Inferring gene regulatory networks from single-cell RNA-seq temporal snapshot data requires higher-order moments

Patterns (N Y). 2021 Aug 18;2(9):100332. doi: 10.1016/j.patter.2021.100332. eCollection 2021 Sep 10.

Abstract

Single-cell RNA sequencing (scRNA-seq) has become ubiquitous in biology. Recently, there has been a push for using scRNA-seq snapshot data to infer the underlying gene regulatory networks (GRNs) steering cellular function. To date, this aspiration remains unrealized due to technical and computational challenges. In this work we focus on the latter, which is under-represented in the literature. We took a systemic approach by subdividing the GRN inference into three fundamental components: data pre-processing, feature extraction, and inference. We observed that the regulatory signature is captured in the statistical moments of scRNA-seq data and requires computationally intensive minimization solvers to extract it. Furthermore, current data pre-processing might not conserve these statistical moments. Although our moment-based approach is a didactic tool for understanding the different compartments of GRN inference, this line of thinking-finding computationally feasible multi-dimensional statistics of data-is imperative for designing GRN inference methods.

Keywords: Markov chains; RNA sequencing; chemical master equation; moment equations; single cell; time-course snapshots.