Gene regulatory network discovery from time-series gene expression Data - A computational intelligence approach

Abstract

The interplay of interactions between DNA, RNA and proteins leads to genetic regulatory networks (GRN) and in turn controls the gene regulation. Directly or indirectly in a cell such molecules either interact in a positive or in repressive manner therefore it is hard to obtain the accurate computational models through which the final state of a cell can be predicted with certain accuracy. This paper describes biological behaviour of actual regulatory systems and we propose a novel method for GRN discovery of a large number of genes from multiple time series gene expression observations over small and irregular time intervals. The method integrates a genetic algorithm (GA) to select a small number of genes and a Kaiman filter to derive the GRN of these genes. After GRNs of smaller number of genes are obtained, these GRNs may be integrated in order to create the GRN of a larger group of genes of interest. © Springer-Verlag Berlin Heidelberg 2004.