Recent development of bioinformatics tools for microRNA target prediction

2021 ◽  
Vol 28 ◽  
Author(s):  
Mst Shamima Khatun ◽  
Md Ashad Alam ◽  
Watshara Shoombuatong ◽  
Md Nurul Haque Mollah ◽  
Hiroyuki Kurata ◽  
...  
Keyword(s):  
Mirna Target ◽  
Target Identification ◽  
Target Prediction ◽  
Mirna Target Prediction ◽  
Microrna Target ◽  
Rna Sequences ◽  
Target Mrnas ◽  
Mirna Targets ◽  
Bioinformatics Tools ◽  
Experimental Approaches

: MicroRNAs (miRNAs) are central players that regulate the post-transcriptional processes of gene expression. Binding of miRNAs to target mRNAs can repress their translation by inducing the degradation or by inhibiting the translation of the target mRNAs. High-throughput experimental approaches for miRNA target identification are costly and time-consuming, depending on various factors. It is vitally important to develop the bioinformatics methods for accurately predicting miRNA targets. With the increase of RNA sequences in the post-genomic era, bioinformatics methods are being developed for miRNA studies specially for miRNA target prediction. This review summarizes the current development of state-of-the-art bioinformatics tools for miRNA target prediction, points out the progress and limitations of the available miRNA databases, and their working principles. Finally, we discuss the caveat and perspectives of the next-generation algorithms for the prediction of miRNA targets.

scholarly journals Comprehensive Overview and Assessment of microRNA Target Prediction Tools in Homo sapiens and Drosophila melanogaster

2019 ◽  
Vol 14 (5) ◽  
pp. 432-445 ◽  
Author(s):  
Muniba Faiza ◽  
Khushnuma Tanveer ◽  
Saman Fatihi ◽  
Yonghua Wang ◽  
Khalid Raza
Keyword(s):  
Drosophila Melanogaster ◽  
Mirna Target ◽  
Homo Sapiens ◽  
Target Prediction ◽  
Computational Prediction ◽  
Transcriptional Level ◽  
Mirna Target Prediction ◽  
Microrna Target ◽  
Prediction Tools ◽  
Mirna Targets

Background: MicroRNAs (miRNAs) are small non-coding RNAs that control gene expression at the post-transcriptional level through complementary base pairing with the target mRNA, leading to mRNA degradation and blocking translation process. Many dysfunctions of these small regulatory molecules have been linked to the development and progression of several diseases. Therefore, it is necessary to reliably predict potential miRNA targets. Objective: A large number of computational prediction tools have been developed which provide a faster way to find putative miRNA targets, but at the same time, their results are often inconsistent. Hence, finding a reliable, functional miRNA target is still a challenging task. Also, each tool is equipped with different algorithms, and it is difficult for the biologists to know which tool is the best choice for their study. Methods: We analyzed eleven miRNA target predictors on Drosophila melanogaster and Homo sapiens by applying significant empirical methods to evaluate and assess their accuracy and performance using experimentally validated high confident mature miRNAs and their targets. In addition, this paper also describes miRNA target prediction algorithms, and discusses common features of frequently used target prediction tools. Results: The results show that MicroT, microRNA and CoMir are the best performing tool on Drosopihla melanogaster; while TargetScan and miRmap perform well for Homo sapiens. The predicted results of each tool were combined in order to improve the performance in both the datasets, but any significant improvement is not observed in terms of true positives. Conclusion: The currently available miRNA target prediction tools greatly suffer from a large number of false positives. Therefore, computational prediction of significant targets with high statistical confidence is still an open challenge.

scholarly journals FilTar: using RNA-Seq data to improve microRNA target prediction accuracy in animals

2020 ◽  
Vol 36 (8) ◽  
pp. 2410-2416
Author(s):  
Thomas Bradley ◽  
Simon Moxon
Keyword(s):  
Programming Languages ◽  
Mirna Target ◽  
Target Prediction ◽  
Supplementary Information ◽  
Mirna Target Prediction ◽  
Rna Seq ◽  
Microrna Target ◽  
R Programming ◽  
High Level ◽  
Transcript Expression Level

