Differential expression analyses for single-ce RNA-Seq： old questions on new data  

作　　者：Zhun Miao Xuegong Zhang 

机构地区：[1]MOE Key Laboratory of Bioinformatics Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST Department of Automation, Tsinghua University, Beijing 100084, China [2]School of Life Sciences, Tsinghua University, Beijing 100084, China

出　　处：《Frontiers of Electrical and Electronic Engineering in China》2016年第4期243-260,共18页中国电气与电子工程前沿（英文版）

摘　　要：Single-cell RNA sequencing （scRNA-seq） is an emerging technology that enables high resolution detection of heterogeneities between ceils. One important application of scRNA-seq data is to detect differential expression （DE） of genes. Currently, some researchers still use DE analysis methods developed for bulk RNA-Seq data on single-cell data, and some new methods for scRNA-seq data have also been developed. Bulk and single-cell RNA-seq data have different characteristics. A systematic evaluation of the two types of methods on scRNA-seq data is needed. Results： In this study, we conducted a series of experiments on scRNA-seq data to quantitatively evaluate 14 popular DE analysis methods, including both of traditional methods developed for bulk RNA-seq data and new methods specifically designed for scRNA-seq data. We obtained observations and recommendations for the methods under different situations. Conclusions： DE analysis methods should be chosen for scRNA-seq data with great caution with regard to different situations of data. Different strategies should be taken for data with different sample sizes and/or different strengths of the expected signals. Several methods for scRNA-seq data show advantages in some aspects, and DEGSeq tends to outperform other methods with respect to consistency, reproducibility and accuracy of predictions on scRNA-seq data.Single-cell RNA sequencing （scRNA-seq） is an emerging technology that enables high resolution detection of heterogeneities between ceils. One important application of scRNA-seq data is to detect differential expression （DE） of genes. Currently, some researchers still use DE analysis methods developed for bulk RNA-Seq data on single-cell data, and some new methods for scRNA-seq data have also been developed. Bulk and single-cell RNA-seq data have different characteristics. A systematic evaluation of the two types of methods on scRNA-seq data is needed. Results： In this study, we conducted a series of experiments on scRNA-seq data to quantitatively evaluate 14 popular DE analysis methods, including both of traditional methods developed for bulk RNA-seq data and new methods specifically designed for scRNA-seq data. We obtained observations and recommendations for the methods under different situations. Conclusions： DE analysis methods should be chosen for scRNA-seq data with great caution with regard to different situations of data. Different strategies should be taken for data with different sample sizes and/or different strengths of the expected signals. Several methods for scRNA-seq data show advantages in some aspects, and DEGSeq tends to outperform other methods with respect to consistency, reproducibility and accuracy of predictions on scRNA-seq data.

关 键 词：SINGLE-CELL RNA-SEQ differential expression 

分 类 号：Q949.751.9[生物学—植物学] S634.1[农业科学—蔬菜学]