Relative R squared method for miRNA target identification and algorithm for tissue-specification of miRNA target interactions

• Main Authors: Hsieh, Wan-Ju, 謝宛茹
• Other Authors: Wang, Hsiu-Ying
• Format: Others
• Language: en_US
• Published: 2012
• Online Access: http://ndltd.ncl.edu.tw/handle/45394147299915812664

博士 === 國立交通大學 === 統計學研究所 === 100 === Recent studies have revealed a small non-coding RNA, microRNA (miRNA) down-regulates its mRNA targets, which is regarded as an important role in various biological processes. In recent years, there have been many studies concentrated on the discovery of new miRNAs and identification of their mRNA targets. Although researchers have identified many miRNAs, few miRNA targets have been identified by actual experimental methods. To expedite the identification of miRNA targets for experimental verification, in the literature approaches based on the sequence or microarray expression analysis have been established to discover the potential miRNA targets. We focus on the human miRNA target prediction and propose a generalized relative R squared method (RRSM) to find many high-confidence targets, which is shown to be superior to some existing methods. Although many high-confidence targets from RRSM have been confirmed from previous studies, the thresholds of RRSM are set to be fixed constants, which do not depend on the characteristic of a gene. To find a more feasible method for real data applications, we propose a variable threshold selection method based on the distribution of the relative R squared statistic, which is shown significantly improvement of the prediction results of RRSM only based on a fixed threshold criterion. In addition, we show that the interactions may be only functional on some specific-tissues which depend on the characteristic of a miRNA. There have been no systematic methods established in the literatures to investigate the relationship between miRNA target interactions and tissue specificity through microarray data. In this study, we propose an algorithm to investigate tissue-specificity of miRNAs based on experimental miRNA target interactions. The tissue-specificity result by our method is in accordance with the literatures.