Identification of non-coding RNAs with a new composite feature in the Hybrid Random Forest Ensemble algorithm

Nucleic Acids Research

Volumn 42, Issue 11, 2014, Pages

  Lertampaiporn, Supatcha ^a   Thammarongtham, Chinae ^a   Nukoolkit, Chakarida ^a   Kaewkamnerdpong, Boonserm ^a   Ruengjitchatchawalya, Marasri ^a  

^a KING MONGKUT'S UNIVERSITY OF TECHNOLOGY THONBURI   (Thailand)

Author keywords

[No Author keywords available]

Indexed keywords

UNTRANSLATED RNA;

ACCURACY; ARTICLE; GENETIC ANALYSIS; GENETIC ASSOCIATION; HUMAN; HYBRID RANDOM FOREST ENSEMBLE ALGORITHM; LEARNING ALGORITHM; MICROBIAL GENOME; NONHUMAN; NUCLEIC ACID STRUCTURE, METABOLISM AND FUNCTION; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; PROCESS OPTIMIZATION; RNA ANALYSIS; RNA CODING POTENTIAL; RNA MODULATION; RNA SEQUENCE; RNA STRUCTURAL ROBUSTNESS; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; SPIRULINA;

ALGORITHMS; CLASSIFICATION; GENOME, BACTERIAL; GENOMICS; HUMANS; LOGISTIC MODELS; RNA, LONG NONCODING; RNA, SMALL UNTRANSLATED; RNA, UNTRANSLATED;

EID: 84903172520     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku325     Document Type: Article

References (77)

