%0 Journal Article
%T A combinatorial approach to determine the context-dependent role in transcriptional and posttranscriptional regulation in Arabidopsis thaliana
%A Le Lu
%A Jinming Li
%J BMC Systems Biology
%D 2009
%I BioMed Central
%R 10.1186/1752-0509-3-43
%X We applied the proposed method to microarray time course gene expression profiles and could correctly predict expression patterns for more than 50% of 1,132 genes, based on the sequence motifs adopted in the network models, which was statistically significant. Our study suggested that the contribution of miRNA regulation towards gene expression in plants may be more restricted than that of transcription factors; however, miRNAs might confer additional layers of robustness on gene regulation networks. The programs written in C++ and PERL implementing methods in this work are available for download from our supplemental data web page.In this study we demonstrated a combinatorial approach to incorporate miRNA target motifs (miRNA-mediated posttranscriptional regulatory sites) and TFBSs (transcription factor binding sites) with gene expression profiles to reconstruct the regulatory networks. The proposed approach may facilitate the incorporation of diverse sources with limited prior knowledge.Transcription factors (TFs) regulate gene expression by binding selectively to DNA sequences in promoters, and genes regulated by the same TFs have been assumed to share the common binding sites in their promoter regions and exhibit similar expression patterns [1]. Numerous experimental and computational studies [2] have been done on locating transcriptional regulator DNA binding sequences and understanding their working mechanisms. These binding motifs can be used as building blocks of gene regulatory networks and several approaches were developed to identify how a set of cis-regulatory elements in a gene's promoter region governed its behavior and explained the observed expression profiles [3-5]. Using different approaches, Segal et al. [3] and Beer and Tavazoie [4] both showed that a substantial fraction of yeast gene expression profiles could be explained in terms of the combination of cis-regulatory elements. However, a limitation of such approaches is that many genes are post
%U http://www.biomedcentral.com/1752-0509/3/43