miReader: Discovering Novel miRNAs in Species without Sequenced Genome

PLoS ONE

Volumn 8, Issue 6, 2013, Pages

  Jha, Ashwani ^a   Shankar, Ravi ^a  

^a CSIR INSTITUTE OF HIMALAYAN BIORESOURCE TECHNOLOGY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

ACCURACY; ALGORITHM; ARABIDOPSIS THALIANA; ARTICLE; CAENORHABDITIS ELEGANS; CLASSIFIER; COMPUTER PROGRAM; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; GENE SEQUENCE; HIGH THROUGHPUT SEQUENCING; HUMAN; MIREADER; NONHUMAN; NUCLEOTIDE SEQUENCE; ORYZA; RNA SEQUENCE; ZEBRA FISH; ANIMAL; AREA UNDER THE CURVE; BIOLOGY; CHEMISTRY; GENOME; METABOLISM; PROCEDURES; RECEIVER OPERATING CHARACTERISTIC; SEQUENCE ANALYSIS;

DANIO RERIO; MISCANTHUS;

ALGORITHMS; ANIMALS; AREA UNDER CURVE; COMPUTATIONAL BIOLOGY; GENOME; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MICRORNAS; ROC CURVE; SEQUENCE ANALYSIS, RNA;

EID: 84879275585     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0066857     Document Type: Article

References (36)

1. Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, et al. (2003) The microRNAs of Caenorhabditis elegans. Genes Dev 17(8): 991-1008.
2. Cullen BR, (2004) Transcription and processing of human microRNA precursors. Mol Cell 16(6): 861-5.
3. Lee Y, Kim M, Han J, Yeom KH, Lee S, et al. (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J 23(20): 4051-4060.
4. Siomi H, Siomi MC, (2010) Posttranscriptional regulation of microRNA biogenesis in animals. Mol Cell 38(3): 323-32.
5. Macrae IJ, Zhou K, Li F, Repic A, Brooks AN, et al. (2006) Structural basis for double-stranded RNA processing by Dicer. Science 311(5758): 195-198.
6. Friedman RC, Farh KK, Burge CB, Bartel DP, (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19(1): 92-105.
7. Kozomara A, Griffiths-Jones S (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39(Database issue): D152-7.
8. Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, et al. (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33(20): e179.
9. Wu Y, Wei B, Liu H, Li T, Rayner S, (2011) MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences. BMC Bioinformatics 12: 107.
10. Xue C, Li F, He T, Liu GP, Li Y, et al. (2005) Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine. BMC Bioinformatics 6: 310.
11. Ritchie W, Theodule FX, Gautheret D, (2008) MirEval: a web tool for simple microRNA prediction in genome sequences. Bioinformatics 24(11): 1394-6.
12. Jha A, Chauhan R, Mehra M, Singh HR, Shankar R, (2012) miR-BAG: Bagging Based Identification of MicroRNA Precursors. PLoS ONE 7(9): e45782 doi: 10.1371/journal.pone.0045782.
13. Gkirtzou K, Tsamardinos I, Tsakalides P, Poirazi P, (2010) MatureBayes: a probabilistic algorithm for identifying the mature miRNA within novel precursors. PLoS One 5(8): e11843.
14. Xuan P, Guo M, Huang Y, Li W, Huang Y, (2011) MaturePred: efficient identification of microRNAs within novel plant pre-miRNAs. PLoS One 6(11): e27422.
15. Terai G, Okida H, Asai K, Mituyama T, (2012) Prediction of Conserved Precursors of miRNAs and Their Mature Forms by Integrating Position-Specific Structural Features. PLoS One. 7(9): e44314.18.
16. Friedländer MR, Chen W, Adamidi C, Maaskola J, Einspanier R, et al. (2008) Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol 26: 407-415.
17. Baigude H, Ahsanullah, Li Z, Zhou Y, Rana TM, (2012) miR-TRAP: a benchtop chemical biology strategy to identify microRNA targets. Angew Chem Int Ed Engl 51(24): 5880-3 doi: 10.1002/anie.201201512.
18. Ronen R, Gan I, Modai S, Sukacheov A, Dror G, et al. (2010) miRNAkey: a software for microRNA deep sequencing analysis. Bioinformatics 26(20): 261 5-6.
19. Wang WC, Lin FM, Chang WC, Lin KY, Huang HD, et al. (2009) miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression. BMC Bioinformatics 10: 328.
20. Wei YY, Chen S, Yang PC, Ma ZY, Kang L, (2009) Characterization and comparative profiling of the small RNA transcriptomes in two phases of locust. Genome Biology 10(1): R6.
21. Lai EC, (2003) microRNAs: runts of the genome assert themselves. Curr Biol 13 (23):: R925-36.
22. Auyeung VC, Ulitsky I, McGeary SE, Bartel DP, (2013) Beyond secondary structure: primary-sequence determinants license pri-miRNA hairpins for processing. Cell. 152(4): 844-58.
23. Jha A, Mehra M, Shankar R, (2011) The regulatory epicenter of miRNAs. J Biosci 36(4): 621-638.
24. Zeng Y, Yi R, Cullen BR, (2005) Recognition and cleavage of primary microRNA precursors by the nuclear processing enzyme Drosha. EMBO J. 24(1): 138-48.
25. Kim VN, (2005) MicroRNA biogenesis: coordinated cropping and dicing. Nat Rev Mol Cell Biol. 6(5): 376-85.
26. Davis BN, Hilyard AC, Nguyen PH, Lagna G, Hata A, (2010) Smad proteins bind a conserved RNA sequence to promote microRNA maturation by Drosha. Mol Cell 39(3): 373-84.
27. Piriyapongsa J, Jordan IK, Conley AB, Ronan T, Smalheiser NR, (2011) Transcription factor binding sites are highly enriched within microRNA precursor sequences. Biol Direct. 6: 61.
28. Shi H (2007) Best-First decision tree learning. Master's thesis, University of Waikato, Hamilton, NZ.
29. Webb GI (2000) MultiBoosting: A Technique for Combining Boosting and Wagging. Machine Learning. 40(No.2).
30. He C, Li YX, Zhang G, Gu Z, Yang R, et al. (2012) MiRmat: mature microRNA sequence prediction. PLoS ONE 7(12): e51673 doi: 10.1371/journal.pone.0051673.
31. Gardner PP, Giegerich R, (2004) A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics 5: 140.
32. Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, et al. (2008) Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stemcells. Genome Res. 2008 18(4): 610-21.
33. Suzuki HI, Miyazono K, (2010) Emerging complexity of microRNA generation cascades. J Biochem 149(1): 15-25.
34. Lai EC, Tomancak P, Williams RW, Rubin GM, (2003) Computational identification of Drosophila microRNA genes. Genome Biol 4(7): R42.
35. Cloonan N, Wani S, Xu Q, Gu J, Lea K, et al. (2011) MicroRNAs and their isomiRs function cooperatively to target common biological pathways. Genome Biol. 12(12): R126.
36. Jha A, Shankar R, (2011) Employing machine learning for reliable miRNA target identification in plants. BMC Genomics 12: 636.