BayMiR: inferring evidence for endogenous miRNA-induced gene repression from mRNA expression profiles.

ABSTRACT:

Background

Popular miRNA target prediction techniques use sequence features to determine the functional miRNA target sites. These techniques commonly ignore the cellular conditions in which miRNAs interact with their targets in vivo. Gene expression data are rich resources that can complement sequence features to take into account the context dependency of miRNAs.

Results

We introduce BayMiR, a new computational method, that predicts the functionality of potential miRNA target sites using the activity level of the miRNAs inferred from genome-wide mRNA expression profiles. We also found that mRNA expression variation can be used as another predictor of functional miRNA targets. We benchmarked BayMiR, the expression variation, Cometa, and the TargetScan "context scores" on two

SUBMITTER: Radfar H 

PROVIDER: S-EPMC3933272 | biostudies-literature | 2013 Aug

REPOSITORIES: biostudies-literature