Inference of genetic networks from time course expression data using functional regression with lasso penalty

2008/04/04 by Heng Lian, Lian, Heng
Biochemistry, Genetics and Molecular Biology · Decision Sciences · #FOS: Biological sciences #Gene Regulatory Network Analysis #Gene expression and cancer classification #Optimal Experimental Design Methods #Quantitative Methods (q-bio.QM)

paper · pdf · doi:10.48550/arxiv.0804.0696

openalex publication_date 2008/04/04 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28

Abstract

Statistical inference of genetic regulatory networks is essential for understanding temporal interactions of regulatory elements inside the cells. For inferences of large networks, identification of network structure is typical achieved under the assumption of sparsity of the networks. When the number of time points in the expression experiment is not too small, we propose to infer the parameters in the ordinary differential equations using the techniques from functional data analysis (FDA) by regarding the observed time course expression data as continuous-time curves. For networks with a large number of genes, we take advantage of the sparsity of the networks by penalizing the linear coefficients with a L₁ norm. The ability of the algorithm to infer network structure is demonstrated using the cell-cycle time course data for Saccharomyces cerevisiae.

Citations

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