1. Mattick, J.S. and Makunin, I.V. (2006) Non-coding RNA. Hum. Mol. Genet., 15, R17-R29.
2. Weinberg, Z. and Ruzzo, W.L. (2006) Sequence-based heuristics for faster annotation of non-coding RNA families. Bioinformatics, 22, 35-39.
3. Brosnan, C.A. and Voinnet, O. (2009) The long and the short of noncoding RNAs. Curr. Opin. Cell Biol., 21, 416-425.
4. Storz, G. (2002) An expanding universe of noncoding RNAs. Science, 296, 1260-1263.
5. Costa, F.F. (2010) Non-coding RNAs: Meet thy masters. BioEssays, 32, 599-608.
6. The ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.
7. Pauli, A., Rinn, J.L. and Schier, A.F. (2011) Non-coding RNAs as regulators of embryogenesis. Nat. Rev. Genet., 12, 136-149.
8. Managadze, D., Rogozin, I.B., Chernikova, D., Shabalina, S.A. and Koonin, E.V. (2011) Negative correlation between expression level and evolutionary rate of long intergenic noncoding RNAs. Genome Biol. Evol., 3, 1390-1404.
9. Mercer, T.R., Dinger, M.E. and Mattick, J.S. (2009) Long non-coding RNAs: insights into functions. . Nat. Rev. Genet., 10, 155-159.
10. Guttman, M. and Rinn, J.L. (2012) Modular regulatory principles of large non-coding RNAs. Nature, 482, 339-346.
11. Gorodkin, J. and Hofacker, I.L. (2011) From structure Prediction to genomic screens for novel non-coding RNAs. PLoS Comput. Biol., 7, e1002100.
12. Ponjavic, J., Ponting, C.P. and Lunter, G. (2007) Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res., 17, 556-565.
13. Sati, S., Ghosh, S., Jain, V., Scaria, V. and Sengupta, S. (2012) Genome-wide analysis reveals distinct patterns of epigenetic features in long non-coding RNA loci. Nucleic Acids Res., 40, 10018-10031.
14. Chen, G., Wang, Z., Wang, D., Qiu, C., Liu, M., Chen, X., Zhang, Q., Yan, G. and Cui, Q. (2013) LncRNADisease: a database for long-non-coding RNA-associated diseases. Nucleic Acids Res., 41, D983-D986.
15. Moran, V.A., Perera, R.J. and Khalil, A.M. (2012) Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs. Nucleic Acids Res., 40, 6391-6400.
16. Zhang, H., Chen, Z., Wang, X., Huang, Z., He, Z. and Chen, Y. (2013) Long non-coding RNA: a new player in cancer. J. Hematol. Oncol. 6, 37.
17. Marques, A.C. and Ponting, C.P. (2009) Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness. Genome Biol., 10, R124.
18. Bernhart, S.H. and Hofacker, I.L. (2009) From consensus structure prediction to RNA gene finding. Brief Funct. Genomic Proteomic, 8, 461-471.
19. Derrien, T., Johnson, R., Bussotti, G., Tanzer, A., Djebali, S., Tilgner, H., Guernec, G., Martin, D., Merkel, A., Knowles, D.G. et al. (2012) The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res., 22, 1775-1789.
20. Rivas, E. and Eddy, S.R. (2001) Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics, 2, 8.
21. Washietl, S., Hofacker, I.L. and Stadler, P.F. (2005) Fast and reliable prediction of noncoding RNAs. Proc. Natl. Acad. Sci. U.S.A., 102, 2454-2459.
22. Coventry, A., Kleitman, D.J. and Berger, B. (2004) MSARI: multiple sequence alignments for statistical detection of RNA secondary structure. Proc. Natl. Acad. Sci. U.S.A., 101, 12102-12107.
23. Pedersen, J.S., Bejerano, G., Siepel, A., Rosenbloom, K., Lindblad-Toh, K., Lander, E.S., Kent, J., Miller, W. and Haussler, D. (2006) Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput. Biol., 2, e33.
24. Tran, T., Zhou, F., Marshburn, S., Stead, M., Kushner, S. and Xu, Y. (2009) De novo computational prediction of non-coding RNA genes in prokaryotic genomes. Bioinformatics, 25, 2897-2905.
25. Saetrom, P., Sneve, R., Kristiansen, K.I., Snøve, O., Gr̈unfeld, T., Rognes, T. and Seeberg, E. (2005) Predicting non-coding RNA genes in Escherichia coli with boosted genetic programming. Nucleic Acids Res., 33, 3263-3270.
26. Wang, C., Ding, C., Meraz, R.F. and Holbrook, S.R. (2006) PSoL: a positive sample only learning algorithm for finding non-coding RNA genes. Bioinformatics, 22, 2590-2596.
27. Washietl, S., Findeiß, S., M̈uller, S.A., Kalkhof, S., Bergen, M.V., Hofacker, I.L., Stadler, P.F. and Goldman, N. (2011) RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data. RNA, 17, 578-594.
