Abstract
BackgroundMicroRNAs (miRNAs) are small non-coding RNA molecules that are ~22-nt-long sequences capable of suppressing protein synthesis. Previous research has suggested that miRNAs regulate 30% or more of the human protein-coding genes. The aim of this work is to consider various analyzing scenarios in the identification of miRNA-target interactions, as well as to provide an integrated system that will aid in facilitating investigation on the influence of miRNA targets by alternative splicing and the biological function of miRNAs in biological pathways.ResultsThis work presents an integrated system, miRTar, which adopts various analyzing scenarios to identify putative miRNA target sites of the gene transcripts and elucidates the biological functions of miRNAs toward their targets in biological pathways. The system has three major features. First, the prediction system is able to consider various analyzing scenarios (1 miRNA:1 gene, 1:N, N:1, N:M, all miRNAs:N genes, and N miRNAs: genes involved in a pathway) to easily identify the regulatory relationships between interesting miRNAs and their targets, in 3'UTR, 5'UTR and coding regions. Second, miRTar can analyze and highlight a group of miRNA-regulated genes that participate in particular KEGG pathways to elucidate the biological roles of miRNAs in biological pathways. Third, miRTar can provide further information for elucidating the miRNA regulation, i.e., miRNA-target interactions, affected by alternative splicing.ConclusionsIn this work, we developed an integrated resource, miRTar, to enable biologists to easily identify the biological functions and regulatory relationships between a group of known/putative miRNAs and protein coding genes. miRTar is now available at http://miRTar.mbc.nctu.edu.tw/.
Highlights
MicroRNAs are small non-coding RNA molecules that are ~22-nt-long sequences capable of suppressing protein synthesis
We aim to provide an integrated resource to allow biologists to elucidate miRNA-target interactions affected by the alternative splicing considering that the location of miRNA target sites may be found in exons, which are alternatively spliced
Case study of alternatively spliced target-containing exon To demonstrate the functionality of miRTar in realizing the functional interactions between mature miRNAs and alternative pre-mRNA splicing, the miRNA
Summary
MicroRNAs (miRNAs) are small non-coding RNA molecules that are ~22-nt-long sequences capable of suppressing protein synthesis. MicroRNAs (miRNAs) are small non-coding RNA molecules that are ~22 nts sequences capable of suppressing protein synthesis. Previous investigations suggest that miRNA target sites in mammalians are preferentially conserved in mRNA sequences, especially in 3’ UTR [3]. Since these miRNA-regulated genes are involved in various crucial cell processes including. TargetScan [9], miRanda [10] and RNAhybrid [11] are three computational tools for determining the most energetically favored hybridization sites of small to large RNAs. PicTar [12] is capable of identifying common targets of known miRNAs. DIANA-microT [13] system utilizes experimentally derived miRNA/mRNA binding rules. DIANA-microT [13] system utilizes experimentally derived miRNA/mRNA binding rules. miRNAMap [14,15] and miRecords [16], miRGen [17,18] and GOmir [19] provide the putative miRNAtarget interactions by combining prediction from multiple programs
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