LncRNA-ID: Long non-coding RNA IDentification using balanced random forests

Bioinformatics

Volumn 31, Issue 24, 2015, Pages 3897-3905

  Achawanantakun, Rujira ^a   Chen, Jiao ^a   Sun, Yanni ^a   Zhang, Yuan ^a  

^a Michigan State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LONG UNTRANSLATED RNA; PROTEIN;

ANIMAL; COMPUTER PROGRAM; EVALUATION STUDY; GENETICS; HUMAN; MACHINE LEARNING; METABOLISM; MOUSE; OPEN READING FRAME; RIBOSOME;

ANIMALS; HUMANS; MACHINE LEARNING; MICE; OPEN READING FRAMES; PROTEINS; RIBOSOMES; RNA, LONG NONCODING; SOFTWARE;

EID: 84950272960     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv480     Document Type: Article

References (65)

1. Arava, Y. et al. (2003) Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA, 100, 3889-3894.
2. Arriaga-Canon, C. et al. (2014) A long non-coding RNA promotes full activation of adult gene expression in the chicken globin domain. Epigenetics, 9, 173-181.
3. Boerner, S. and McGinnis, K.M. (2012) Computational identification and functional predictions of long noncoding RNA in Zea mays. PLoS ONE, 7, e43047.
4. Borsani, G. et al. (1991) Characterization of a murine gene expressed from the inactive X chromosome. Nature, 351, 325-329.
5. Breiman, L. (2001) Random forests. Mach. Learn., 45, 5-32.
6. Brockdorff, N. et al. (1992) The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus. Cell, 71, 515-526.
7. Bu, D. et al. (2012) NONCODE v3.0: integrative annotation of long noncoding RNAs. Nucleic Acids Res., 40, D210-D215.
8. Cabili, M.N. et al. (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev., 25, 1915-1927.
9. Chen, C. et al. (2004) Using random forest to learn imbalanced data. Technical report, Department of Statistics, University of Berkeley.
10. Chen, G. et al. (2013) Lnc RNADisease: a database for long-non-coding RNAassociated diseases. Nucleic Acids Res., 41, D983-D986.
11. Chen, X. and Ishwaran, H. (2012) Random forests for genomic data analysis. Genomics, 99, 323-329.
12. Chodroff, R.A. et al. (2010) Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes. Genome Biol., 11, R72.
13. De Angioletti, M. et al. (2004) Beta+45 G-C: a novel silent betathalassaemia mutation, the first in the Kozak sequence. Br. J. Haematol., 124, 224-231.
14. Derrien, T. 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.
15. Dinger, M.E. et al. (2008) Differentiating protein-coding and noncoding RNA: challenges and ambiguities. PLoS Comput. Biol., 4, e1000176.
16. Djebali, S. et al. (2012) Landscape of transcription in human cells. Nature, 489, 101-108.
17. Durbin, R. et al. (1998) Biological Sequence Analysis Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, UK.
18. Eddy, S.R. (2009) A new generation of homology search tools based on probabilistic inference. Genome Inf., 23, 205-211.
19. Finn, R.D. et al. (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res., 39, 29-37.
20. Gonen, M. (2007) Analyzing Receiver Operating Characteristic Curves With SAS. SAS Press Series, USA.
21. Guttman, M. et al. (2010) Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of linc RNAs. Nat. Biotechnol., 28, 503-510.
22. Guttman, M. et al. (2013) Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins. Cell, 154(1), 240-251.
23. Hall, M. et al. (2009) The WEKA data mining software: An update. SIGKDD Explorations, 11.
24. Huang, K.-Z. et al. (2008) Machine Learning: Modeling Data Locally and Globally. Springer Science and Business Media, Germany.
25. Humann, F.C. et al. (2013) Sequence and expression characteristics of long noncoding RNAs in honey bee caste development-potential novel regulators for transgressive ovary size. PLoS ONE, 8, e78915.
26. Hung, T. and Chang, H.Y. (2010) Long noncoding RNA in genome regulation: prospects and mechanisms. RNA Biol., 7, 582-585.
27. Ingolia, N.T. et al. (2011) Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell, 147, 789-802.
28. Kapranov, P. et al. (2007) RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science, 316, 1484-1488.
29. Kong, L. et al. (2007) CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res., 35, W345-W349.
30. Kozak, M. (1989) Context effects and inefficient initiation at non-aug codons in eucaryotic cell-free translation systems. Genome Res., 9, 5073-5080.
31. Kozak, M. (1997) Recognition of aug and alternative initiator codons is augmented by g in position +4 but is not generally affected by the nucleotides in positions +5 and +6. EMBO J., 16, 2482-2492.
