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

文献类型：期刊论文

作者Zeng, Wanwen3,4; Chen, Xi4; Duren, Zhana4; Wang, Yong1,2; Jiang, Rui3; Wong, Wing Hung4
刊名NATURE COMMUNICATIONS
出版日期2019-10-10
卷号10页码:11
ISSN号2041-1723
DOI10.1038/s41467-019-12547-1
英文摘要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.
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
语种英语
WOS记录号WOS:000489557800006
出版者NATURE PUBLISHING GROUP
源URL[http://ir.amss.ac.cn/handle/2S8OKBNM/35766]  
专题应用数学研究所
通讯作者Jiang, Rui; Wong, Wing Hung
作者单位1.Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming 650223, Yunnan, Peoples R China
2.Chinese Acad Sci, Acad Math & Syst Sci, MDIS, CEMS,NCMIS, Beijing 100080, Peoples R China
3.Tsinghua Univ, MOE Key Lab Bioinformat, Beijing Natl Res Ctr Informat Sci & Technol, Bioinformat Div,Dept Automat, Beijing 100084, Peoples R China
4.Stanford Univ, Dept Stat, Dept Biomed Data Sci, Biox Program, Stanford, CA 94305 USA
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.

入库方式： OAI收割

来源：数学与系统科学研究院

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