Beyond comparisons of means: understanding changes in gene expression at the single-cell level. Issue 1 (December 2016)

• Record Type: Journal Article
• Authors: Vallejos, Catalina; Richardson, Sylvia; Marioni, John
• Is Part Of: Genome biology. Volume 17:Issue 1(2016)
• Page Start: 1
• Page End: 14
• Publication Date: 2016-12
• Subjects: Single-cell RNA-seq -- Differential expression -- Cellular heterogeneity; Genomes -- Periodicals; Biology -- Periodicals; Molecular biology -- Periodicals; 572.8633
• DOI: 10.1186/s13059-016-0930-3
• Languages: English
• ISSNs: 1474-760X

Abstract

Abstract Traditional differential expression tools are limited to detecting changes in overall expression, and fail to uncover the rich information provided by single-cell level data sets. We present a Bayesian hierarchical model that builds upon BASiCS to study changes that lie beyond comparisons of means, incorporating built-in normalization and quantifying technical artifacts by borrowing information from spike-in genes. Using a probabilistic approach, we highlight genes undergoing changes in cell-to-cell heterogeneity but whose overall expression remains unchanged. Control experiments validate our method's performance and a case study suggests that novel biological insights can be revealed. Our method is implemented in R and available athttps://github.com/catavallejos/BASiCS .