Abstract Motivation MicroRNA (miRNA) target prediction algorithms do not generally consider biological context and therefore generic target prediction based on seed binding can lead to a high level of false-positive predictions. Here, we present FilTar, a method that incorporates RNA-Seq data to make miRNA target prediction specific to a given cell type or tissue of interest. Results We demonstrate that FilTar can be used to: (i) provide sample specific 3′-UTR reannotation; extending or truncating default annotations based on RNA-Seq read evidence and (ii) filter putative miRNA target predictions by transcript expression level, thus removing putative interactions where the target transcript is not expressed in the tissue or cell line of interest. We test the method on a variety of miRNA transfection datasets and demonstrate increased accuracy versus generic miRNA target prediction methods. Availability and implementation FilTar is freely available and can be downloaded from https://github.com/TBradley27/FilTar. The tool is implemented using the Python and R programming languages, and is supported on GNU/Linux operating systems. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals miTAR: a hybrid deep learning-based approach for predicting miRNA targets

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Tongjun Gu ◽  
Xiwu Zhao ◽  
William Bradley Barbazuk ◽  
Ji-Hyun Lee
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Mirna Target ◽  
Target Prediction ◽  
Hybrid Models ◽  
Mirna Target Prediction ◽  
Max Pooling ◽  
Mirna Targets ◽  
Spatial Features ◽  
Wide Range

Abstract Background microRNAs (miRNAs) have been shown to play essential roles in a wide range of biological processes. Many computational methods have been developed to identify targets of miRNAs. However, the majority of these methods depend on pre-defined features that require considerable efforts and resources to compute and often prove suboptimal at predicting miRNA targets. Results We developed a novel hybrid deep learning-based (DL-based) approach that is capable of predicting miRNA targets at a higher accuracy. This approach integrates convolutional neural networks (CNNs) that excel in learning spatial features and recurrent neural networks (RNNs) that discern sequential features. Therefore, our approach has the advantages of learning both the intrinsic spatial and sequential features of miRNA:target. The inputs for our approach are raw sequences of miRNAs and genes that can be obtained effortlessly. We applied our approach on two human datasets from recently miRNA target prediction studies and trained two models. We demonstrated that the two models consistently outperform the previous methods according to evaluation metrics on test datasets. Comparing our approach with currently available alternatives on independent datasets shows that our approach delivers substantial improvements in performance. We also show with multiple evidences that our approach is more robust than other methods on small datasets. Our study is the first study to perform comparisons across multiple existing DL-based approaches on miRNA target prediction. Furthermore, we examined the contribution of a Max pooling layer in between the CNN and RNN and demonstrated that it improves the performance of all our models. Finally, a unified model was developed that is robust on fitting different input datasets. Conclusions We present a new DL-based approach for predicting miRNA targets and demonstrate that our approach outperforms the current alternatives. We supplied an easy-to-use tool, miTAR, at https://github.com/tjgu/miTAR. Furthermore, our analysis results support that Max Pooling generally benefits the hybrid models and potentially prevents overfitting for hybrid models.

scholarly journals miTAR: a hybrid deep learning-based approach for predicting miRNA targets

2020 ◽  
Author(s):  
Tongjun Gu ◽  
Xiwu Zhao ◽  
William Bradley Barbazuk ◽  
Ji-Hyun Lee
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Mirna Target ◽  
Target Prediction ◽  
Unified Model ◽  
Brier Score ◽  
Mirna Target Prediction ◽  
Learning Methods ◽  
Mirna Targets ◽  
Wide Range

AbstractmicroRNAs (miRNAs) are a major type of small RNA that alter gene expression at the post-transcriptional or translational level. They have been shown to play important roles in a wide range of biological processes. Many computational methods have been developed to predict targets of miRNAs in order to understand miRNAs’ function. However, the majority of the methods depend on a set of pre-defined features that require considerable effort and resources to compute, and these methods often do not effectively on the prediction of miRNA targets. Therefore, we developed a novel hybrid deep learning-based approach that is capable to predict miRNA targets at a higher accuracy. Our approach integrates two deep learning methods: convolutional neural networks (CNNs) that excel in learning spatial features, and recurrent neural networks (RNNs) that discern sequential features. By combining CNNs and RNNs, our approach has the advantages of learning both the intrinsic spatial and sequential features of miRNA:target. The inputs for the approach are raw sequences of miRNA and gene sequences. Data from two latest miRNA target prediction studies were used in our study: the DeepMirTar dataset and the miRAW dataset. Two models were obtained by training on the two datasets separately. The models achieved a higher accuracy than the methods developed in the previous studies: 0.9787 vs. 0.9348 for the DeepMirTar dataset; 0.9649 vs. 0.935 for the miRAW dataset. We also calculated a series of model evaluation metrics including sensitivity, specificity, F-score and Brier Score. Our approach consistently outperformed the current methods. In addition, we compared our approach with earlier developed deep learning methods, resulting in an overall better performance. Lastly, a unified model for both datasets was developed with an accuracy higher than the current methods (0.9545). We named the unified model miTAR for miRNA target prediction. The source code and executable are available at https://github.com/tjgu/miTAR.