28. Raasch, P., Schmitz, U., Patenge, N., Vera, J., Kreikemeyer, B. and Wolkenhauer, O. (2010) Non-coding RNA detection methods combined to improve usability, reproducibility and precision. BMC Bioinformatics, 11, 491.
29. Salari, R., Aksay, C., Karakoc, E., Unrau, P.J., Hajirasouliha, I. and Sahinalp, S.C. (2009) smyRNA: A Novel Ab Initio ncRNA Gene Finder. PLoS ONE, 4, e5433.
30. Bao, M., Cervantes-Cervantes, M., Zhong, L. and Wang, J.T.L. (2012) Searching for non-coding RNAs in genomic sequences using ncRNAscout. Genomics, Proteomics Bioinformatics, 10, 114-121.
31. Lertampaiporn, S., Thammarongtham, C., Nukoolkit, C., Kaewkamnerdpong, B. and Ruengjitchatchawalya, M. (2013) Heterogeneous ensemble approach with discriminative features and modified-SMOTEbagging for pre-miRNA classification. Nucleic Acids Res., 41, e21.
32. Rivas, E. and Eddy, S.R. (2000) Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs. Bioinformatics, 16, 583-605.
33. Burge, S., Daub, J., Eberhardt, R., Tate, J., Barquist, L., Nawrocki, E., Eddy, S., Gardner, P. and Bateman, A. (2013) Rfam 11.0: 10 years of RNA families. Nucleic Acids Res., 41, D226-D232.
34. Fu, L., Niu, B., Zhu, Z., Wu, S. and Li, W. (2012) CD-HIT: accelerated for clustering the next generation sequencing data. Bioinformatics, 28, 3150-3152.
35. Pruitt, K.D., Tatusova, T., Brown, G.R. and Maglott, D.R. (2012) NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res., 40, D130-D135.
36. Amaral, P.P., Clark, M.B., Gascoigne, D.K., Dinger, M.E. and Mattick, J.S. (2011) lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res., 39, D146-D151.
37. Ferrara, S., Brugnoli, M., De Bonis, A., Righetti, F., Delvillani, F., Deho, G., Horner, D., Briani, F. and Bertoni, G. (2012) Comparative profiling of Pseudomonas aeruginosa strains reveals differential expression of novel unique and conserved small RNAs. PLoS One, 7, e36553.
38. Hall, M.A. (2000) Correlation-based feature selection for discrete and numeric class machine learning. In: Proceedings of the Seventeenth International Conference on Machine Learning. Morgan Kaufmann, San Francisco, CA. pp. 359-366.
39. Bishop, C.M. (2006) Pattern Recognition and Machine Learning. Springer, New York.
40. R Development Core Team. (2006) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Vienna, Austria.
41. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Libman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
42. Nawrocki, E.P., Kolbe, D.L. and Eddy, S.R. (2009) Infernal 1.0: Inference of RNA alignments. Bioinformatics, 25, 1335-1337.
43. Eddy, S.R. and Durbin, R. (1994) RNA sequence analysis using covariance models. Nucleic Acids Res., 22, 2079-2088.
44. Yao, Z., Weinberg, Z. and Ruzzo, W.L. (2006) CMfinder-a covariance model based RNA motif finding algorithm. Bioinformatics, 22, 445-452.
45. Lee, M.T. and Kim, J. (2008) Self containment, a property of modular RNA structures, distinguishes microRNAs. PLoS Comput. Biol., 4, e1000150.
46. Freyhult, E., Gardner, P.P. and Moulton, V. (2005) A comparison of RNA folding measures. BMC Bioinformatics, 6, 241.
47. Kong, L., Zhang, Y., Ye, Z., Liu, X., Zhao, S., Wei, L. and Gao, G. (2007) CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res., 35, W345-W349.
48. Slater, G.C. (2000) Algorithms for the Analysis of Expressed Sequence Tags. University of Cambridge, Cambridge.
49. Breiman, L. (2001) Random forests. Mach. Learning, 45, 5-32.
50. Larrañaga, P., Calvo, B., Santana, R., Bielza, C., Galdiano, J., Inza, I., Lozano, J.A., Armañanzas, R., Santaf́e, G., Ṕerez, A. et al. (2006) Machine learning in bioinformatics. Brief. Bioinform., 7, 86-112.
51. Liaw, A. and Wiener, M. (2002) Classification and regression by randomForest.R News, 2, 18-22.
52. Yang, P., Hwa Yang, Y., Zhou, B. and Zomaya, A. (2010) A review of ensemble methods in bioinformatics. Curr. Bioinformatics, 5, 296-308.
53. Frank, E., Hall, M., Trigg, l. E., Holmes, G. and Witten, I.H. (2004) Data mining in bioinformatics using Weka. Bioinformatics, 20, 2479-2481.
