Temporal clustering of gene expression patterns using short-time segments Online publication date: Tue, 20-Nov-2012
by Nguyen Nguyen; Ying Ann Chiao; Yufei Huang; Shou-Jiang Gao; Merry Lindsey; Yidong Chen; Yufang Jin
International Journal of Functional Informatics and Personalised Medicine (IJFIPM), Vol. 4, No. 1, 2012
Abstract: Temporal clustering of time series data is a powerful tool to delaminate the dynamics of transcription and interactions among genes on a large scale. Different algorithms have been proposed to organise experimental data with meaningful biological clusters; however, these approaches often fail to generate well-defined temporal clusters, especially when genes exert their functions or response to stimuli coordinately only in a short period of time span. In this study, we proposed an algorithm using sliding windows to identify different temporal patterns based on fold changes of gene expressions. The algorithm was applied to simulated data and real experimental data. Furthermore, a comparison study has been carried out with the clusters obtained from commercial software packages. The identified clusters using our algorithm demonstrated better temporal matching and consistency.
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