ANIMAL MICRORNA TARGET PREDICTION USING DIVERSE SEQUENCE-SPECIFIC DETERMINANTS

2010 ◽  
Vol 08 (04) ◽  
pp. 763-788 ◽  
Author(s):  
YUN ZHENG ◽  
WEIXIONG ZHANG
Keyword(s):  
Drosophila Melanogaster ◽  
Protein Level ◽  
Mirna Target ◽  
Homo Sapiens ◽  
Target Prediction ◽  
Prediction Algorithm ◽  
Mirna Target Prediction ◽  
Microrna Target ◽  
Microrna Target Prediction ◽  
Target Prediction Algorithm

Many recent studies have shown that access of animal microRNAs (miRNAs) to their complementary sites in target mRNAs is determined by several sequence-specific determinants beyond the seed regions in the 5′ end of miRNAs. These factors have been related to the repressive power of miRNAs and used in some programs to predict the efficacy of miRNA complementary sites. However, these factors have not been systematically examined regarding their capacities for improving miRNA target prediction. We develop a new miRNA target prediction algorithm, called Hitsensor, by incorporating many sequence-specific features that determine complementarities between miRNAs and their targets, in addition to the canonical seed regions in the 5′ ends of miRNAs. We evaluate the performance of our algorithm on 720 known animal miRNA:target pairs in four species, Homo sapiens, Mus musculus, Drosophila melanogaster and Caenorhabditis elegans. Our experimental results show that Hitsensor outperforms five popular existing algorithms, indicating that our unique scheme for quantifying the determinants of complementary sites is effective in improving the performance of a miRNA target prediction algorithm. We also examine the effectiveness of miRNA-mediated repression for the predicted targets by using a published quantitative protein expression dataset of miR-223 knockout in mouse neutrophils. Hitsensor identifies more targets than the existing algorithms, and the predicted targets of Hitsensor show comparable protein level changes to those of the existing algorithms.

scholarly journals miRDB: an online database for prediction of functional microRNA targets

2019 ◽  
Vol 48 (D1) ◽  
pp. D127-D131 ◽  
Author(s):  
Yuhao Chen ◽  
Xiaowei Wang
Keyword(s):  
Mirna Target ◽  
Expression Profiles ◽  
Target Prediction ◽  
Prediction Algorithm ◽  
Specific Cell ◽  
Mirna Target Prediction ◽  
Online Database ◽  
Functional Annotations ◽  
Small Noncoding Rnas ◽  
Mirna Targets

Abstract MicroRNAs (miRNAs) are small noncoding RNAs that act as master regulators in many biological processes. miRNAs function mainly by downregulating the expression of their gene targets. Thus, accurate prediction of miRNA targets is critical for characterization of miRNA functions. To this end, we have developed an online database, miRDB, for miRNA target prediction and functional annotations. Recently, we have performed major updates for miRDB. Specifically, by employing an improved algorithm for miRNA target prediction, we now present updated transcriptome-wide target prediction data in miRDB, including 3.5 million predicted targets regulated by 7000 miRNAs in five species. Further, we have implemented the new prediction algorithm into a web server, allowing custom target prediction with user-provided sequences. Another new database feature is the prediction of cell-specific miRNA targets. miRDB now hosts the expression profiles of over 1000 cell lines and presents target prediction data that are tailored for specific cell models. At last, a new web query interface has been added to miRDB for prediction of miRNA functions by integrative analysis of target prediction and Gene Ontology data. All data in miRDB are freely accessible at http://mirdb.org.

scholarly journals TarDB: an online database for plant miRNA targets and miRNA-triggered phased siRNAs

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jing Liu ◽  
Xiaonan Liu ◽  
Siju Zhang ◽  
Shanshan Liang ◽  
Weijiang Luan ◽  
...  
Keyword(s):  
Stress Responses ◽  
Mirna Target ◽  
Target Prediction ◽  
Mirna Target Prediction ◽  
Online Database ◽  
Small Interfering Rnas ◽  
High Confidence ◽  
Web Resource ◽  
Mirna Targets ◽  
Plant Mirna

