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Accurate microRNA target prediction correlates with protein repression levels

Manolis Maragkakis, Panagiotis Alexiou, Giorgio L Papadopoulos, Martin Reczko, Theodore Dalamagas, George Giannopoulos, George Goumas, Evangelos Koukis, Kornilios Kourtis, Victor A Simossis, Praveen Sethupathy, Thanasis Vergoulis (+4 others)
2009 BMC Bioinformatics  
Conclusion: Recently, several computational target prediction programs were benchmarked based on a set of microRNA target genes identified by the pSILAC method.  ...  Results: DIANA-microT 3.0 is an algorithm for microRNA target prediction which is based on several parameters calculated individually for each microRNA and combines conserved and non-conserved microRNA  ...  An MRE X is considered conserved in species A if X can also be identified at the exact same position on the ortholog 3'UTR sequence of species A.  ... 
doi:10.1186/1471-2105-10-295 pmid:19765283 pmcid:PMC2752464 fatcat:k2s6urwysfcvhkangiybl2cazq

STarMir Tools for Prediction of microRNA Binding Sites [chapter]

Shaveta Kanoria, William Rennie, Chaochun Liu, C. Steven Carmack, Jun Lu, Ye Ding
2016 Msphere  
This chapter provides protocols for using the STarMir web server for improved predictions of miRNA binding sites on a target mRNA.  ...  the protein. 6 A specific database is under development, based on a recent study on genetic variants within and near miRNA binding sites [24] .  ...  The results are categorized as seed and seedless sites for each of the three target mRNA regions, i.e. 3' UTR, CDS and 5' UTR.  ... 
doi:10.1007/978-1-4939-6433-8_6 pmid:27665594 pmcid:PMC5353976 fatcat:hslplso2bjhfnbl2fxalbe2n6i

STarMirDB: A database of microRNA binding sites

William Rennie, Shaveta Kanoria, Chaochun Liu, Bibekanand Mallick, Dang Long, Adam Wolenc, C. Steven Carmack, Jun Lu, Ye Ding
2016 RNA Biology  
The search results are categorized into seed and seedless sites in 3 0 UTR, CDS and 5 0 UTR.  ...  For each predicted site, STarMirDB provides a comprehensive list of sequence, thermodynamic and target structural features that are known to influence miRNA: target interaction.  ...  L. and A.W. wrote the initial software for the computation of several target site features used by the database, and C.C. provided hardware and system support. W.  ... 
doi:10.1080/15476286.2016.1182279 pmid:27144897 pmcid:PMC4962797 fatcat:5te2kia6snd6jf7dmsbfjuvqtq

Crosstalk between codon optimality and cis-regulatory elements dictates mRNA stability

Santiago Gerardo Medina-Muñoz, Gopal Kushawah, Luciana Andrea Castellano, Michay Diez, Michelle Lynn DeVore, María José Blanco Salazar, Ariel Alejandro Bazzini
2021 Genome Biology  
Regulatory sequences in 3′ untranslated regions (3UTRs) have long been considered the central determinants of mRNA stability.  ...  Furthermore, we show that microRNA targeting efficacy can be affected by substantial enrichment of optimal (stabilizing) or non-optimal (destabilizing) codons.  ...  In total, 68 features were used as predictors: 3 categorical features (species, cell type, and experimental technique) and 65 numerical features (64 codon frequencies and 3UTR length).  ... 
doi:10.1186/s13059-020-02251-5 pmid:33402205 pmcid:PMC7783504 fatcat:gn2pfz7wbvfm7p376nilfs5kyy

Distinguishing between MicroRNA Targets from Diverse Species using Sequence Motifs and K-mers

Malik Yousef, Waleed Khalifa, İlhan Erkin Acar, Jens Allmer
2017 Proceedings of the 10th International Joint Conference on Biomedical Engineering Systems and Technologies  
For machine learning, many features for parameterization of the miRNA targets are available and k-mers and sequence motifs have previously been used.  ...  Unrelated organisms like intracellular pathogens and their hosts may communicate via miRNAs and, therefore, we investigated whether miRNA targets from one species can be differentiated from miRNA targets  ...  Thus, it is our aim to differentiate between miRNA targets of one species by using another species as negative training data employing only sequence-based features, which means that positive and negative  ... 
doi:10.5220/0006137901330139 dblp:conf/biostec/YousefKAA17 fatcat:mqd5kprog5fsxbwstpzu6ztjoe

