miRAW: A deep learning-based approach to predict microRNA targets by analyzing whole microRNA transcripts

PLoS Computational Biology
Albert PlaSimon Rayner

Abstract

MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression by binding to partially complementary regions within the 3'UTR of their target genes. Computational methods play an important role in target prediction and assume that the miRNA "seed region" (nt 2 to 8) is required for functional targeting, but typically only identify ∼80% of known bindings. Recent studies have highlighted a role for the entire miRNA, suggesting that a more flexible methodology is needed. We present a novel approach for miRNA target prediction based on Deep Learning (DL) which, rather than incorporating any knowledge (such as seed regions), investigates the entire miRNA and 3'TR mRNA nucleotides to learn a uninhibited set of feature descriptors related to the targeting process. We collected more than 150,000 experimentally validated homo sapiens miRNA:gene targets and cross referenced them with different CLIP-Seq, CLASH and iPAR-CLIP datasets to obtain ∼20,000 validated miRNA:gene exact target sites. Using this data, we implemented and trained a deep neural network-composed of autoencoders and a feed-forward network-able to automatically learn features describing miRNA-mRNA interactions and assess functionality. Predictions were then re...Continue Reading

References

Feb 22, 2005·PLoS Biology·Julius BrenneckeStephen M Cohen
Jul 29, 2006·Science·G E Hinton, R R Salakhutdinov
Jul 7, 2007·Molecular Cell·Andrew GrimsonDavid P Bartel
Sep 26, 2007·Nature Genetics·Michael KerteszEran Segal
Sep 22, 2009·BMC Bioinformatics·Manolis MaragkakisArtemis G Hatzigeorgiou
Sep 2, 2010·Nucleic Acids Research·Ray M Marín, Jirí Vanícek
Mar 19, 2011·BMC Bioinformatics·Xavier RobinMarkus Müller
Sep 13, 2011·Nature Structural & Molecular Biology·David M GarciaDavid P Bartel
Nov 26, 2011·Algorithms for Molecular Biology : AMB·Ronny LorenzIvo L Hofacker
Mar 1, 2012·Nucleic Acids Research·Sita J LangeRolf Backofen
May 18, 2013·Nucleic Acids Research·Maria D ParaskevopoulouA G Hatzigeorgiou
May 30, 2013·Nucleic Acids Research·Charles E VejnarEvgeny M Zdobnov
Nov 28, 2013·Nucleic Acids Research·Ana Kozomara, Sam Griffiths-Jones
Feb 1, 2014·Computers in Biology and Medicine·Quan ZouZhiliang Ji
Nov 2, 2014·Science·Nicole T SchirleIan J MacRae
Nov 25, 2014·Nucleic Acids Research·Ioannis S VlachosArtemis G Hatzigeorgiou
Dec 23, 2014·IEEE Transactions on Neural Networks and Learning Systems·Jan Chorowski, Jacek M Zurada
May 8, 2015·Nucleic Acids Research·Miroslav ŠulcJiří Vaníček
May 29, 2015·Nature·Yann LeCunGeoffrey Hinton
Jul 28, 2015·Nature Biotechnology·Babak AlipanahiBrendan J Frey
Aug 1, 2015·Nature Methods·Harsh Dweep, Norbert Gretz
Aug 13, 2015·ELife·Vikram AgarwalDavid P Bartel
Nov 22, 2015·Nucleic Acids Research·Chih-Hung ChouHsien-Da Huang
Feb 14, 2016·Bioinformatics·Yifei ChenXiaohui Xie
Apr 28, 2016·Molecules and Cells·Heeyoung SeokSung Wook Chi
Jun 25, 2016·Database : the Journal of Biological Databases and Curation·Bronwen L AkenStephen M J Searle
Oct 22, 2016·Molecular Cell·James P BroughtonAmy E Pasquinelli
Apr 4, 2018·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Lijun ZhangXuemei Huang

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Citations

Jul 15, 2020·Biochemical Society Transactions·Shir Bahiri-Elitzur, Tamir Tuller
Sep 11, 2019·Briefings in Bioinformatics·Juan Cui, Jiang Shu
Apr 12, 2020·Cancers·Shahzad Nawaz Syed, Bernhard Brüne
May 6, 2020·PloS One·Xueming ZhengXinxiang Huang
Dec 4, 2019·Briefings in Bioinformatics·Fabian KernAndreas Keller
Jul 18, 2020·Scientific Reports·Daniel G KyrollosJames R Green
Mar 27, 2020·Computational and Structural Biotechnology Journal·Moritz Schäfer, Constance Ciaudo
Sep 10, 2020·Heliyon·Rodolfo S Allendes OsorioYayoi Natsume-Kitatani
Mar 1, 2021·BMC Bioinformatics·Tongjun GuJi-Hyun Lee
Oct 23, 2021·Bioinformatics·Seonwoo MinSungroh Yoon
Jan 28, 2022·BMC Bioinformatics·Niloofar BorhaniYousof Gheisari

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Methods Mentioned

BETA
CLIP
CLASH
Transfection
PAR-CLIP

Software Mentioned

TS
Micro
TDS
ViennaRNA package
Vienna
PAR
NLL
TargetScanHuman
miRAW miRAW
mirza

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