A Methodology Based on MP Theory for Gene Expression Analysis

In this paper we develop an application of the MP theory to gene expression analysis. After introducing some general concepts about transcriptome analysis and about gene networks, we delineate a methodology for modelling such kind of networks by means of Metabolic P systems. MP systems were initially introduced as models of metabolic processes, but they can be successfully used in each context where we want to infer models of a system from a given set of time series. In thecase of gene expression analysis, we found a standard way for translating MP grammars involving gene expressions into corresponding quantitative gene networks. Pre-processing methods of raw time series have been also elaborated in order to achieve a successful MP modelling of theunderlying gene network.