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This article is part of the supplement: Selected articles from the IEEE International Conference on Bioinformatics and Biomedicine 2012: Bioinformatics

Open Access Research

An efficient method for mining cross-timepoint gene regulation sequential patterns from time course gene expression datasets

Chun-Pei Cheng1, Yu-Cheng Liu12, Yi-Lin Tsai1 and Vincent S Tseng13*

Author Affiliations

1 Department of Computer Science and Information Engineering, National Cheng Kung University, No.1, University Road, Tainan City 701, Taiwan

2 Department of Environmental and Occupational Health, National Cheng Kung University, No.1, University Road, Tainan City 701, Taiwan

3 Institute of Medical Informatics, National Cheng Kung University, No.1, University Road, Tainan City 701, Taiwan

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BMC Bioinformatics 2013, 14(Suppl 12):S3  doi:10.1186/1471-2105-14-S12-S3

Published: 24 September 2013

Abstract

Background

Observation of gene expression changes implying gene regulations using a repetitive experiment in time course has become more and more important. However, there is no effective method which can handle such kind of data. For instance, in a clinical/biological progression like inflammatory response or cancer formation, a great number of differentially expressed genes at different time points could be identified through a large-scale microarray approach. For each repetitive experiment with different samples, converting the microarray datasets into transactional databases with significant singleton genes at each time point would allow sequential patterns implying gene regulations to be identified. Although traditional sequential pattern mining methods have been successfully proposed and widely used in different interesting topics, like mining customer purchasing sequences from a transactional database, to our knowledge, the methods are not suitable for such biological dataset because every transaction in the converted database may contain too many items/genes.

Results

In this paper, we propose a new algorithm called CTGR-Span (Cross-Timepoint Gene Regulation Sequential pattern) to efficiently mine CTGR-SPs (Cross-Timepoint Gene Regulation Sequential Patterns) even on larger datasets where traditional algorithms are infeasible. The CTGR-Span includes several biologically designed parameters based on the characteristics of gene regulation. We perform an optimal parameter tuning process using a GO enrichment analysis to yield CTGR-SPs more meaningful biologically. The proposed method was evaluated with two publicly available human time course microarray datasets and it was shown that it outperformed the traditional methods in terms of execution efficiency. After evaluating with previous literature, the resulting patterns also strongly correlated with the experimental backgrounds of the datasets used in this study.

Conclusions

We propose an efficient CTGR-Span to mine several biologically meaningful CTGR-SPs. We postulate that the biologist can benefit from our new algorithm since the patterns implying gene regulations could provide further insights into the mechanisms of novel gene regulations during a biological or clinical progression. The Java source code, program tutorial and other related materials used in this program are available at http://websystem.csie.ncku.edu.tw/CTGR-Span.rar webcite.