A fast and efficient gene-network reconstruction method from multiple over-expression experiments

Details A fast and efficient gene-network reconstruction method from multiple over-expression experiments A fast and efficient gene-network reconstruction method from multiple over-expression experiments

2008-06-18

arxiv.org/abs/0806.3048v1

Biology

Quantitative Biology

Molecular Networks

10 pages, 3 figures

Scientific paper

Reverse engineering of gene regulatory networks presents one of the big challenges in systems biology. Gene regulatory networks are usually inferred from a set of single-gene over-expressions and/or knockout experiments. Functional relationships between genes are retrieved either from the steady state gene expressions or from respective time series. We present a novel algorithm for gene network reconstruction on the basis of steady-state gene-chip data from over-expression experiments. The algorithm is based on a straight forward solution of a linear gene-dynamics equation, where experimental data is fed in as a first predictor for the solution. We compare the algorithm's performance with the NIR algorithm, both on the well known E.Coli experimental data and on in-silico experiments. We show superiority of the proposed algorithm in the number of correctly reconstructed links and discuss computational time and robustness. The proposed algorithm is not limited by combinatorial explosion problems and can be used in principle for large networks of thousands of genes.

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