Abstract Background In plants, microRNAs (miRNAs) are pivotal regulators of plant development and stress responses. Different computational tools and web servers have been developed for plant miRNA target prediction; however, in silico prediction normally contains false positive results. In addition, many plant miRNA target prediction servers lack information for miRNA-triggered phased small interfering RNAs (phasiRNAs). Creating a comprehensive and relatively high-confidence plant miRNA target database is much needed. Results Here, we report TarDB, an online database that collects three categories of relatively high-confidence plant miRNA targets: (i) cross-species conserved miRNA targets; (ii) degradome/PARE (Parallel Analysis of RNA Ends) sequencing supported miRNA targets; (iii) miRNA-triggered phasiRNA loci. TarDB provides a user-friendly interface that enables users to easily search, browse and retrieve miRNA targets and miRNA initiated phasiRNAs in a broad variety of plants. TarDB has a comprehensive collection of reliable plant miRNA targets containing previously unreported miRNA targets and miRNA-triggered phasiRNAs even in the well-studied model species. Most of these novel miRNA targets are relevant to lineage-specific or species-specific miRNAs. TarDB data is freely available at http://www.biosequencing.cn/TarDB. Conclusions In summary, TarDB serves as a useful web resource for exploring relatively high-confidence miRNA targets and miRNA-triggered phasiRNAs in plants.

A new approach to human microRNA target prediction using ensemble pruning and rotation forest

2015 ◽  
Vol 13 (06) ◽  
pp. 1550017 ◽  
Author(s):  
Reza Mousavi ◽  
Mahdi Eftekhari ◽  
Mehdi Ghezelbash Haghighi
Keyword(s):  
Mirna Target ◽  
Target Prediction ◽  
Research Area ◽  
Majority Voting ◽  
Mirna Target Prediction ◽  
Microrna Target ◽  
Rotation Forest ◽  
New Approach ◽  
Ensemble Pruning ◽  
Heterogeneous Ensemble

MicroRNAs (miRNAs) are small non-coding RNAs that have important functions in gene regulation. Since finding miRNA target experimentally is costly and needs spending much time, the use of machine learning methods is a growing research area for miRNA target prediction. In this paper, a new approach is proposed by using two popular ensemble strategies, i.e. Ensemble Pruning and Rotation Forest (EP-RTF), to predict human miRNA target. For EP, the approach utilizes Genetic Algorithm (GA). In other words, a subset of classifiers from the heterogeneous ensemble is first selected by GA. Next, the selected classifiers are trained based on the RTF method and then are combined using weighted majority voting. In addition to seeking a better subset of classifiers, the parameter of RTF is also optimized by GA. Findings of the present study confirm that the newly developed EP-RTF outperforms (in terms of classification accuracy, sensitivity, and specificity) the previously applied methods over four datasets in the field of human miRNA target. Diversity-error diagrams reveal that the proposed ensemble approach constructs individual classifiers which are more accurate and usually diverse than the other ensemble approaches. Given these experimental results, we highly recommend EP-RTF for improving the performance of miRNA target prediction.

Identification of BAP1-associated MicroRNAs and Implications in Cancer Development

2019 ◽  
pp. 1-4
Author(s):  
Tikam Chand ◽  
Tikam Chand
Keyword(s):  
Gene Regulation ◽  
In Silico ◽  
Mirna Target ◽  
Target Prediction ◽  
Differential Regulation ◽  
Cancer Development ◽  
Mirna Target Prediction ◽  
Cancer Types ◽  
In Silico Tools

Having role in gene regulation and silencing, miRNAs have been implicated in development and progression of a number of diseases, including cancer. Herein, I present potential miRNAs associated with BAP1 gene identified using in-silico tools such as TargetScan and Exiqon miRNA Target Prediction. I identified fifteen highly conserved miRNA (hsa-miR-423-5p, hsa-miR-3184-5p, hsa-miR-4319, hsa-miR125b-5p, hsa-miR-125a-5p, hsa-miR-6893-3p, hsa-miR-200b-3p, hsa-miR-200c-3p, hsa-miR-505-3p.1, hsa-miR-429, hsa-miR-370-3p, hsa-miR-125a-5p, hsa-miR-141-3p, hsa-miR-200a-3p, and hsa-miR-429) associated with BAP1 gene. We also predicted the differential regulation of these twelve miRNAs in different cancer types.

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