Abstract
This paper presents a simple and novel least squares fitting-based modeling approach for the extraction simple gene regulatory sub- networks from biclusters in microarray time series gene expression data. Preprocessing helps in retaining the strongly interacting gene regulatory pairs. The methodology was applied to public-domain data sets of Yeast and the experimental results were biologically validated based on standard databases and information from literature.
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Mitra, S., Das, R., Hayashi, Y.: Genetic networks and soft computing. IEEE/ACM Transactions on Computational Biology and Bioinformatics (to appear)
Mitra, S., Banka, H.: Multi-objective evolutionary biclustering of gene expression data. Pattern Recognition 39, 2464–2477 (2006)
Kohane, I.S., Kho, A.T., Butte, A.J.: Microarrays for an Integrative Genomics. MIT Press, Cambridge (2003)
Filkov, V., Skiena, S., Zhi, J.: Analysis techniques for microarray time-series data. Journal of Computational Biology 9, 317–330 (2002)
Mitra, S., Das, R., Banka, H., Mukhopadhyay, S.: Gene interaction - An evolutionary biclustering approach. Information Fusion 10, 242–249 (2009)
Cho, R.J., Campbell, M.J., Winzeler, L.A., Steinmetz, L., Conway, A., Wodicka, L., Wolfsberg, T.G., Gabrielian, A.E., Landsman, D., Lockhart, D.J., Davis, R.W.: A genome-wide transcriptional analysis of the mitotic cell cycle. Molecular Cell 2, 65–73 (1998)
Bo, T., Dysvik, B., Jonassen, I.: LSimpute: accurate estimation of missing values in microarray data with least squares methods. Nucleic Acids Research 32, 1–8 (2004)
Yu, H., Gerstein, M.: Genomic analysis of the hierarchical structure of regulatory networks. Proceedings of National Academy of Sciences USA 103, 14724–14731 (2006)
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Das, R., Mitra, S., Murthy, C.A., Mukhopadhyay, S. (2009). A Least Squares Fitting-Based Modeling of Gene Regulatory Sub-networks. In: Chaudhury, S., Mitra, S., Murthy, C.A., Sastry, P.S., Pal, S.K. (eds) Pattern Recognition and Machine Intelligence. PReMI 2009. Lecture Notes in Computer Science, vol 5909. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-11164-8_27
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DOI: https://doi.org/10.1007/978-3-642-11164-8_27
Publisher Name: Springer, Berlin, Heidelberg
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Online ISBN: 978-3-642-11164-8
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