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Reveal cell type-specific regulatory elements and their characterized histone code classes via a hidden Markov model
Wang, Can1,2; Zhang, Shihua1,2,3
2018-12-31
Source PublicationBMC GENOMICS
ISSN1471-2164
Volume19Pages:13
AbstractBackgroundWith 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.
KeywordEpigenomics Cell type-specific regulatory elements Hidden Markov model Histone modification
DOI10.1186/s12864-018-5274-9
Language英语
Funding ProjectNational 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 Research AreaBiotechnology & Applied Microbiology ; Genetics & Heredity
WOS SubjectBiotechnology & Applied Microbiology ; Genetics & Heredity
WOS IDWOS:000454632500003
PublisherBMC
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Document Type期刊论文
Identifierhttp://ir.amss.ac.cn/handle/2S8OKBNM/31629
Collection应用数学研究所
Affiliation1.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
Recommended Citation
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.
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