54. Strobl, C., Boulesteix, A., Zeileis, A. and Hothorn, T. (2007) Bias in random forest variable importance measures: illustrations, sources and a solution. BMC Bioinformatics, 8, 25.
55. Strobl, C., Boulesteix, A., Kneib, T., Augustin, T. and Zeileis, A. (2008) Conditional variable importance for random forests. BMC Bioinformatics, 9, 307.
56. Hothorn, T., Hornik, K. and Zeileis, A. (2006) party: a laboratory for recursive part(y)tioning. [R package version 0.9-0].
57. Lu, Z.J., Yip, K.Y., Wang, G., Shou, C., Hillier, L.W., Khurana, E., Agarwal, A., Auerbach, R., Rozowsky, J., Cheng, C. et al. (2011) Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data. Genome Res., 21, 276-285.
58. Babak, T., Blencowe, B.J. and Hughes, T.R. (2007) Considerations in the identification of functional RNA structural elements in genomic alignments. BMC Bioinformatics, 8, 33.
59. Clote, P., Ferŕe, F., Kranakis, E. and Krizanc, D. (2005) Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency. RNA, 11, 578-591.
60. Klein, R.J., Misulovin, Z. and Eddy, S.R. (2002) Noncoding RNA genes identified in AT-rich hyperthermophiles. Proc. Natl. Acad. Sci. U.S.A., 99, 7542-7547.
61. Schattner, P. (2002) Searching for RNA genes using base-composition statistics. Nucleic Acids Res., 30, 2076-2082.
62. Larsson, P., Hinas, A., Ardell, D.H., Kirsebom, L.A., Virtanen, A. and S̈oderbom, F. (2008) De novo search for non-coding RNA genes in the AT-rich genome of Dictyostelium discoideum: performance of Markov-dependent genome feature scoring. Genome Res., 18, 888-899.
63. Gardner, P.P. (2009) The use of covariance models to annotate RNAs in whole genomes. Brief. Funct. Genomic Proteomic, 8, 444-450.
64. Menzel, P., Gorodkin, J. and Stadler, P.F. (2009) The tedious task of finding homologous noncoding RNA genes. RNA, 15, 2075-2082.
65. Zhong, C. and Zhang, S. (2012) Clustering RNA structural motifs in ribosomal RNAs using secondary structural alignment. Nucleic Acids Res., 40, 1307-1317.
66. Miler, T.L. (2009) Modular organization and composability of RNA. Publicly Accessible Penn Dissertations. Paper 244.
67. Bhartiya, D., Pal, K., Ghosh, S., Kapoor, S., Jalali, S., Panwar, B., Jain, S., Sati, S., Sengupta, S., Sachidanandan, C. et al. (2013) lncRNome: a comprehensive knowledgebase of human long noncoding RNAs. Database, 11, doi: 10.1093/database/bat034.
68. Novikova, I.V., Hennelly, S.P. and Sanbonmatsu, K.Y. (2012) Structural architecture of the human long non-coding RNA, steroid receptor RNA activator. Nucleic Acids Res., 40, 5034-5051.
69. William, G.J. (2009) Rattle: a data mining GUI for R. R J. 1, 45-55.
70. Bu, D., Yu, K., Sun, S., Xie, C., Skogerbø, G., Miao, R., Xiao, H., Liao, Q., Luo, H., Zhao, G. et al. (2012) NONCODE v3.0: integrative annotation of long noncoding RNAs. Nucleic Acids Res., 40, D210-D215.
71. Kin, T., Yamada, K., Terai, G, Okida, H., Yoshinari, Y., Ono, Y., Kojima, A., Kimura, Y., Komori, T. and Asai, K. (2007) fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences. Nucleic Acids Res., 35, D145-D148.
72. Kaczkowski, B., Torarinsson, E., Reiche, K., Havgaard, J., Stadler, P. and Gorodkin, J. (2009) Structural profiles of human miRNA families from pairwise clustering. Bioinformatics, 25, 291-294.
73. Will, S., Joshi, T. and Hofacker, I. (2012) locaARNA-P: accurate boundary prediction and improved detection of structural RNAs. RNA, 18, 900-914.
74. Kavanaugh, L.A. and Dietrich, F.S. (2009) Non-coding RNA prediction and verification in Saccharomyces cerevisiae. PLoS Genet., 5, e1000321.
75. Waters, L.S. and Storz, G. (2009) Regulatory RNAs in bacteria. Cell, 136, 615-628.
76. Kawano, M., Reynolds, A.A., Miranda-Rios, J. and Storz, G. (2005) Detection of 5-and3-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli. Nucleic Acids Res., 33, 1040-1050.
77. Georg, J., Voss, B., Scholz, I., Mitschke, J., Wilde, A. and Hess, W.R. (2009) Evidence for a major role of antisense RNAs in cyanobacterial gene regulation. Mol. Syst. Biol., 5, 305.