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Recommendations of scRNA-seq Differential Gene Expression Analysis Based on Comprehensive Benchmarking.

Authors :
Gagnon, Jake
Pi, Lira
Ryals, Matthew
Wan, Qingwen
Hu, Wenxing
Ouyang, Zhengyu
Zhang, Baohong
Li, Kejie
Source :
Life (2075-1729). Jun2022, Vol. 12 Issue 6, p850. 25p.
Publication Year :
2022

Abstract

To guide analysts to select the right tool and parameters in differential gene expression analyses of single-cell RNA sequencing (scRNA-seq) data, we developed a novel simulator that recapitulates the data characteristics of real scRNA-seq datasets while accounting for all the relevant sources of variation in a multi-subject, multi-condition scRNA-seq experiment: the cell-to-cell variation within a subject, the variation across subjects, the variability across cell types, the mean/variance relationship of gene expression across genes, library size effects, group effects, and covariate effects. By applying it to benchmark 12 differential gene expression analysis methods (including cell-level and pseudo-bulk methods) on simulated multi-condition, multi-subject data of the 10x Genomics platform, we demonstrated that methods originating from the negative binomial mixed model such as glmmTMB and NEBULA-HL outperformed other methods. Utilizing NEBULA-HL in a statistical analysis pipeline for single-cell analysis will enable scientists to better understand the cell-type-specific transcriptomic response to disease or treatment effects and to discover new drug targets. Further, application to two real datasets showed the outperformance of our differential expression (DE) pipeline, with unified findings of differentially expressed genes (DEG) and a pseudo-time trajectory transcriptomic result. In the end, we made recommendations for filtering strategies of cells and genes based on simulation results to achieve optimal experimental goals. [ABSTRACT FROM AUTHOR]

Details

Language :
English
ISSN :
20751729
Volume :
12
Issue :
6
Database :
Academic Search Index
Journal :
Life (2075-1729)
Publication Type :
Academic Journal
Accession number :
157777848
Full Text :
https://doi.org/10.3390/life12060850