Open AccessProperties of sparse penalties on inferring gene regulatory networks from time‐course gene expression data
Author(s) -
Liu LiZhi,
Wu FangXiang,
Zhang WenJun
Publication year - 2015
Publication title -
iet systems biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.367
H-Index - 50
eISSN - 1751-8857
pISSN - 1751-8849
DOI - 10.1049/iet-syb.2013.0060
Subject(s) - gene regulatory network , computer science , in silico , biological data , least absolute deviations , oracle , lasso (programming language) , computational biology , systems biology , data mining , gene expression , machine learning , artificial intelligence , regression , gene , biology , mathematics , bioinformatics , statistics , genetics , software engineering , world wide web
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 time‐course 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.