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BMC Research Notes

, 3:142

First Online: 25 May 2010Received: 08 April 2010Accepted: 25 May 2010DOI: 10.1186-1756-0500-3-142

Cite this article as: Huang, T., Liu, L., Qian, Z. et al. BMC Res Notes 2010 3: 142. doi:10.1186-1756-0500-3-142


BackgroundUnderstanding gene expression and regulation is essential for understanding biological mechanisms. Because gene expression profiling has been widely used in basic biological research, especially in transcription regulation studies, we have developed GeneReg, an easy-to-use R package, to construct gene regulatory networks from time course gene expression profiling data; More importantly, this package can provide information about time delays between expression change in a regulator and that of its target genes.

FindingsThe R package GeneReg is based on time delay linear regression, which can generate a model of the expression levels of regulators at a given time point against the expression levels of their target genes at a later time point. There are two parameters in the model, time delay and regulation coefficient. Time delay is the time lag during which expression change of the regulator is transmitted to change in target gene expression. Regulation coefficient expresses the regulation effect: a positive regulation coefficient indicates activation and negative indicates repression. GeneReg was implemented on a real Saccharomyces cerevisiae cell cycle dataset; more than thirty percent of the modeled regulations, based entirely on gene expression files, were found to be consistent with previous discoveries from known databases.

ConclusionsGeneReg is an easy-to-use, simple, fast R package for gene regulatory network construction from short time course gene expression data. It may be applied to study time-related biological processes such as cell cycle, cell differentiation, or causal inference.

AbbreviationsODEOrdinary differential equation

AICAkaike Information Criterion

ORFopen reading frame.

Electronic supplementary materialThe online version of this article doi:10.1186-1756-0500-3-142 contains supplementary material, which is available to authorized users.

Tao Huang, Lei Liu contributed equally to this work.

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Autor: Tao Huang - Lei Liu - Ziliang Qian - Kang Tu - Yixue Li - Lu Xie


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