Comparison and integration of target prediction algorithms for microRNA studies

Yanju Zhang, Fons J Verbeek
2010 Journal of Integrative Bioinformatics  
microRNAs are short RNA fragments that have the capacity of regulating hundreds of target gene expression.  ...  Among different integration strategies, the application of Bayesian Network classifier on the features calculated from multiple prediction methods significantly improved target prediction accuracy.  ...  Acknowledgements We thank Amalia Kallergi, Joris Slob and Kuan Yan for their critical discussions on methodology and results.  ... 
doi:10.2390/biecoll-jib-2010-127 pmid:20375447 fatcat:bmaba6soevdt3kwweapqrvlbei

The relationship between the evolution of microRNA targets and the length of their UTRs

Chao Cheng, Nitin Bhardwaj, Mark Gerstein
2009 BMC Genomics  
Conclusion: Our analysis suggests a two-way evolutionary mechanism for miRNA targets on the basis of their cellular roles and the length of their 3' UTRs.  ...  However, they have a distinctly different type of regulation, with shorter 3'UTRs to avoid miRNA targeting.  ...  To repress expression of mRNAs, miRNAs recognize target sites in their 3' un-translated region (3'UTR) via base pair-ing, leading to their degradation or inhibition of their translation [3] [4] [5] .  ... 
doi:10.1186/1471-2164-10-431 pmid:19751524 pmcid:PMC2758905 fatcat:nvok3f3epvgs5p5xpfwsvzzcpi

Comparison and Integration of Target Prediction Algorithms for microRNA Studies

Yanju Zhang, Fons J. Verbeek
2010 Journal of Integrative Bioinformatics  
Among different integration strategies, the application of Bayesian Network classifier on the features calculated from multiple prediction methods significantly improved target prediction accuracy.  ...  In this paper, three commonly used target prediction algorithms are evaluated and further integrated using algorithm combination, ranking aggregation and Bayesian Network classification.  ...  Acknowledgements We thank Amalia Kallergi, Joris Slob and Kuan Yan for their critical discussions on methodology and results.  ... 
doi:10.1515/jib-2010-127 fatcat:y44ysnangvhzxlgy6zmmw4vmha

Bioinformatic tools for microRNA dissection

Most Mauluda Akhtar, Luigina Micolucci, Md Soriful Islam, Fabiola Olivieri, Antonio Domenico Procopio
2015 Nucleic Acids Research  
Recently, microRNAs (miRNAs) have emerged as important elements of gene regulatory networks.  ...  Recent technological advances, especially highthroughput sequencing, have led to an exponential growth in the generation of miRNA-related data.  ...  SVM is a classifier that categorizes objects based on a set of features for each object.  ... 
doi:10.1093/nar/gkv1221 pmid:26578605 pmcid:PMC4705652 fatcat:kbmr3qnfffgeriy5d5o5owezke

Bioinformatics Methods for Studying MicroRNA and ARE-Mediated Regulation of Post-Transcriptional Gene Expression

Richipal Singh Bindra, Jason T. L. Wang, Paramjeet Singh Bagga
2010 International Journal of Knowledge Discovery in Bioinformatics  
AU-rich elements (AREs) are regulatory RNA motifs found in the 3' untranslated regions (UTRs) of mRNAs; they play dominant roles in the regulated decay of short-lived human mRNAs via specific interactions  ...  Next we present a data mining method for identifying the co-occurrences of miRNA target sites in ARE containing genes.  ...  Scoring of the targets was done based on three features: seed topology (S), structural accessibility (A), and total interaction energy (E). A site score was calculated as S × A × E.  ... 
doi:10.4018/jkdb.2010070106 fatcat:a52gc5r2x5aa7nnjrtmre2hxiu

