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Bioinformatics Advance Access published online on November 15, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm507
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Genome-wide co-expression based prediction of differential expressions

Yinglei Lai *

Department of Statistics and Biostatistics Center, The George Washington University, 2140Pennsylvania Avenue, N.W. Washington, D.C. 20052

*To whom correspondence should be addressed. Dr. Yinglei Lai E-mail: ylai{at}gwu.edu


  Abstract

Motivation: Microarrays have been widely used for medical studies to detect novel disease related genes. They enable us to study differential gene expressions at a genomic level. They also provide us with informative genome-wide co-expressions. Although many statistical methods have been proposed for identifying differentially expressed genes, genome-wide co-expressions have not been well considered for this issue. Incorporating genome-wide co-expression information in the differential expression analysis may improve the detection of disease related genes.

Results: In this study, we proposed a statistical method for predicting differential expressions through the local regression between differential expression and co-expression measures. The smoother span parameter was determined by optimizing the rank correlation between the observed and predicted differential expression measures. A mixture normal quantile based method was used to transform data. We used the gene-specific permutation procedure to evaluate the significance of a prediction. Two published microarray data sets were analyzed for applications. For the data set collected for a prostate cancer study, the proposed method identified many genes with weak differential expressions. Several of these genes have been shown in literature to be associated with the disease. For the data set collected for a type 2 diabetes study, no significant genes could be identified by the traditiona methods. However, the proposed method identified many genes with ignificantly low false discovery rates.

Availability: The R codes are freely available at http://home.gwu.edu/~ylai/research/CoDiff, where the gene lists ranked by our method are also provided as the Supplementary Data.

Contact: ylai{at}gwu.edu

Associate Editor: Dr. Trey Ideker

Received on May 31, 2007; revised on September 9, 2007; accepted on October 4, 2007

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