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Bioinformatics Advance Access originally published online on November 22, 2005
Bioinformatics 2006 22(3):332-340; doi:10.1093/bioinformatics/bti792
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

A bi-dimensional regression tree approach to the modeling of gene expression regulation

Jianhua Ruan 1 and Weixiong Zhang 1,2,*

1Department of Computer Science and Engineering, Washington University in St Louis St Louis, MO 63130, USA
2Department of Genetics, Washington University in St Louis St Louis, MO 63130, USA

*To whom correspondence should be addressed.

Motivation: The transcriptional regulation of a gene depends on the binding of cis-regulatory elements on its promoter to some transcription factors and the expression levels of the transcription factors. Most existing approaches to studying transcriptional regulation model these dependencies separately, i.e. either from promoters to gene expression or from the expression levels of transcription factors to the expression levels of genes. Little effort has been devoted to a single model for integrating both dependencies.

Results: We propose a novel method to model gene expression using both promoter sequences and the expression levels of putative regulators. The proposed method, called bi-dimensional regression tree (BDTree), extends a multivariate regression tree approach by applying it simultaneously to both genes and conditions of an expression matrix. The method produces hypotheses about the condition-specific binding motifs and regulators for each gene. As a side-product, the method also partitions the expression matrix into small submatrices in a way similar to bi-clustering. We propose and compare several splitting functions for building the tree. When applied to two microarray datasets of the yeast Saccharomyces cerevisiae, BDTree successfully identifies most motifs and regulators that are known to regulate the biological processes underlying the datasets. Comparing with an existing algorithm, BDTree provides a higher prediction accuracy in cross-validations.

Availability: The software is available upon request from the authors.

Contact: zhang{at}cse.wustl.edu

Supplementary information: http://cic.cs.wustl.edu/bdtree/

Received on March 16, 2005; revised on October 10, 2005; accepted on November 15, 2005

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