Context-specific microRNA analysis: identification of functional microRNAs and their mRNA targets.

ABSTRACT: MicroRNAs (miRs) function primarily as post-transcriptional negative regulators of gene expression through binding to their mRNA targets. Reliable prediction of a miR's targets is a considerable bioinformatic challenge of great importance for inferring the miR's function. Sequence-based prediction algorithms have high false-positive rates, are not in agreement, and are not biological context specific. Here we introduce CoSMic (Context-Specific MicroRNA analysis), an algorithm that combines sequence-based prediction with miR and mRNA expression data. CoSMic differs from existing methods--it identifies miRs that play active roles in the specific biological system of interest and predicts with less false positives their functional targets. We applied CoSMic to search for miRs that regulate th

SUBMITTER: Bossel Ben-Moshe N 

PROVIDER: S-EPMC3505984 | biostudies-literature | 2012 Nov

REPOSITORIES: biostudies-literature