Transcriptional perturbation effects remain structured beyond the leading global trend

Abstract

Prior work has described a global transcriptional response to gene perturbation, with many perturbations moving cells along a common direction. We find that perturbations contribute differently to this leading global trend and that substantial organization remains beyond it, including transferable perturbation-specific effects across datasets and a common hierarchy of responsive genes across perturbations. These patterns make simple strategies surprisingly competitive even in predicting effects beyond the leading global component.

Qiyuan Liu

Ph.D. student

Jingshu Wang

Assistant Professor in Statistics