Building genetic networks for gene expression patterns

Abstract

Building genetic regulatory networks from time series data of gene expression patterns is an important topic in bioinformatics. Probabilistic Boolean networks (PBNs) have been developed as a model of gene regulatory networks. PBNs are able to cope with uncertainty, corporate rule-based dependencies between genes and uncover the relative sensitivity of genes in their interactions with other genes. However, PBNs are unlikely used in practice because of huge number of possible predictors and their computed probabilities. In this paper, we propose a multivariate Markov chain model to govern the dynamics of a genetic network for gene expression patterns. The model preserves the strength of PBNs and reduce the complexity of the networks. Parameters of the model are quadratic with respect to the number of genes. We also develop an efficient estimation method for the model parameters. Simulation results on yeast data are given to illustrate the effectiveness of the model. © Springer-Verlag Berlin Heidelberg 2004.