KMS Of Academy of mathematics and systems sciences, CAS
| Imputing single-cell RNA-seq data by considering cell heterogeneity and prior expression of dropouts | |
Zhang, Lihua1,2; Zhang, Shihua1,2,3,4
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| 2021 | |
| Source Publication | JOURNAL OF MOLECULAR CELL BIOLOGY
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| ISSN | 1674-2788 |
| Volume | 13Issue:1Pages:29-40 |
| Abstract | 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. |
| Keyword | single-cell RNA-seq dropout imputation low-rank systems biology |
| DOI | 10.1093/jmcb/mjaa052 |
| Indexed By | SCI |
| Language | 英语 |
| Funding Project | 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 Research Area | Cell Biology |
| WOS Subject | Cell Biology |
| WOS ID | WOS:000644518000004 |
| Publisher | OXFORD UNIV PRESS |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.amss.ac.cn/handle/2S8OKBNM/58627 |
| Collection | 应用数学研究所 |
| Corresponding Author | Zhang, Shihua |
| Affiliation | 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 |
| 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. |
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