Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Highly Accessed Methodology article

Detecting multivariate differentially expressed genes

Roland Nilsson1*, José M Peña1, Johan Björkegren2 and Jesper Tegnér12

Author Affiliations

1 Computational Biology, Department of Physics, Linköping University, SE-581 53 Linköping, Sweden

2 Unit of Computational Medicine, King Gustaf V Research Institute, Department of Medicine, Karolinska Institutet, SE-171 76 Stockholm, Sweden

For all author emails, please log on.

BMC Bioinformatics 2007, 8:150  doi:10.1186/1471-2105-8-150

Published: 9 May 2007

Abstract

Background

Gene expression is governed by complex networks, and differences in expression patterns between distinct biological conditions may therefore be complex and multivariate in nature. Yet, current statistical methods for detecting differential expression merely consider the univariate difference in expression level of each gene in isolation, thus potentially neglecting many genes of biological importance.

Results

We have developed a novel algorithm for detecting multivariate expression patterns, named Recursive Independence Test (RIT). This algorithm generalizes differential expression testing to more complex expression patterns, while still including genes found by the univariate approach. We prove that RIT is consistent and controls error rates for small sample sizes. Simulation studies confirm that RIT offers more power than univariate differential expression analysis when multivariate effects are present. We apply RIT to gene expression data sets from diabetes and cancer studies, revealing several putative disease genes that were not detected by univariate differential expression analysis.

Conclusion

The proposed RIT algorithm increases the power of gene expression analysis by considering multivariate effects while retaining error rate control, and may be useful when conventional differential expression tests yield few findings.