CPAT: Coding-potential assessment tool using an alignment-free logistic regression model

Nucleic Acids Research

Volumn 41, Issue 6, 2013, Pages

  Wang, Liguo ^a,b   Park, Hyun Jung ^b   Dasari, Surendra ^a   Wang, Shengqin ^c   Kocher, Jean Pierre ^a   Li, Wei ^b  

^a MAYO CLINIC   (United States)

^b BAYLOR COLLEGE OF MEDICINE   (United States)

^c SOUTHEAST UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; GENE SEQUENCE; GENETIC CODE; GENETIC TRANSCRIPTION; INFORMATION PROCESSING; INTERMETHOD COMPARISON; LOGISTIC REGRESSION ANALYSIS; OPEN READING FRAME; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; STATISTICAL MODEL;

LOGISTIC MODELS; OPEN READING FRAMES; RNA, UNTRANSLATED; SEQUENCE ANALYSIS, RNA; SOFTWARE;

PHYLO;

EID: 84876020023     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt006     Document Type: Article

References (26)

1. Bertone, P., Stolc, V., Royce, T.E., Rozowsky, J.S., Urban, A.E., Zhu, X., Rinn, J.L., Tongprasit, W., Samanta, M., Weissman, S. et al. (2004) Global identification of human transcribed sequences with genome tiling arrays. Science (New York, NY), 306, 2242-2246.
2. Kapranov, P., St Laurent, G., Raz, T., Ozsolak, F., Reynolds, C.P., Sorensen, P.H.B., Reaman, G., Milos, P., Arceci, R.J., Thompson, J.F. et al. (2010) The majority of total nuclear-encoded non-ribosomal RNA in a human cell is dark matter' un-annotated RNA. BMC Biol., 8, 149.
3. Kapranov, P., Cheng, J., Dike, S., Nix, D.A., Duttagupta, R., Willingham, A.T., Stadler, P.F., Hertel, J., Hackermüller, J., Hofacker, I.L. et al. (2007) RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science (New York, NY), 316, 1484-1488.
4. Mercer, T.R., Gerhardt, D.J., Dinger, M.E., Crawford, J., Trapnell, C., Jeddeloh, J.A., Mattick, J.S. and Rinn, J.L. (2012) Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat. Biotechnol., 30, 99-104.
5. 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.
6. Ulitsky, I., Shkumatava, A., Jan, C.H., Sive,H. and Bartel, D.P. (2011) Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell, 147, 1537-1550.
7. 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.
8. Guttman, M., Garber, M., Levin, J.Z., Donaghey, J., Robinson, J., Adiconis, X., Fan, L., Koziol, M.J., Gnirke, A., Nusbaum, C. et al. (2010) Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotechnol., 28, 503-510.
9. Gupta, R.A., Shah, N., Wang, K.C., Kim, J., Horlings, H.M., Wong, D.J., Tsai,M.-C., Hung, T., Argani, P., Rinn, J.L. et al. (2010) Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature, 464, 1071-1076.
10. Chu, C., Qu, K., Zhong, F.L., Artandi, S.E. and Chang, H.Y. (2011) Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol. Cell, 44, 667-678.
11. Ørom, U.A., Derrien, T., Beringer M., Gumireddy, K., Gardini, A., Bussotti, G., Lai, F., Zytnicki, M., Notredame, C., Huang, Q. et al. (2010) Long noncoding RNAs with enhancer-like function in human cells. Cell. 143:46-58.
12. Huarte, M., Guttman, M., Feldser, D., Garber, M., Koziol, M.J., Kenzelmann-Broz, D., Khalil, A.M., Zuk, O., Amit, I., Rabani, M. et al. (2010) A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell, 142, 409-419.
13. Pauli, A., Rinn, J.L. and Schier, A.F. (2011) Non-coding RNAs as regulators of embryogenesis. Nat. Rev. Genet., 12, 136-149.
14. Hung,T. and Chang, H.Y. (2010) Long noncoding RNA in genome regulation: prospects and mechanisms. RNA Biol., 7, 582-585.
15. Arrial, R.T., Togawa, R.C. and Brigido,M.deM. (2009) Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus Paracoccidioides brasiliensis. BMC Bioinformatics, 10, 239.
16. 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.
17. Lin, M.F., Jungreis,I. and Kellis, M. (2011) PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics (Oxford, England), 27, i275-i282.
18. Washietl, S., Findeiss, S., Müller, S.A., Kalkhof, S., Bergen,von, M., 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.
19. The FANTOM Consortium. (2005) The transcriptional landscape of the mammalian genome. Science, 309, 1559-1563.
20. Schloss, P.D. (2010) The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput. Biol., 6, e1000844.
21. Frith, M.C., Bailey, T.L., Kasukawa, T., Mignone, F., Kummerfeld, S.K., Madera, M., Sunkara, S., Furuno, M., Bult, C.J., Quackenbush, J. et al. (2006) Discrimination of non-protein-coding transcripts from protein-coding mRNA. RNA Biol., 3, 40-48.
22. Fickett, J.W. (1982) Recognition of protein coding regions in DNA sequences. Nucleic Acids Res., 10, 5303-5318.
23. Fickett, J.W. and Tung,C.-S. (1992) Assessment of protein coding measures. Nucleic Acids Res., 20, 6441-6450.
24. Sing, T., Sander, O., Beerenwinkel,N. and Lengauer, T. (2005) ROCR: visualizing classifier performance in R. Bioinformatics (Oxford, England), 21, 3940-3941.
25. Lin, M.F., Deoras, A.N., Rasmussen, M.D. and Kellis, M. (2008) Performance and scalability of discriminative metrics for comparative gene identification in 12 Drosophila genomes. PLoS Comput. Biol., 4, e1000067.
26. 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.