原创力文档a two-step site and mrna-level model for predicting microrna targets一个两步网站和mrna-level模型预测microrna的目标.pdfVIP
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a two-step site and mrna-level model for predicting microrna targets一个两步网站和mrna-level模型预测microrna的目标
Saito and Sætrom BMC Bioinformatics 2010, 11:612
/1471-2105/11/612
RESEARCH ARTICLE Open Access
A two-step site and mRNA-level model for
predicting microRNA targets
1 1,2*
Takaya Saito , Pål Sætrom
Abstract
Background: Despite experiments showing that the number of microRNA (miRNA) target sites is critical for miRNA
targeting, most existing methods focus on identifying individual miRNA target sites and do not model
contributions of multiple target sites to miRNA regulation. To address this possible fault, we developed a miRNA
target prediction model that recognizes the individual characteristics of functional binding sites and the global
characteristics of miRNA-targeted mRNAs.
Results: Benchmark experiments showed that this two-step model generally had a higher overall performance
than other established miRNA target prediction algorithms and that the model was especially suited to identify
true miRNA targets among genes that all contain conserved target sites.
Conclusions: This improved performance could partly be explained by the model not relying on conservation
when predicting targets. The critical factors for the model’s performance, however, were mRNA-level features that
characterized the number and strength of individual target sites within the mRNA. The model is available for
online predictions or as pre-computed predictions on the human genome http://tare.medisin.ntnu.no/mirna_target.
Background miRNA target predictions in animals [4,8,9]. Most exist-
MicroRNAs (miRNAs) are a class of non-coding RNAs ing algorithms first perform sequence search on 3’
that can regulate many protein coding genes by base- UTRs to find regions that have complementarity to
paring
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