Email updates

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

This article is part of the supplement: The 2007 International Conference on Bioinformatics & Computational Biology (BIOCOMP'07)

Open Access Research

Identification of transcription factor and microRNA binding sites in responsible to fetal alcohol syndrome

Guohua Wang123, Xin Wang124, Yadong Wang3, Jack Y Yang2, Lang Li1, Kenneth P Nephew5, Howard J Edenberg67, Feng C Zhou8* and Yunlong Liu127*

Author Affiliations

1 Division of Biostatistics Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA

2 Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA

3 School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, 150001, China

4 College of Automation, Harbin Engineering University, Harbin, Heilongjiang 150001, China

5 Medical Sciences, Indiana University School of Medicine, Bloomington, IN 47405, USA

6 Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA

7 Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, IN 46202, USA

8 Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA

For all author emails, please log on.

BMC Genomics 2008, 9(Suppl 1):S19  doi:10.1186/1471-2164-9-S1-S19

Published: 20 March 2008

Abstract

This is a first report, using our MotifModeler informatics program, to simultaneously identify transcription factor (TF) and microRNA (miRNA) binding sites from gene expression microarray data. Based on the assumption that gene expression is controlled by combinatorial effects of transcription factors binding in the 5'-upstream regulatory region and miRNAs binding in the 3'-untranslated region (3'-UTR), we developed a model for (1) predicting the most influential cis-acting elements under a given biological condition, and (2) estimating the effects of those elements on gene expression levels. The regulatory regions, TF and miRNA, which mediate the differential genes expression in fetal alcohol syndrome were unknown; microarray data from alcohol exposure paradigm was used. The model predicted strong inhibitory effects of 5' cis-acting elements and stimulatory effects of 3'-UTR under alcohol treatment. Current predictive model derived a key hypothesis for the first time a novel role of miRNAs in gene expression changes associated with abnormal mouse embryo development after alcohol exposure. This suggests that disturbance of miRNA functions may contribute to the alcohol-induced developmental deficiencies.