Distinguishing mirtrons from canonical miRNAs with data exploration and machine learning methods

Scientific Reports
Grzegorz RorbachBogumil M Konopka

Abstract

Mirtrons are non-canonical microRNAs encoded in introns the biogenesis of which starts with splicing. They are not processed by Drosha and enter the canonical pathway at the Exportin-5 level. Mirtrons are much less evolutionary conserved than canonical miRNAs. Due to the differences, canonical miRNA predictors are not applicable to mirtron prediction. Identification of differences is important for designing mirtron prediction algorithms and may help to improve the understanding of mirtron functioning. So far, only simple, single-feature comparisons were reported. These are insensitive to complex feature relations. We quantified miRNAs with 25 features and showed that it is impossible to distinguish the two miRNA species using simple thresholds on any single feature. However, when using the Principal Component Analysis mirtrons and canonical miRNAs are grouped separately. Moreover, several methodologically diverse machine learning classifiers delivered high classification performance. Using feature selection algorithms we found features (e.g. bulges in the stem region), previously reported divergent in two classes, that did not contribute to improving classification accuracy, which suggests that they are not biologically meaning...Continue Reading

References

Sep 17, 2004·The EMBO Journal·Yoontae LeeV Narry Kim
Nov 9, 2004·Nature·Ahmet M DenliGregory J Hannon
Jun 26, 2007·Nature·J Graham RubyDavid P Bartel
Oct 30, 2007·Molecular Cell·Eugene BerezikovEric C Lai
Jul 1, 2008·Bioinformatics·Yunpen XuWeixiong Zhang
Sep 27, 2008·Annual Review of Pathology·Yong Sun Lee, Anindya Dutta
Feb 24, 2009·Bioinformatics·Rukshan Batuwita, Vasile Palade
Nov 6, 2010·Journal of Cardiovascular Pharmacology·Shanshan Qin, Chunxiang Zhang
Nov 30, 2010·Surgery for Obesity and Related Diseases : Official Journal of the American Society for Bariatric Surgery·Ismael CourtRaul J Rosenthal
Dec 1, 2010·Nature Reviews. Genetics·Benjamin Czech, Gregory J Hannon
Dec 22, 2010·Expert Review of Molecular Diagnostics·Md Saha JamaluddinChangyi Chen
Jun 30, 2011·Biochimie·Jakub O Westholm, Eric C Lai
Mar 6, 2012·BMC Genomics·Sung-Chou LiWen-chang Lin
Sep 8, 2012·Genome Research·Erik LadewigEric C Lai
Mar 19, 2013·BMC Bioinformatics·Adam GudyśIzabela Makałowska
Sep 21, 2013·Bioinformatics·Dadi GaoWilliam Ritchie
Jul 17, 2014·Trends in Molecular Medicine·Josie HayesSean Lawler
Jan 2, 2015·Therapeutic Advances in Gastroenterology·Christopher G Chapman, Joel Pekow
May 12, 2015·Cancer Cell International·Kaladhar B Reddy
Sep 4, 2015·IEEE Transactions on Nanobioscience·Leyi WeiQuan Zou
Jan 1, 2014·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Leyi WeiQuan Zou
Sep 13, 2015·Journal of Theoretical Biology·Bin LiuKuo-Chen Chou
Dec 22, 2016·International Journal of Molecular Sciences·Leyi Wei, Quan Zou
Jan 21, 2017·BMC Musculoskeletal Disorders·Shomi OkaShigeto Tohma
Apr 10, 2017·Digestive Diseases and Sciences·Bo CaoLiu Hong
Aug 26, 2017·Nature Communications·Müşerref Duygu Saçar DemirciJens Allmer
Sep 18, 2017·Molecular Therapy. Nucleic Acids·Chiranjib ChakrabortySang-Soo Lee
Oct 13, 2017·Frontiers in Microbiology·Maggie R WilliamsSyed A Hashsham
Jan 28, 2016·Signal Transduction and Targeted Therapy·Yong Peng, Carlo M Croce

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Citations

Mar 16, 2019·Bioinformatics·Bruno Henrique Ribeiro Da FonsecaAlexandre Rossi Paschoal
Apr 18, 2019·Bioinformatics·Ali M YazbeckJörg Fallmann
Aug 23, 2019·Wiley Interdisciplinary Reviews. RNA·Shama Prasada KabekkoduKapaettu Satyamoorthy
Oct 31, 2018·Nature Communications·Quan Q GaoMarcus E Peter
Jan 27, 2019·Scientific Reports·Xueming ZhengXinxiang Huang
Nov 23, 2019·Cells·Christiaan J Stavast, Stefan J Erkeland
Apr 18, 2020·Seminars in Cancer Biology·Faheem Hyder PottooFirdos Alam Khan
Oct 31, 2020·Frontiers in Endocrinology·Gabriella Simões HeynKelly Grace Magalhães
Dec 18, 2020·Frontiers in Oncology·Tiziana AnneseDomenico Ribatti
Mar 23, 2021·Frontiers in Cardiovascular Medicine·Wei Wang, Hao Zheng
Sep 6, 2020·Life Sciences·Aysan SalamatiBahman Yousefi
May 11, 2021·Autoimmunity Reviews·Cristian PaparaAdrian Baican
Jul 22, 2021·Biochemistry. Biokhimii︠a︡·Ekaterina V SeminaKseniya A Rubina
Jul 10, 2021·Scientific Reports·Abdulkadir Tasdelen, Baha Sen

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Methods Mentioned

BETA
PCA

Software Mentioned

RNAfold
house R script
ViennaRNA Package
miRank
e1071
in
R
Boruta
Ensemble
izMIR

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