A novel pattern based clustering methodology for time-series microarray data

Authors:
Sieu Phan;Fazel Famili;Zoujian Tang;Youlian Pan;Ziying Liu;Junjun Ouyang;Anne Lenferink;Maureen Mc-Court O'connor
Affiliations:
Institute for Information Technology, National Research Council Canada, Ottawa, Ontario, Canada;Institute for Information Technology, National Research Council Canada, Ottawa, Ontario, Canada;Institute for Information Technology, National Research Council Canada, Ottawa, Ontario, Canada;Institute for Information Technology, National Research Council Canada, Ottawa, Ontario, Canada;Institute for Information Technology, National Research Council Canada, Ottawa, Ontario, Canada;Institute for Information Technology, National Research Council Canada, Ottawa, Ontario, Canada;Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada;Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
Venue:
International Journal of Computer Mathematics - Bioinformatics
Year:
2007

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Abstract

Identification of co-expressed genes sharing similar biological behaviours is an essential step in functional genomics. Traditional clustering techniques are generally based on overall similarity of expression levels and often generate clusters with mixed profile patterns. A novel pattern recognition method for selecting co-expressed genes based on rate of change and modulation status of gene expression at each time interval is proposed in this paper. This method is capable of identifying gene clusters consisting of highly similar shapes of expression profiles and modulation patterns. Furthermore, we develop a quality index based on the semantic similarity in gene annotations to assess the likelihood of a cluster being a co-regulated group. The effectiveness of the proposed methodology is demonstrated by applying it to the well-known yeast sporulation dataset and an in-house cancer genomics dataset.