Space-log: a novel approach to inferring gene-gene net-works using SPACE model with log penalty [version 2; peer review: 2 approved, 1 approved with reservations]

Abstract

Gene expression data have been used to infer gene-gene networks (GGN) where an edge between two genes implies the conditional dependence of these two genes given all the other genes. Such gene-gene networks are of-ten referred to as gene regulatory networks since it may reveal expression regulation. Most of existing methods for identifying GGN employ penalized regression with L1 (lasso), L2 (ridge), or elastic net penalty, which spans the range of L1 to L2 penalty. However, for high dimensional gene expression data, a penalty that spans the range of L0 and L1 penalty, such as the log penalty, is often needed for variable selection consistency. Thus, we develop a novel method that em-ploys log penalty within the framework of an earlier network identification method space (Sparse PArtial Correlation Estimation), and implement it into a R package space-log. We show that the space-log is computationally efficient (source code implemented in C), and has good performance comparing with other methods, particularly for networks with hubs.Space-log is open source and available at GitHub, https://github.com/wuqian77/SpaceLog

Keywords

• Gene-gene network
• gene regulation
• penalized regression
• log penalty
• partial correlation
• R package
• eng