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Open Access Methodology article

Difference-based clustering of short time-course microarray data with replicates

Jihoon Kim12 and Ju Han Kim1*

Author Affiliations

1 Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of Medicine, Seoul 110-799, Korea

2 Department of Statistics, University of Wisconsin-Madison, Medical Science Center, 1300 University Ave., Madison, WI 53706, USA

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BMC Bioinformatics 2007, 8:253  doi:10.1186/1471-2105-8-253

Published: 14 July 2007

Abstract

Background

There are some limitations associated with conventional clustering methods for short time-course gene expression data. The current algorithms require prior domain knowledge and do not incorporate information from replicates. Moreover, the results are not always easy to interpret biologically.

Results

We propose a novel algorithm for identifying a subset of genes sharing a significant temporal expression pattern when replicates are used. Our algorithm requires no prior knowledge, instead relying on an observed statistic which is based on the first and second order differences between adjacent time-points. Here, a pattern is predefined as the sequence of symbols indicating direction and the rate of change between time-points, and each gene is assigned to a cluster whose members share a similar pattern. We evaluated the performance of our algorithm to those of K-means, Self-Organizing Map and the Short Time-series Expression Miner methods.

Conclusions

Assessments using simulated and real data show that our method outperformed aforementioned algorithms. Our approach is an appropriate solution for clustering short time-course microarray data with replicates.