CSpace  > 应用数学研究所
Imputing single-cell RNA-seq data by considering cell heterogeneity and prior expression of dropouts
Zhang, Lihua1,2; Zhang, Shihua1,2,3,4
AbstractSingle-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.
Keywordsingle-cell RNA-seq dropout imputation low-rank systems biology
Indexed BySCI
Funding ProjectNational 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 Research AreaCell Biology
WOS SubjectCell Biology
WOS IDWOS:000644518000004
Citation statistics
Document Type期刊论文
Corresponding AuthorZhang, Shihua
Affiliation1.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
Recommended Citation
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.
Files in This Item:
There are no files associated with this item.
Related Services
Recommend this item
Usage statistics
Export to Endnote
Google Scholar
Similar articles in Google Scholar
[Zhang, Lihua]'s Articles
[Zhang, Shihua]'s Articles
Baidu academic
Similar articles in Baidu academic
[Zhang, Lihua]'s Articles
[Zhang, Shihua]'s Articles
Bing Scholar
Similar articles in Bing Scholar
[Zhang, Lihua]'s Articles
[Zhang, Shihua]'s Articles
Terms of Use
No data!
Social Bookmark/Share
All comments (0)
No comment.

Items in the repository are protected by copyright, with all rights reserved, unless otherwise indicated.