Accurate Prediction of Transposon-Derived piRNAs by Integrating Various Sequential and Physicochemical Features

PLoS ONE

Volumn 11, Issue 4, 2016, Pages

  Luo, Longqiang ^a   Li, Dingfang ^a   Zhang, Wen ^a   Tu, Shikui ^b   Zhu, Xiaopeng ^b   Tian, Gang ^a  

^a WUHAN UNIVERSITY   (China)

^b UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PIWI INTERACTING RNA; UNTRANSLATED RNA; DROSOPHILA PROTEIN; SMALL INTERFERING RNA; TRANSPOSON;

ARTICLE; CONTROLLED STUDY; DROSOPHILA; HUMAN; MACHINE LEARNING; MOUSE; NONHUMAN; PHYSICAL CHEMISTRY; PREDICTION; RNA ANALYSIS; RNA SEQUENCE; SEQUENCE ALIGNMENT; TRANSPOSON; VALIDATION PROCESS; ANIMAL; BIOLOGICAL MODEL; GENETICS;

ANIMALS; DNA TRANSPOSABLE ELEMENTS; DROSOPHILA; DROSOPHILA PROTEINS; HUMANS; MICE; MODELS, GENETIC; RNA, SMALL INTERFERING;

EID: 84963736173     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0153268     Document Type: Article

References (44)

