Improving microRNA target prediction by modeling with unambiguously identified microRNA-target pairs from CLIP-ligation studies

Bioinformatics

Volumn 32, Issue 9, 2016, Pages 1316-1322

  Wang, Xiaowei ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

ALGORITHM; ANIMAL; BIOLOGY; HUMAN;

ALGORITHMS; ANIMALS; COMPUTATIONAL BIOLOGY; HUMANS; MICRORNAS;

EID: 84964891414     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btw002     Document Type: Article

References (35)

1. Agarwal, V. et al. (2015) Predicting effective microRNA target sites in mammalian mRNAs. Elife, 4, e05005.
2. Ambros, V. (2004) The functions of animal microRNAs. Nature, 431, 350-355.
3. Baek, D. et al. (2008) The impact of microRNAs on protein output. Nature, 455, 64-71.
4. Barrett, T. et al. (2013) NCBI GEO: archive for functional genomics data sets-update. Nucleic Acids Res., 41, D991-D995.
5. Bartel, D.P. (2009) MicroRNAs: target recognition and regulatory functions. Cell, 136, 215-233.
6. Betel, D. et al. (2010) Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol., 11, R90.
7. Breda, J. et al. (2015) Quantifying the strength of miRNA-Target interactions, Methods, 85, 90-99.
8. Chi, S.W. et al. (2009) Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature, 460, 479-486.
9. Gaidatzis, D. et al. (2007) Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC Bioinformatics, 8, 69.
10. Grimson, A. et al. (2007) MicroRNA Targeting Specificity in Mammals: Determinants beyond Seed Pairing. Mol Cell, 27, 91-105.
11. Grosswendt, S. et al. (2014) Unambiguous identification of miRNA:target site interactions by different types of ligation reactions. Mol. Cell, 54, 1042-1054.
12. Gumienny, R. and Zavolan, M. (2015) Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-Targets with MIRZAG. Nucleic Acids Res., 43, 1380-1391.
13. Hafner, M. et al. (2010) Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell, 141, 129-141.
14. Helwak, A. et al. (2013) Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell, 153, 654-665.
15. Hofacker, I.L. (2003) Vienna RNA secondary structure server. Nucleic Acids Res., 31, 3429-3431.
16. Kent, W.J. (2002) BLAT-The BLAST-like alignment tool. Genome Res., 12, 656-664.
17. Kertesz, M. et al. (2007) The role of site accessibility in microRNA target recognition. Nat. Genet., 39, 1278-1284.
18. Khorshid, M. et al. (2013) A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets. Nat. Methods, 10, 253-255.
19. Kozomara, A. and Griffiths-Jones, S. (2014) miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res., 42, D68-D73.
20. Lim, L.P. et al. (2005) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature, 433, 769-773.
21. Linsley, P.S. et al. (2007) Transcripts targeted by the microRNA-16 family cooperatively regulate cell cycle progression. Mol Cell Biol, 27, 2240-2252.
22. Liu, C. et al. (2013) CLIP-based prediction of mammalian microRNA binding sites. Nucleic Acids Res., 41, e138.
23. Long, D. et al. (2007) Potent effect of target structure on microRNA function. Nat. Struct. Mol. Biol., 14, 287-294.
24. Miranda, K.C. et al. (2006) A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell, 126, 1203-1217.
25. NCBI Resource Coordinators. (2015) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 43, D6-D17.
26. Reczko, M. et al. (2012) Functional microRNA targets in protein coding sequences. Bioinformatics, 28, 771-776.
27. Robins, H. et al. (2005) Incorporating structure to predict microRNA targets. Proc. Natl. Acad. Sci. USA, 102, 4006-4009.
28. Salmena, L. et al. (2011) A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell, 146, 353-358.
29. Selbach, M. et al. (2008) Widespread changes in protein synthesis induced by microRNAs. Nature, 455, 58-63.
30. Wang, X. (2014) Composition of seed sequence is a major determinant of microRNA targeting patterns. Bioinformatics, 30, 1377-1383.
31. Wang, X. and El Naqa, I.M. (2008) Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics, 24, 325-332.
32. Wang, X. and Wang, X. (2006) Systematic identification of microRNA functions by combining target prediction and expression profiling. Nucleic Acids Res., 34, 1646-1652.
33. Xia, T. et al. (1998) Thermodynamic parameters for an expanded nearestneighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry, 37, 14719-14735.
34. Zhang, L. et al. (2007) Systematic identification of C. elegans miRISC proteins, miRNAs, and mRNA targets by their interactions with GW182 proteins AIN-1 and AIN-2. Mol. Cell, 28, 598-613.
35. Zhao, Y. et al. (2005) Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature, 436, 214-220.