Two-phase differential expression analysis for single cell RNA-seq

Single-cell RNA-sequencing (scRNA-seq) has brought the study of the transcriptome to higher resolution and makes it possible for scientists to provide answers with more clarity to the question of ‘differential expression’. Specifically, it allows us to observe binary (On/Off) as well as continuous (the amount of expression) regulations. We present a method, SC2P, that identifies the phase of expression a gene is in, by taking into account of both cell- and gene-specific contexts, in a model-based and data-driven fashion. We then identify two forms of transcription regulation: phase transition, and magnitude tuning. We demonstrate that compared with existing methods, SC2P provides substantial improvement in sensitivity without sacrificing the control of false discovery, as well as better robustness. The ability to separately detect different forms of differential expression provides better interpretation of the nature of expression regulation.

Speaker: Dr. Zhijin (Jean) Wu, Brown Univ.