Analyzing Time Course Gene Expression Data with Biological and Technical Replicates to Estimate Gene Networks by State Space Models
Asia International Conference on Modelling & Simulation (2008)
May 13, 2008 to May 15, 2008
DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/AMS.2008.150
In order to estimate accurate gene networks from time course gene expression data, replicated time course data are useful. However, existing methods do not clearly distinguish between biological and technical replicates, while these two kinds of replicates have different features. In this paper, we propose a statistical model based on state space models to use biologically and technically replicated time course data and show an algorithm to estimate a gene network that is a graphical representation of gene-gene regulation. To our knowledge, for estimating gene networks, the proposed model is the first model that can simultaneously use two types of replicated time course data. We show the effectiveness of the proposed method through the analysis of the microarray human T-cell data.
state space model, time course gene expression data, technical and biological replicates, gene networks
S. Imoto, O. Hirose, S. Miyano, R. Yamaguchi, T. Higuchi and R. Yoshida, "Analyzing Time Course Gene Expression Data with Biological and Technical Replicates to Estimate Gene Networks by State Space Models," 2008 Second Asia International Conference on Modeling & Simulation(AMS), Kuala Lumpur, 2008, pp. 940-946.