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Open Access Research article

Predicting state transitions in the transcriptome and metabolome using a linear dynamical system model

Ryoko Morioka1, Shigehiko Kanaya2, Masami Y Hirai1, Mitsuru Yano3, Naotake Ogasawara2 and Kazuki Saito13*

Author Affiliations

1 RIKEN Plant Science Center, Yokohama, Kanagawa, Japan

2 Department of Bioinformatics and Genomics, Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan

3 Department of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Science, Chiba University, Inage-ku, Chiba, Japan

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BMC Bioinformatics 2007, 8:343  doi:10.1186/1471-2105-8-343

Published: 18 September 2007



Modelling of time series data should not be an approximation of input data profiles, but rather be able to detect and evaluate dynamical changes in the time series data. Objective criteria that can be used to evaluate dynamical changes in data are therefore important to filter experimental noise and to enable extraction of unexpected, biologically important information.


Here we demonstrate the effectiveness of a Markov model, named the Linear Dynamical System, to simulate the dynamics of a transcript or metabolite time series, and propose a probabilistic index that enables detection of time-sensitive changes. This method was applied to time series datasets from Bacillus subtilis and Arabidopsis thaliana grown under stress conditions; in the former, only gene expression was studied, whereas in the latter, both gene expression and metabolite accumulation. Our method not only identified well-known changes in gene expression and metabolite accumulation, but also detected novel changes that are likely to be responsible for each stress response condition.


This general approach can be applied to any time-series data profile from which one wishes to identify elements responsible for state transitions, such as rapid environmental adaptation by an organism.