Genomics Inform Search


Genomics Inform > Volume 3(1); 2005 > Article
Identification of Caenorhabditis elegans MicroRNA Targets Using a Kernel Method.
Wha Jin Lee, Jin Wu Nam, Sung Kyu Kim, Byoung Tak Zhang
1Center for Bioinformation Technology (CBIT), Korea.
2Biointelligence Laboratory, School of Computer Science and Engineering, Seoul National University, Seoul 151-742, Korea.
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.
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.
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.
Share :
Facebook Twitter Linked In Google+
METRICS Graph View
  • 1,555 View
  • 17 Download
Related articles in GNI


Browse all articles >

Editorial Office
Room No. 806, 193 Mallijae-ro, Jung-gu, Seoul 04501, Korea
Tel: +82-2-558-9394    Fax: +82-2-558-9434    E-mail:                

Copyright © 2024 by Korea Genome Organization.

Developed in M2PI

Close layer
prev next