Properties of sparse penalties on inferring gene regulatory networks from time-course gene expression data

Abstract

Genes regulate each other and form a gene regulatory network (GRN) to realise biological functions. Elucidating GRN from experimental data remains a challenging problem in systems biology. Numerous techniques have been developed and sparse linear regression methods become a promising approach to infer accurate GRNs. However, most linear methods are either based on steady-state gene expression data or their statistical properties are not analysed. Here, two sparse penalties, adaptive least absolute shrinkage and selection operator and smoothly clipped absolute deviation, are proposed to infer GRNs from timecourse gene expression data based on an auto-regressive model and their Oracle properties are proved under mild conditions. The effectiveness of those methods is demonstrated by applications to in silico and real biological data.