Dataset Information

TarHunter, a tool for predicting conserved microRNA targets and target mimics in plants.

ABSTRACT: Summary:In plants, the targets of deeply conserved microRNAs (miRNAs) were comprehensively studied. Evidence is emerging that targets of less conserved miRNAs, endogenous target mimics (eTM) and non-canonical targets play functional roles. Existing plant miRNA prediction tools lack a cross-species conservation filter and eTM prediction function. We developed a tool named TarHunter that features a strict cross-species conservation filter and capability of predicting eTMs. TarHunter has higher recall or precision rate as compared with other tools, and the conservation filter effectively increases prediction precision. TarHunter prediction combined with degradome analysis uncovered previously neglected miRNA targets including non-canonical target sites from various plant species, which are available at the TarHunter website (http://tarhunter.genetics.ac.cn/). Availability and implementation:The code of TarHunter is available on Github (https://github.com/XMaBio). Contact:xuemei.chen@ucr.edu. Supplementary information:Supplementary data are available at Bioinformatics online.

SUBMITTER: Ma X

PROVIDER: S-EPMC6248703 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

TarHunter, a tool for predicting conserved microRNA targets and target mimics in plants.

Ma Xuan X Liu Chunyan C Gu Lianfeng L Mo Beixin B Cao Xiaofeng X Chen Xuemei X

Bioinformatics (Oxford, England) 20180501 9

<h4>Summary</h4>In plants, the targets of deeply conserved microRNAs (miRNAs) were comprehensively studied. Evidence is emerging that targets of less conserved miRNAs, endogenous target mimics (eTM) and non-canonical targets play functional roles. Existing plant miRNA prediction tools lack a cross-species conservation filter and eTM prediction function. We developed a tool named TarHunter that features a strict cross-species conservation filter and capability of predicting eTMs. TarHunter has hi ...[more]

PMID: 29236948

Similar Datasets

Project description:Variation in gene expression has been observed in natural populations and associated with complex traits or phenotypes such as disease susceptibility and drug response. Gene expression itself is controlled by various genetic and non-genetic factors. The binding of a class of small RNA molecules, microRNAs (miRNAs), to mRNA transcript targets has recently been demonstrated to be an important mechanism of gene regulation. Because individual miRNAs may regulate the expression of multiple gene targets, a comprehensive and reliable catalogue of miRNA-regulated targets is critical to understanding gene regulatory networks. Though experimental approaches have been used to identify many miRNA targets, due to cost and efficiency, current miRNA target identification still relies largely on computational algorithms that aim to take advantage of different biochemical/thermodynamic properties of the sequences of miRNAs and their gene targets. A novel approach, ExprTarget, therefore, is proposed here to integrate some of the most frequently invoked methods (miRanda, PicTar, TargetScan) as well as the genome-wide HapMap miRNA and mRNA expression datasets generated in our laboratory. To our knowledge, this dataset constitutes the first miRNA expression profiling in the HapMap lymphoblastoid cell lines. We conducted diagnostic tests of the existing computational solutions using the experimentally supported targets in TarBase as gold standard. To gain insight into the biases that arise from such an analysis, we investigated the effect of the choice of gold standard on the evaluation of the various computational tools. We analyzed the performance of ExprTarget using both ROC curve analysis and cross-validation. We show that ExprTarget greatly improves miRNA target prediction relative to the individual prediction algorithms in terms of sensitivity and specificity. We also developed an online database, ExprTargetDB, of human miRNA targets predicted by our approach that integrates gene expression profiling into a broader framework involving important features of miRNA target site predictions.

Dataset Information

TarHunter, a tool for predicting conserved microRNA targets and target mimics in plants.

Publications

TarHunter, a tool for predicting conserved microRNA targets and target mimics in plants.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure