Imputing single-cell RNA-seq data by considering cell heterogeneity and prior expression of dropouts

doi:10.1093/jmcb/mjaa052

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	Imputing single-cell RNA-seq data by considering cell heterogeneity and prior expression of dropouts
	Zhang, Lihua 1,2; Zhang, Shihua1,2,3,4
	2021
发表期刊	JOURNAL OF MOLECULAR CELL BIOLOGY
ISSN	1674-2788
卷号	13 期号:1 页码:29-40
摘要	Single-cell RNA sequencing (scRNA-seq) provides a powerful tool to determine expression patterns of thousands of individual cells. However, the analysis of scRNA-seq data remains a computational challenge due to the high technical noise such as the presence of dropout events that lead to a large proportion of zeros for expressed genes. Taking into account the cell heterogeneity and the relationship between dropout rate and expected expression level, we present a cell sub-population based bounded low-rank (PBLR) method to impute the dropouts of scRNA-seq data. Through application to both simulated and real scRNA-seq datasets, PBLR is shown to be effective in recovering dropout events, and it can dramatically improve the low-dimensional representation and the recovery of genegene relationships masked by dropout events compared to several state-of-the-art methods. Moreover, PBLR also detects accurate and robust cell sub-populations automatically, shedding light on its flexibility and generality for scRNA-seq data analysis.
关键词	single-cell RNA-seq dropout imputation low-rank systems biology
DOI	10.1093/jmcb/mjaa052
收录类别	SCI
语种	英语
资助项目	National Key R&D Program of China[2019YFA0709501] ; National Natural Science Foundation of China[11661141019] ; National Natural Science Foundation of China[61621003] ; National Ten Thousand Talent Program for Young Top-notch Talents ; CAS Frontier Science Research Key Project for Top Young Scientist[QYZDB-SSW-SYS008] ; Shanghai Municipal Science and Technology Major Project[2017SHZDZX01]
WOS研究方向	Cell Biology
WOS类目	Cell Biology
WOS记录号	WOS:000644518000004
出版者	OXFORD UNIV PRESS
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/58627
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, RCSDS, NCMIS,CEMS, Beijing 100190, Peoples R China 2.Univ Chinese Acad Sci, Sch Math Sci, Beijing 100049, Peoples R China 3.Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming 650223, Yunnan, Peoples R China 4.Chinese Acad Sci, Univ Chinese Acad Sci, Hangzhou Inst Adv Study, Key Lab Syst Biol, Hangzhou 310024, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Lihua,Zhang, Shihua. Imputing single-cell RNA-seq data by considering cell heterogeneity and prior expression of dropouts[J]. JOURNAL OF MOLECULAR CELL BIOLOGY,2021,13(1):29-40.
APA	Zhang, Lihua,&Zhang, Shihua.(2021).Imputing single-cell RNA-seq data by considering cell heterogeneity and prior expression of dropouts.JOURNAL OF MOLECULAR CELL BIOLOGY,13(1),29-40.
MLA	Zhang, Lihua,et al."Imputing single-cell RNA-seq data by considering cell heterogeneity and prior expression of dropouts".JOURNAL OF MOLECULAR CELL BIOLOGY 13.1(2021):29-40.