Genomics Inform.  2005 Mar;3(1):15-23.

Identification of Caenorhabditis elegans MicroRNA Targets Using a Kernel Method

• Lee WJ
• Nam JW
• Kim SK
• Zhang BT

Abstract

BACKGROUND
MicroRNAs (miRNAs)are a class of noncoding RNAs found in various organisms such as plants and mammals. However, most of the mRNAs regulated by miRNAs are unknown. Furthermore, miRNA targets in genomes cannot be identified by standard sequence comparison since their complementarity to the target sequence is imperfect in general. In thi s paper, we propose a kernel-based method for the efficient prediction of miRNA targets. To help in distinguishing the false positives from potentially valid targets, we elucidate the features common in experimentally confirmed targets.
RESULTS
The performance of our prediction method was evaluated by five-fold cross-validation. Our method showed 0.64 and 0.98 in sensitivity and in specificity, respectively. Also, the proposed method reduced the number of false positives by half compared with TargetScan. We investigated the effect of feature sets on the classification of miRNA targets. Finally, we predicted miRNA targets for several miRNAs in the Caenorhabditis elegans (C.elegans )3'untranslated region (3'UTR) database.
CONCLUSIONS
The targets predicted by the suggested method will help in validating more miRNA targets and ultimately in revealing the role of small RNAs in the regulation of genomes. Our algorithm for miRNA target site detection will be able to be improved by additional experimental-knowledge. Also, the increase of the number of confirmed targets is expected to reveal general structural features that can be used to improve their detection.

MeSH Terms

Caenorhabditis elegans*
Caenorhabditis*
Classification
Genome
Mammals
MicroRNAs*
RNA
RNA, Messenger
RNA, Untranslated
Sensitivity and Specificity
MicroRNAs
RNA
RNA, Messenger
RNA, Untranslated