应用数学研究所

	Reveal cell type-specific regulatory elements and their characterized histone code classes via a hidden Markov model
	Wang, Can 1,2; Zhang, Shihua1,2,3
刊名	BMC GENOMICS
	2018-12-31
卷号	19 页码:13
关键词	Epigenomics Cell type-specific regulatory elements Hidden Markov model Histone modification
ISSN号	1471-2164
DOI	10.1186/s12864-018-5274-9
英文摘要	BackgroundWith the maturity of next generation sequencing technology, a huge amount of epigenomic data have been generated by several large consortia in the last decade. These plenty resources leave us the opportunity about sufficiently utilizing those data to explore biological problems.ResultsHere we developed an integrative and comparative method, CsreHMM, which is based on a hidden Markov model, to systematically reveal cell type-specific regulatory elements (CSREs) along the whole genome, and simultaneously recognize the histone codes (mark combinations) charactering them. This method also reveals the subclasses of CSREs and explicitly label those shared by a few cell types. We applied this method to a data set of 9 cell types and 9 chromatin marks to demonstrate its effectiveness and found that the revealed CSREs relates to different kinds of functional regulatory regions significantly. Their proximal genes have consistent expression and are likely to participate in cell type-specific biological functions.ConclusionsThese results suggest CsreHMM has the potential to help understand cell identity and the diverse mechanisms of gene regulation.
资助项目	National Natural Science Foundation of China[11661141019] ; National Natural Science Foundation of China[61621003] ; National Natural Science Foundation of China[61422309] ; National Natural Science Foundation of China[61379092] ; Strategic Priority Research Program of the Chinese Academy of Sciences (CAS)[XDB13040600] ; National Ten Thousand Talent Program for Young Top-notch Talents ; Key Research Program of the Chinese Academy of Sciences[KFZD-SW-219] ; National Key Research and Development Program of China[2017YFC0908405] ; CAS Frontier Science Research Key Project for Top Young Scientist[QYZDB-SSW-SYS008]
WOS研究方向	Biotechnology & Applied Microbiology ; Genetics & Heredity
语种	英语
出版者	BMC
WOS记录号	WOS:000454632500003
内容类型	期刊论文
源URL	[http://ir.amss.ac.cn/handle/2S8OKBNM/31628]
专题	应用数学研究所
通讯作者	Zhang, Shihua
作者单位	1.Chinese Acad Sci, Acad Math & Syst Sci, Beijing 100190, Peoples R China 2.Univ Chinese Acad Sci, Sch Math Sci, Beijing 100049, Peoples R China 3.Chinese Acad Sci, Ctr Excel Lence Anim Evolut & Genet, Kunming 650223, Yunnan, Peoples R China
推荐引用方式 GB/T 7714	Wang, Can,Zhang, Shihua. Reveal cell type-specific regulatory elements and their characterized histone code classes via a hidden Markov model[J]. BMC GENOMICS,2018,19:13.
APA	Wang, Can,&Zhang, Shihua.(2018).Reveal cell type-specific regulatory elements and their characterized histone code classes via a hidden Markov model.BMC GENOMICS,19,13.
MLA	Wang, Can,et al."Reveal cell type-specific regulatory elements and their characterized histone code classes via a hidden Markov model".BMC GENOMICS 19(2018):13.