32. Kozak, M. (1999) Initiation of translation in prokaryotes and eukaryotes. Gene, 234, 187-208.
33. Leung, Y.Y. et al. (2013) CoRAL: predicting non-coding RNAs from small RNA-sequencing data. Nucleic Acids Res., 41, e137.
34. Li, A. et al. (2014) PLEK: a tool for predicting long non-coding RNAs andmessenger RNAs based on an improved k-mer scheme. BMC Bioinformatics, 15, 311.
35. Lin, M.F. et al. (2011) Phylocsf: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics, 27, i275-i282.
36. Liu, J. et al. (2012) Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell, 24, 4333-4345.
37. Liu, Y. et al. (2013) Inheritable and precise large genomic deletions of non-coding RNA genes in zebrafish using TALENs. PLoS One, 8, e76387.
38. Magrane, M. and Consortium, U. (2011) UniProt knowledgebase: a hub of integrated protein data. Database, 2011, bar009.
39. Marchler-Bauer, A. and Bryant, S.H. (2004) CD-Search: protein domain annotations on the fly. Nucleic Acids Res., 32, W327-W331.
40. Marchler-Bauer, A. et al. (2013) CDD: conserved domains and protein threedimensional structure. Nucleic Acids Res., 41, D348-D352.
41. MATLAB (2010) version 7.10.0 (R2010a). The Math Works Inc., Natick, MA.
42. Muckstein, U. et al. (2006) Thermodynamics of RNA-RNA binding. Bioinformatics, 22, 1177-1182.
43. Okazaki, Y. et al. (2002) Analysis of the mouse transcriptome based on functional annotation of 60 770 full-length cDNAs. Nature, 420, 563-573.
44. Pauli, A. et al. (2011) Non-coding RNAs as regulators of embryogenesis. Nat. Rev. Genet., 12, 136-149.
45. Pauli, A. et al. (2012) Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Res., 22, 577-591.
46. Pennisi, E. (2012) Genomics. ENCODE project writes eulogy for junk DNA. Science, 337, 1159-1161.
47. Prasanth, K.V. and Spector, D.L. (2007) Eukaryotic regulatory RNAs: an answer to the 'genome complexity' conundrum. Genes Dev., 21, 11-42.
48. Probost, F. (2000) Machine learning from imbalanced data sets 101, Proc. Learning from Imbalanced Data Sets: Papers from the Am. Assoc. for Artificial Intelligence Workshop, 2000.
49. Pruitt, K.D. et al. (2007) NCBI reference sequences (Ref Seq): a curated nonredundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 35, 61-65.
50. Punta, M. et al. (2012) The Pfam protein families database. Nucleic Acids Res., 40, 290-301.
51. Schloss, P.D. (2010) The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA genebased studies. PLoS Comput. Biol., 6.
52. Shaw, K. (2008) Biological applications of support vector machines. Nat. Educ., 1, 201.
53. Suzek, B.E. et al. (2007) Uni Ref: comprehensive and non-redundant Uni Prot reference clusters. Bioinformatics, 23, 1282-1288.
54. Tuv, E. et al. (2009) Feature selection with ensembles, artificial variables, and redundancy elimination. J. Mach. Learn. Res., 10, 1341-1366.
55. Vasquez, J. et al. (2014) Comparative ribosome profiling reveals extensive translational complexity in different Trypanosoma brucei life cycle stages. Nucl. Acids Res., 42, 3623-3637.
56. Wang, L. et al. (2013) CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model. Nucleic Acids Res., 41, e74.
57. Wapinski, O. and Chang, H.Y. (2011) Long noncoding RNAs and human disease. Trends Cell Biol., 21, 354-361.
58. Wilusz, J.E. et al. (2009) Long noncoding RNAs: functional surprises from the RNA world. Genes Dev., 23, 1494-1504.
59. Wu, J. et al. (2009) Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature. Bioinformatics, 25, 30-35.
60. Xing, C. et al. (2009) Identification of protein-coding sequences using the hybridization of 18S rRNA and mRNA during translation. Nucleic Acids Res., 37, 591-601.
61. Xu, H. et al. (2010) Length of the ORF, position of the first AUG and the Kozak motif are important factors in potential dual-coding transcripts. Cell Res., 20, 445-457.
62. Zhang, Y. and Sun, Y. (2011)HMM-FRAME: accurate protein domain classification for metagenomic sequences containing frameshift errors. BMC Bioinformatics, 12, 198.
63. Zhang, Y. and Sun, Y. (2012) Meta Domain: a profile HMM-based protein domain classification tool for short sequences. In: Proceedings of Pacific Symposium on Biocomputing (PSB).
64. Zhang, Y. et al. (2013) A Sensitive and Accurate protein domain cLassification Tool (SALT) for short reads. Bioinformatics, 29, 2103-2111.
65. Zhang, Y. et al. (2014) A scalable and accurate targeted gene assembly tool (SAT-Assembler) for next-generation sequencing data. PLoS Comput. Biol., 10, e1003737.