DC3 is a method for deconvolution and coupled clustering from bulk and single-cell genomics data

doi:10.1038/s41467-019-12547-1

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	DC3 is a method for deconvolution and coupled clustering from bulk and single-cell genomics data
	Zeng, Wanwen 1,2; Chen, Xi 1; Duren, Zhana 1; Wang, Yong3,4 ; Jiang, Rui 2; Wong, Wing Hung 1
	2019-10-10
发表期刊	NATURE COMMUNICATIONS
ISSN	2041-1723
卷号	10 页码:11
摘要	Characterizing and interpreting heterogeneous mixtures at the cellular level is a critical problem in genomics. Single-cell assays offer an opportunity to resolve cellular level heterogeneity, e.g., scRNA-seq enables single-cell expression profiling, and scATAC-seq identifies active regulatory elements. Furthermore, while scHi-C can measure the chromatin contacts (i.e., loops) between active regulatory elements to target genes in single cells, bulk HiChIP can measure such contacts in a higher resolution. In this work, we introduce DC3 (De-Convolution and Coupled-Clustering) as a method for the joint analysis of various bulk and single-cell data such as HiChIP, RNA-seq and ATAC-seq from the same heterogeneous cell population. DC3 can simultaneously identify distinct subpopulations, assign single cells to the subpopulations (i.e., clustering) and de-convolve the bulk data into subpopulation-specific data. The subpopulation-specific profiles of gene expression, chromatin accessibility and enhancer-promoter contact obtained by DC3 provide a comprehensive characterization of the gene regulatory system in each subpopulation.
DOI	10.1038/s41467-019-12547-1
语种	英语
资助项目	NIH[P50HG007735] ; NIH[R01HG010359] ; NIH[R01GM109836] ; VA Palo Alto Health Care System ; Strategic Priority Research Program of the Chinese Academy of Sciences[XDB13000000] ; National Key Research and Development Program of China[2018YFC0910404] ; National Natural Science Foundation of China[61873141] ; National Natural Science Foundation of China[61721003] ; National Natural Science Foundation of China[61573207] ; Tsinghua-Fuzhou Institute for Data Technology ; RONG professorship at the Institute for Data Science of Tsinghua University
WOS研究方向	Science & Technology - Other Topics
WOS类目	Multidisciplinary Sciences
WOS记录号	WOS:000489557800006
出版者	NATURE PUBLISHING GROUP
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/35767
专题	应用数学研究所
通讯作者	Jiang, Rui; Wong, Wing Hung
作者单位	1.Stanford Univ, Dept Stat, Dept Biomed Data Sci, Biox Program, Stanford, CA 94305 USA 2.Tsinghua Univ, MOE Key Lab Bioinformat, Beijing Natl Res Ctr Informat Sci & Technol, Bioinformat Div,Dept Automat, Beijing 100084, Peoples R China 3.Chinese Acad Sci, Acad Math & Syst Sci, MDIS, CEMS,NCMIS, Beijing 100080, Peoples R China 4.Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming 650223, Yunnan, Peoples R China
推荐引用方式 GB/T 7714	Zeng, Wanwen,Chen, Xi,Duren, Zhana,et al. DC3 is a method for deconvolution and coupled clustering from bulk and single-cell genomics data[J]. NATURE COMMUNICATIONS,2019,10:11.
APA	Zeng, Wanwen,Chen, Xi,Duren, Zhana,Wang, Yong,Jiang, Rui,&Wong, Wing Hung.(2019).DC3 is a method for deconvolution and coupled clustering from bulk and single-cell genomics data.NATURE COMMUNICATIONS,10,11.
MLA	Zeng, Wanwen,et al."DC3 is a method for deconvolution and coupled clustering from bulk and single-cell genomics data".NATURE COMMUNICATIONS 10(2019):11.