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Open Access Highly Accessed Research article

A temporal precedence based clustering method for gene expression microarray data

Ritesh Krishna1, Chang-Tsun Li1* and Vicky Buchanan-Wollaston2

Author Affiliations

1 Department of Computer Science, Warwick University, Coventry CV4 7AL, UK

2 Warwick Horticulture Research Institute, University of Warwick, Wellesbourne CV35 9EF, UK

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BMC Bioinformatics 2010, 11:68  doi:10.1186/1471-2105-11-68

Published: 30 January 2010

Abstract

Background

Time-course microarray experiments can produce useful data which can help in understanding the underlying dynamics of the system. Clustering is an important stage in microarray data analysis where the data is grouped together according to certain characteristics. The majority of clustering techniques are based on distance or visual similarity measures which may not be suitable for clustering of temporal microarray data where the sequential nature of time is important. We present a Granger causality based technique to cluster temporal microarray gene expression data, which measures the interdependence between two time-series by statistically testing if one time-series can be used for forecasting the other time-series or not.

Results

A gene-association matrix is constructed by testing temporal relationships between pairs of genes using the Granger causality test. The association matrix is further analyzed using a graph-theoretic technique to detect highly connected components representing interesting biological modules. We test our approach on synthesized datasets and real biological datasets obtained for Arabidopsis thaliana. We show the effectiveness of our approach by analyzing the results using the existing biological literature. We also report interesting structural properties of the association network commonly desired in any biological system.

Conclusions

Our experiments on synthesized and real microarray datasets show that our approach produces encouraging results. The method is simple in implementation and is statistically traceable at each step. The method can produce sets of functionally related genes which can be further used for reverse-engineering of gene circuits.