QWENDY: Gene Regulatory Network Inference by Quadruple Covariance Matrices

Abstract

Knowing gene regulatory networks (GRNs) is important for understanding various biological mechanisms. In this paper, we present a method, QWENDY, that uses single-cell gene expression data measured at four time points to infer GRNs. Based on a linear gene expression model, it solves the transformation of the covariance matrices. Unlike its predecessor WENDY, QWENDY avoids solving a non-convex optimization problem and produces a unique solution. We test the performance of QWENDY on three experimental data sets and two synthetic data sets. Compared to previously tested methods on the same data sets, QWENDY ranks the first on experimental data, although it does not perform well on synthetic data.