Analysis of putative miRNA function using a novel approach, GAPPS-miRTarGE
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Deciphering the function of miRNA is one of the most important research subjects directed toward understanding the regulation of gene expression. Several experimental methodologies and bioinformatics programs have been developed, however, elucidating miRNA function has not been an easy task. Herein, we suggest a new method, GAPPS-miRTarGE, which is a novel methodology for predicting miRNA function based on the proportion of mRNA targets expressed during embryonic developmental stages, the Theilers stages (TS), in mice. GAPPS-miRTarGE is essentially a computational approach that groups miRNAs using shared expression patterns of their target genes during the 28 different TS. In this study, we present not only several examples derived from the GAPPS-miRTarGE analyses that confirm previously known miRNA functions but also examples of function prediction for valid but functionally unknown miRNAs. Furthermore, we show that tissue-centered GAPPS-miRTarGE, such as brain-centered or heart-centered, is useful for predicting miRNA function on a more detailed level.
KeywordsPrediction of microRNA function miRNA target mRNA expression profile Embryonic developmental stage
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- Betel D, Wilson M, Gabow A, Marks DS and Sander C (2008) The microRNA.org resource: targets and expression. Nucleic Acids Res. 36: D149–D153.Google Scholar
- Griffiths-Jones S (2010) miRBase: microRNA sequences and annotation. Curr. Protoc. Bioinformatics Chapter 12: Unit 12 9 1–10.Google Scholar
- Theiler K (1989) The house mouse: atlas of embryonic development. Iintelligence 1: 1.Google Scholar
- Thompson JD, Gibson TJ and Higgins DG (2002) Multiple sequence alignment using ClustalW and ClustalX. Curr. Protoc. Bioinformatics Chapter 2: Unit 2 3.Google Scholar