1. Claverie J. Fewer genes, more noncoding RNA. Science. 2005; 309(5740):1529-1530. PMID: 16141064
2. Mattick J. The functional genomics of noncoding RNA. Science. 2005; 309(5740):1527-1528. PMID: 16141063
3. Xie C, Yuan J, Li H, Li M, Zhao G, Bu D, et al. NONCODEv4: Exploring the world of long non-coding RNA genes. Nucleic Acids Research. 2014; 42(D1):D98-D103.
4. Huang Y, Liu N, Wang J, Wang Y, Yu X, Wang Z, et al. Regulatory long non-coding RNA and its functions. Journal of Physiology & Biochemistry. 2012; 68(4):611-618.
5. Meenakshisundaram K, Carmen L, Michela B, Diego D, Gabriella M, Rosaria V. Existence of snoRNA, microRNA, piRNA characteristics in a novel non-coding RNA: X-ncRNA and its biological implication in Homo sapiens. Journal of Bioinformatics & Sequence Analysis. 2009; 1(2):31-40.
6. Alexei A, Dimos G, Sébastien P, Mariana L, Pablo L, Nicola I, et al. A novel class of small RNAs bind to MILI protein in mouse testes. Nature. 2006; 442(7099):203-207. PMID: 16751777
7. Lau N, Seto A, Kim J, Kuramochi-Miyagawa S, Nakano T, P. Bartel D, et al. Characterization of the piRNA Complex from Rat Testes. Science. 2006; 313(5785):363-367. PMID: 16778019
8. Grivna S, Beyret E, Wang Z, Lin H. A novel class of small RNAs in mouse spermatogenic cells. Genes & Development. 2006; 20(13):1709-1714.
9. Seto A, Kingston R, Lau N. The Coming of Age for Piwi Proteins. Molecular Cell. 2007; 26(5):603-609. PMID: 17560367
10. Ruby J, Jan C, Player C, Axtell M, Lee W, Nusbaum C, et al. Large-scale sequencing reveals 21URNAs and additional Micro-RNAs and endogenous siRNAs in C. elegans. Cell. 2007; 127(6):1193-1207.
11. Cox D, Chao A, Baker J, Chang L, Qiao D, Lin H. A novel class of evolutionarily conserved genes defined by piwi are essential for stem cell self-renewal. Genes & Development. 1998; 12(23):3715-3727.
12. Klattenhoff C, Theurkauf W. Biogenesis and germline functions of piRNAs. Development. 2008; 135 (1):3-9. PMID: 18032451
13. Brennecke BJ, Aravin A, Stark A, Dus M, Kellis M. Sachidanandam R, Hannon G. Discrete Small RNAGenerating Loci as Master Regulators of Transposon Activity in Drosophila. Cell. 2007; 128(6):1089-1103. PMID: 17346786
14. Thomson T, Lin H. The biogenesis and function of PIWI proteins and piRNAs: Progress and prospect. Annual Review of Cell & Developmental Biology. 2009; 25(1):355-376.
15. Houwing S, Kamminga L, Berezikov E, Cronembold D, Girard A, Elst H, et al. A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in Zebrafish. Cell. 2007; 129(1):69-82. PMID: 17418787
16. Das P, Bagijn M, Goldstein L, Woolford J, Lehrbach N, Sapetschnig A, et al. Piwi and piRNAs Act Upstream of an Endogenous siRNA Pathway to Suppress Tc3 Transposon Mobility in the Caenorhabditis elegans Germline. Molecular Cell. 2008; 31(1):79-90. doi: 10.1016/j.molcel.2008.06.003 PMID: 18571451
17. Robine N, Lau N, Balla S, Jin Z, Okamura K, Kuramochi-Miyagawa S, et al. A Broadly Conserved Pathway Generates 30UTR-Directed Primary piRNAs. Current Biology. 2009; 19(24):2066-2076. doi: 10. 1016/j.cub.2009.11.064 PMID: 20022248
18. Yin H, Lin H. An epigenetic activation role of Piwi and a Piwi-associated piRNA in Drosophila melanogaster. Nature. 2007; 450(7167):304-308. PMID: 17952056
19. Betel D, Sheridan R, Marks DS, Sander C. Computational Analysis of Mouse piRNA Sequence and Biogenesis. Plos Computational Biology. 2007; 3(11):e222-e222. PMID: 17997596
20. Zhang Y, Wang X, Kang L. A k-mer scheme to predict piRNAs and characterize locust piRNAs. Bioinformatics. 2011; 27(6):771-776. doi: 10.1093/bioinformatics/btr016 PMID: 21224287
21. Wang K, Liang C, Liu J, Xiao H, Huang S, Xu J, Li F. Prediction of piRNAs using transposon interaction and a support vector machine. BMC Bioinformatics. 2014; 15(1):6593-6593.
22. Leslie C, Eskin E, Noble WS. The spectrum kernel: A string kernel for SVM protein classification. Pacific Symposium on Biocomputing. 2002; 7:564-575.
23. Liu B, Liu F, Wang X, Chen J, Fang L, Chou K. Pse-in-One: A web server for generating various modes of pseudo components of DNA, RNA, and protein sequences. Nucleic Acids Research. 2015; 43(W1): W65-W71. doi: 10.1093/nar/gkv458 PMID: 25958395
24. Liu B, Liu F, Fang L, Wang X, Chou K. repDNA: A Python package to generate various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties and sequenceorder effects. Bioinformatics. 2015; 31(8):1307-1309. doi: 10.1093/bioinformatics/btu820 PMID: 25504848
25. EL-Manzalawy Y, Dobbs D, Honavar V. Predicting flexible length linear B-cell epitopes. Computational Systems Bioinformatics; 2008; 7(7):121-132.
26. Leslie CS, Eskin E, Cohen A, Weston J, Noble WS. Mismatch string kernels for discriminative protein classification. Bioinformatics. 2004; 20(4):467-476. PMID: 14990442
27. Lodhi H, Saunders CJ, Shawe-Taylor J. Cristianini N, Watkins C. Text classification using string kernels. Journal of Machine Learning Research. 2002; 2(3):563-569.
28. Stormo GD. DNA binding sites: Representation and discovery. Bioinformatics. 2000; 16(1):16-23. PMID: 10812473
29. Sinha S. On counting position weight matrix matches in a sequence, with application to discriminative motif finding. Bioinformatics. 2006; 22(14):e454-e463. PMID: 16873507
30. Xia X. Position Weight Matrix, Gibbs Sampler, and the Associated Significance Tests in Motif Characterization and Prediction. Scientifica. 2012; 2012:917540-917540. doi: 10.6064/2012/917540 PMID: 24278755
31. Xue C, Li F, He T, Liu G, Li Y, Zhang X. Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine. BMC Bioinformatics. 2005; 6(2):1-7.
32. Bu D, Yu K, Sun S, Xie C, Skogerbø G, Miao R, et al. NONCODE v3.0: Integrative annotation of long noncoding RNAs. Nucleic Acids Research. 2012; 40(D1):D210-D215.
33. Karolchik D, Barber G, Casper J, Clawson H, Cline M, Diekhans M, et al. The UCSC Genome Browser database: 2014 update. Nucleic Acids Research. 2014; 42(suppl 1):D590-D598.
34. Jiang H, Wong WH. SeqMap: Mapping massive amount of oligonucleotides to the genome. Bioinformatics. 2008; 24(20):2395-2396. doi: 10.1093/bioinformatics/btn429 PMID: 18697769
35. Wei L, Liao M, Gao Y, Ji R, He Z, Zou Q. Improved and Promising Identification of Human MicroRNAs by Incorporating a High-quality Negative Set. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2014; 11(1):192-201. doi: 10.1109/TCBB.2013.146 PMID: 26355518
36. Song L, Li D, Zeng X, Wu Y, Guo L, Zou Q. nDNA-prot: Identification of DNA-binding proteins based on unbalanced classification. BMC Bioinformatics. 2014; 15(1):1-10.
37. Abeel T, Helleputte T, De Peer Y, Dupont P, Saeys Y. Robust biomarker identification for cancer diagnosis with ensemble feature selection methods. Bioinformatics. 2010; 26(3):392-398. doi: 10.1093/bioinformatics/btp630 PMID: 19942583
38. Zhang W, Niu Y, Xiong Y, Zhao M, Yu R, Liu J. Computational Prediction of Conformational B-Cell Epitopes from Antigen Primary Structures by Ensemble Learning. Plos One. 2012; 7(8):e43575-e43575. doi: 10.1371/journal.pone.0043575 PMID: 22927994
39. Zhang W, Liu J, Xiong Y, Ke M, Zhang K. Predicting immunogenic T-cell epitopes by combining various sequence-derived features. IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2013; pp:4-9.
40. Zhang W, Niu Y, Zou H, Luo L, Liu Q, Wu W. Accurate Prediction of Immunogenic T-Cell Epitopes from Epitope Sequences Using the Genetic Algorithm-Based Ensemble Learning. Plos One. 2015; 10(5): E0128194-e0128194. doi: 10.1371/journal.pone.0128194 PMID: 26020952
41. Zou Q, Guo J, Ju Y, Wu M, Zeng X, Hong Z. Improving tRNAscan-SE Annotation Results via Ensemble Classifiers. Molecular Informatics. 2015; 2003(16):2992-3000.
42. Breiman L. Random forests. Machine Learning. 2001; 45:5-32.
43. Chang C, Lin C, et al. LIBSVM: A library for Support Vector Machines. ACM Transactions on Intelligent Systems and Technology. 2011; 2(3):389-396.
44. Cucchiara A. Applied Logistic Regression. Journal of Flow Chemistry. 2012; 34(3):358-359.