A Dimension Reduction Method for Inferring Biochemical Networks

Details A Dimension Reduction Method for Inferring Biochemical Networks A Dimension Reduction Method for Inferring Biochemical Networks

2009-02-25

arxiv.org/abs/0902.4417v1

Biology

Quantitative Biology

Molecular Networks

12 pages and 4 figures

Scientific paper

We present herein an extension of an algebraic statistical method for inferring biochemical reaction networks from experimental data, proposed recently in [3]. This extension allows us to analyze reaction networks that are not necessarily full-dimensional, i.e., the dimension of their stoichiometric space is smaller than the number of species. Specifically, we propose to augment the original algebraic-statistical algorithm for network inference with a preprocessing step that identifies the subspace spanned by the correct reaction vectors, within the space spanned by the species. This dimension reduction step is based on principal component analysis of the input data and its relationship with various subspaces generated by sets of candidate reaction vectors. Simulated examples are provided to illustrate the main ideas involved in implementing this method, and to asses its performance.

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