Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts

Nucleic Acids Research

Volumn 41, Issue 17, 2013, Pages

  Sun, Liang ^a,b   Luo, Haitao ^a   Bu, Dechao ^a   Zhao, Guoguang ^a   Yu, Kuntao ^a   Zhang, Changhai ^b   Liu, Yuanning ^b   Chen, Runsheng ^c   Zhao, Yi ^a  

^a INSTITUTE OF COMPUTING TECHNOLOGY   (China)

^b JILIN UNIVERSITY   (China)

^c INSTITUTE OF BIOPHYSICS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

LONG UNTRANSLATED RNA; TRANSCRIPTOME;

ADJOINING NUCLEOTIDE TRIPLET SCORE; ARTICLE; CODING DOMAIN SEQUENCE; CODING NONCODING INDEX; CONTROLLED STUDY; GENETIC CODE; GENETIC PARAMETERS; GENETIC VARIABILITY; HUMAN; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN CODING SEQUENCE; PROTEIN NONCODING SEQUENCE; RECEIVER OPERATING CHARACTERISTIC; RNA SEQUENCE; SCORING SYSTEM; SEQUENCE ANALYSIS; SEQUENCE SCORE;

ANIMALS; GENE EXPRESSION PROFILING; HUMANS; MICE; PONGO; PROTEINS; RNA, LONG UNTRANSLATED; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 84884915826     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt646     Document Type: Article

References (26)

1. Dunham,I., Kundaje,A., Aldred,S.F., Collins,P.J., Davis,C.A., Doyle,F., Epstein,C.B., Frietze,S., Harrow,J., Kaul,R. et al. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.
2. Djebali,S., Davis,C.A., Merkel,A., Dobin,A., Lassmann,T., Mortazavi,A., Tanzer,A., Lagarde,J., Lin,W., Schlesinger,F. et al. (2012) Landscape of transcription in human cells. Nature, 489, 101-108.
3. Brawand,D., Soumillon,M., Necsulea,A., Julien,P., Csardi,G., Harrigan,P., Weier,M., Liechti,A., Aximu-Petri,A., Kircher,M. et al. (2011) The evolution of gene expression levels in mammalian organs. Nature, 478, 343-348.
4. Kong,L., Zhang,Y., Ye,Z.Q., Liu,X.Q., Zhao,S.Q., 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.
5. Lin,M.F., Jungreis,I. and Kellis,M. (2011) PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics, 27, i275-i282.
6. Dinger,M.E., Pang,K.C., Mercer,T.R. and Mattick,J.S. (2008) Differentiating protein-coding and noncoding RNA: challenges and ambiguities. PLoS Comput. Biol., 4, e1000176.
7. Guttman,M. and Rinn,J.L. (2012) Modular regulatory principles of large non-coding RNAs. Nature, 482, 339-346.
8. Guttman,M., Amit,I., Garber,M., French,C., Lin,M.F., Feldser,D., Huarte,M., Zuk,O., Carey,B.W., Cassady,J.P. et al. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature, 458, 223-227.
9. 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.
10. Kersey,P.J., Staines,D.M., Lawson,D., Kulesha,E., Derwent,P., Humphrey,J.C., Hughes,D.S., Keenan,S., Kerhornou,A., Koscielny,G. et al. (2012) Ensembl genomes: an integrative resource for genome-scale data from non-vertebrate species. Nucleic Acids Res., 40, D91-D97.
11. Cabili,M.N., Trapnell,C., Goff,L., Koziol,M., Tazon-Vega,B., Regev,A. and Rinn,J.L. (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev., 25, 1915-1927.
12. Mukherjee,S. and Zhang,Y. (2009) MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming. Nucleic Acids Res., 37, e83.
13. Chang,C.C. and Lin,C.J. (2011) LIBSVM: A Library for Support Vector Machines. Acm T Intel Syst Tec, 2.
14. Trapnell,C., Pachter,L. and Salzberg,S.L. (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105-1111.
15. Trapnell,C., Williams,B.A., Pertea,G., Mortazavi,A., Kwan,G., van Baren,M.J., Salzberg,S.L., Wold,B.J. and Pachter,L. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol., 28, 511-515.
16. Flicek,P., Amode,M.R., Barrell,D., Beal,K., Brent,S., Chen,Y., Clapham,P., Coates,G., Fairley,S., Fitzgerald,S. et al. (2011) Ensembl 2011. Nucleic Acids Res., 39, D800-D806.
17. Trapnell,C., Roberts,A., Goff,L., Pertea,G., Kim,D., Kelley,D.R., Pimentel,H., Salzberg,S.L., Rinn,J.L. and Pachter,L. (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc., 7, 562-578.
18. Bu,D., Yu,K., Sun,S., Xie,C., Skogerbo,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.
19. Liao,Q., Liu,C., Yuan,X., Kang,S., Miao,R., Xiao,H., Zhao,G., Luo,H., Bu,D., Zhao,H. et al. (2011) Large-scale prediction of long non-coding RNA functions in a coding-noncoding gene co-expression network. Nucleic Acids Res., 39, 3864-3878.
20. Guo,X., Gao,L., Liao,Q., Xiao,H., Ma,X., Yang,X., Luo,H., Zhao,G., Bu,D., Jiao,F. et al. (2013) Long non-coding RNAs function annotation: a global prediction method based on bi-colored networks. Nucleic Acids Res., 41, e35.
21. Liao,Q., Xiao,H., Bu,D., Xie,C., Miao,R., Luo,H., Zhao,G., Yu,K., Zhao,H., Skogerbo,G. et al. (2011) ncFANs: a web server for functional annotation of long non-coding RNAs. Nucleic Acids Res., 39, W118-W124.
22. Buchan,J.R., Aucott,L.S. and Stansfield,I. (2006) tRNA properties help shape codon pair preferences in open reading frames. Nucleic Acids Res., 34, 1015-1027. (Pubitemid 43380684)
23. Re,M., Pesole,G. and Horner,D.S. (2009) Accurate discrimination of conserved coding and non-coding regions through multiple indicators of evolutionary dynamics. BMC Bioinformatics, 10, 282.
24. Wang,L., Park,H.J., Dasari,S., Wang,S., Kocher,J.P. and Li,W. (2013) CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model. Nucleic Acids Res., 41, e74.
25. Burge,C. and Karlin,S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol., 268, 78-94. (Pubitemid 27192680)
26. Bussotti,G., Raineri,E., Erb,I., Zytnicki,M., Wilm,A., Beaudoing,E., Bucher,P. and Notredame,C. (2011) BlastR-fast and accurate database searches for non-coding RNAs. Nucleic Acids Res., 39, 6886-6895.