CLIP-based prediction of mammalian microRNA binding sites

Chaochun Liu, Bibekanand Mallick, Dang Long, William A. Rennie, Adam Wolenc, C. Steven Carmack, Ye Ding
2013 Nucleic Acids Research  
region (3 0 UTR), coding sequence (CDS) region and 5 0 untranslated region (5 0 UTR) of target messenger RNA (mRNA).  ...  By analysing data from CLIP studies, we identified a comprehensive list of sequence, thermodynamic and target structure features that are essential for target binding by miRNAs in the 3 0 untranslated  ...  Other sequence features have been proposed based on their enhancement of targeting specificity.  ... 
doi:10.1093/nar/gkt435 pmid:23703212 pmcid:PMC3737542 fatcat:wzglxfl5dfa7jg4af2djfcv3au

miTarget: microRNA target gene prediction using a support vector machine

Sung-Kyu Kim, Jin-Wu Nam, Je-Keun Rhee, Wha-Jin Lee, Byoung-Tak Zhang
2006 BMC Bioinformatics  
It uses a radial basis function kernel as a similarity measure for SVM features, categorized by structural, thermodynamic, and position-based features.  ...  The functions of animal miRNAs are generally based on complementarity for their 5' components.  ...  One of the main limitations in miRNA target prediction for the human genome is the prevalence of long 3' UTR sequences compared with other species.  ... 
doi:10.1186/1471-2105-7-411 pmid:16978421 pmcid:PMC1594580 fatcat:fbk34qt5frfrdkeygwltpxfqvy

A bioinformatics-based update on microRNAs and their targets in rainbow trout (Oncorhynchus mykiss)

Liandong Yang, Shunping He
2014 Gene  
a r t i c l e i n f o MicroRNAs (miRNAs) participate in various vitally biological processes via controlling target genes activity and thousands of miRNAs have been identified in many species to date,  ...  In present study, we systematically investigated the miRNAs in rainbow trout using a well-developed comparative genome-based homologue search.  ...  Both the 3UTRs, 5′UTRs and CDS regions were used to predict targets by two widely used miRNA target prediction algorithms, miRanda (http://www.microrna.org/microrna/home.do) and PITA (Kertesz et al.  ... 
doi:10.1016/j.gene.2013.09.060 pmid:24064144 fatcat:dw2kehcx2jgwdgcpnmdsero7t4

A comprehensive joint analysis of the long and short RNA transcriptomes of human erythrocytes

Jennifer F. Doss, David L. Corcoran, Dereje D. Jima, Marilyn J. Telen, Sandeep S. Dave, Jen-Tsan Chi
2015 BMC Genomics  
To comprehensively define the erythrocyte transcriptome, we used high-throughput sequencing to identify both short (18-24 nt) and long (>200 nt) RNAs in mature erythrocytes.  ...  We show that miR-4732-3p targets both SMAD2 and SMAD4, two critical components of the TGF-β pathway implicated in erythropoiesis.  ...  Acknowledgements We thank the Duke GCB Genome Sequencing Shared Resource for sequencing assistance, Chi lab members for feedback, Lauren Ord and Shannon McNulty for technical assistance, Jude Jonaissant  ... 
doi:10.1186/s12864-015-2156-2 pmid:26573221 pmcid:PMC4647483 fatcat:7uxatmihijcppkd26t3nyw5nje

MicroRNAs and other mechanisms regulate interleukin-17 cytokines and receptors

Jietang Mai
2012 Frontiers in Bioscience (Elite Edition)  
microRNAs-mRNA interactions in the 3UTRs of IL-17 cytokine and receptor mRNAs.  ...  of several RNA binding proteins are found in the 3UTRs of the mRNAs of IL-17 cytokines and receptors; and vi) numerous microRNA binding sites are statistically equivalent to that of experimentally verified  ...  Similarly, three out of eight microRNAs targeted to the same sequence region (bases 216-225) in the 3UTR of human IL-17C, and six out of nine microRNAs targeted to the same sequence region (bases 167-  ... 
doi:10.2741/474 pmid:22201969 pmcid:PMC3289104 fatcat:o3jyflp72bhz3dmrwads2cvsey
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