Computational identification of condition-specific miRNA targets based on gene ezpression profiles and sequence information
Background: MicroRNAs (miRNAs) are small and noncoding RNAs that play important roles in various biological processes. They regulate target mRNAs post-transcriptionally through complementary base pairing. Since the changes of miRNAs affect the expression of target genes,the expression levels of target genes in specific biological processes could be different from those of non-target genes. Here we demonstrate that gene expression profiles contain useful information in separating rniRNA targets from non-targets.Results: The gene expression profiles related to various developmental processes and stresses,as well as the sequences of miRNAs and mRNAs in Arabidopsis, were used to determine whether a given gene is a miRNA target. It is based on the model combining the support vector machine (SVM) classifier and the scoring method based on complementary base pairing between miRNAs and mRNAs. The proposed model yielded low false positive rate and retrieved condition-specific candidate targets through a genome-wide screening.Conclusions: Our approach provides a novel framework into screening target genes by considering the gene regulation of miRNAs. It can be broadly applied to identify condition-specific targets computationally by embedding information of gene expression profiles.
Je-Gun Joung Zhangjun Fei
Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA USDA Robert W
国际会议
The 7th Asia-Pacific Bioinformatics Conference(第七届亚太生物信息学大会)
北京
英文
392-400
2009-01-01（万方平台首次上网日期，不代表论文的发表时间）