A Fast Reconstruction Algorithm for Gene Networks

2004/01/30 by Lorenzo Farina, Ilaria Mogno, Farina, Lorenzo +1
Biochemistry, Genetics and Molecular Biology · #Bioinformatics and Genomic Networks #FOS: Biological sciences #Gene Regulatory Network Analysis #Gene expression and cancer classification #Genomics (q-bio.GN) #Quantitative Methods (q-bio.QM) #q-bio.GN #q-bio.QM

paper · pdf · doi:10.48550/arxiv.q-bio/0401044

12 pages, 3 figures

arxiv created 2004/01/30 · openalex publication_date 2004/01/30 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28

Abstract

This paper deals with gene networks whose dynamics is assumed to be generated by a continuous-time, linear, time invariant, finite dimensional system (LTI) at steady state. In particular, we deal with the problem of network reconstruction in the typical practical situation in which the number of available data is largely insufficient to uniquely determine the network. In order to try to remove this ambiguity, we will exploit the biologically a priori assumption of network sparseness, and propose a new algorithm for network reconstruction having a very low computational complexity (linear in the number of genes) so to be able to deal also with very large networks (say, thousands of genes). Its performances are also tested both on artificial data (generated with linear models) and on real data obtained by Gardner et al. from the SOS pathway in Escherichia coli.

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