Gene Regulatory Network modelling: A state-space approach

International Journal of Data Mining and Bioinformatics

Volumn 2, Issue 1, 2008, Pages 1-14

  Wu, Fang Xiang ^a  

^a UNIVERSITY OF SASKATCHEWAN   (Canada)

Author keywords

Bayesian Information Criterion; BIC; Bioinformatics; Controllability; Data mining; Gene Regulatory Network; GRN; Observability; Periodicity; PPCA; Probabilistic Principal Component Analysis; Robustness; Stability; State space approach; Time course gene expression data

Indexed keywords

EID: 39149105974     PISSN: 17485673     EISSN: 17485681     Source Type: Journal    
DOI: 10.1504/IJDMB.2008.016753     Document Type: Article

References (33)

1. Akutsu, T., Miyano, S. and Kuhara, S. (1999) 'Identification of gene networks from a small number of gene expression patterns under the Boolean network model', Pacific Symposium on Biocomputing, Vol. 4, pp. 17-28.
2. Alberts, B., Johnson, A., Lewis, J., Raff, M., Bray, D., Hopkin, K., Roberts, K. and Walter, P. (1998) Essential Cell Biology, Garland Science, New York.
3. Baldi, P. and Hatfield, G.W. (2002) DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling, Cambridge University Press, New York.
4. Burnham, K.P. and Anderson, D.R. (1998) Model Selection and Inference: A Practical Information-theoretic Approach, Springer, New York.
5. Chen, C.T. (1999) Linear System Theory and Design, 3rd ed., Oxford University Press, New York.
6. Chen, T., He, H.L. and Church, G.M. (1999) 'Modeling gene expression with differential equations', Pacific Symposium on Biocomputing, Vol. 4, pp.29-40.
7. D'haeseleer, P., Wen, X., Fuhrman, S. and Somogyi, R. (1999) 'Linear modeling of mRNA expression levels during CNS development and injury', Pacific Symposium on Biocomputing, Vol. 4, pp.41-52.
8. Duda, R.O., Hart, P.E. and Stork, D.G. (2001) Pattern Classification Wiley Press, New York.
9. Durbin, J. and Koopman, S.J. (2001) Time-series Analysis by State Space Model, Oxford University Press, New York.
10. Eisen, M.B., Spellman, P.T., Brown, P.O. and Botstein, D. (1998) 'Cluster analysis and display of genome-wide expression patterns', Proc. Natl. Acad. Sci. USA, Vol. 95, pp. 14863-14868.
11. Everitt, B.S. and Dunn, G. (1992) Applied Multivariate Data Analysis Oxford University Press, New York.
12. Gardner T.S., di Bernardo, D., Lorenz, D. and Collins, J.J. (2003) 'Inferring genetic networks and identifying compound mode of action via expression profiling', Science, Vol. 301, pp.102-105.
13. Harvey, A.C. (1993) Time Series Models, 2nd ed., The MIT Press, Cambridge, MA.
14. Kauffman, S.A. (1993) The Origins of Order: Self-Organization and Selection in Evolution, Oxford University Press, Oxford.
15. Kitano, H. (2002) 'Computational systems biology', Nature, Vol. 420, pp.206-210.
16. Langmead, C.J., Yan, A.K., McClung, C.R. and Donald, B.R. (2002) 'Phase-independent rhythmic analysis of genome-wide expression patterns', Proceedings of the Sixth Annual International Conference on Research in Computational Molecular Biology, Washington DC, USA, Vol. 1, pp.205-215.
17. Laub, M.T., McAdams, H.H., Feldblyum, T., Fraser, C.M. and Shapiro, L. (2000) 'Global analysis of the genetic network controlling a bacterial cell cycle', Science, Vol. 290, pp.2144 2148.
18. Liang, S., Fuhrman, S. and Somogyi, R. (1998) 'REVEAL, a general reverse engineering algorithm for inference of genetic network architectures', Pacific Symposium on Biocomputing, Vol. 3, pp. 18-29.
19. Liebler, D.C. (2002) Introduction to Proteomics, Humana Press, Totowa, NJ.
20. Press, W.H., Flannery, B.P., Teukolsky, S.A. and Vetterling, W.T. (1992) Numerical Recipes in C: The Art of Scientific Computing, 2nd ed., Cambridge University Press, Cambridge, UK.
21. Schwarz, G. (1978) 'Estimating the dimension of a model', Annals of Statistics, Vol. 6, pp.461-464.
22. Somogyi, R. and Sniegoski, C.A. (1996) 'Modeling the complexity of genetic networks: Understanding multigenic and pleiotropic regulation', Complexity, Vol. 1, pp.45-63.
23. Spellman, P.T., Sherlock, G., Zhang, M.Q., Iyer, V.R., Anders, K., Eisen, M.B., Brown, P.O., Botstein, D. and Futcher, B. (1998) 'Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization', Mol. Biol., Vol. 9, pp.3273-3297.
24. Spieth, C., Streichert, F., Speer, N. and Zell, A. (2004) 'Iteratively inferring gene regulatory networks with virtual knockout experiments', Proc. 2nd European Workshop on Evolutionary Bioinformatics, Coimbra, Portugal, April 5-7, pp. 104-112.
25. Tavazoie, S., Hughes, J.D., Campbell, M.J., Cho, R.J. and Church, G.M. (1999) 'Systematic determination of genetic network architecture', Nature Genetics, Vol. 22, pp.281-285.
26. Tipping, M.E. and Bishop, C.M. (1999) 'Probabilistic principal component analysis', Journal of the Royal Statistical Society, Series B, Vol. 61, pp.611-622.
27. Tozeren, A. and Byers, S.W. (2004) New Biology for Engineers and Computer Scientists, Pearson Education Inc., New Jersey.
28. Wessels, L.F.A., van Someren, E.P. and Reinders, M.J.T. (2001) 'A comparison of genetic network models', Pacific Symposium on Biocomputing, Vol. 6, pp.508-519.
29. Wichert, S., Fokianos, K. and Strimmer, K. (2004) 'Identifying periodically expressed transcripts in microarray time series data', Bioinformatics, Vol. 20, pp. 5-20.
30. Wu, F.X., Zhang, W.J. and Kusalik, A.J. (2004a) 'Modeling gene expression from microarray expression data with state-space equations', Pacific Symposium on Biocomputing, Vol. 9, pp.581-592.
31. Wu, F.X., Zhang, W.J. and Kusalik, A.J. (2004b) 'State-space model with time delays for gene regulatory networks', Journal of Biological Systems, Vol. 12, pp.483-499.
32. Wu, F.X., Poirier, G.G. and Zhang, W.J. (2005) 'Inferring gene regulatory networks with time delays using a genetic algorithm', IEE Proc. Systems Biology, Vol. 152, pp.67-74.
33. Yeung, K.Y., Fraley, C., Murua, A., Rafterym, A.E. and Ruzzo, W.L. (2001) 'Model-based clustering and data transformations for gene expression data', Bioinformatics, Vol. 17, pp.977-987.