Communications of the Korean Institute of Information Scientists and Engineers (정보과학회지)

Korean Institute of Information Scientists and Engineers (한국정보과학회)
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Long non-coding RNA 예측을 위한 실험적-전산학적 방법

  • Published : 2014.10.16
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Abstract

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References

  1. The ENCODE Project Consortium, The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, 2004. 306(5696): p. 636-640. https://doi.org/10.1126/science.1105136
  2. Gerstein, M.B., et al., Architecture of the human regulatory network derived from ENCODE data. Nature, 2012. 489(7417): p. 91-100. https://doi.org/10.1038/nature11245
  3. Khalil, A.M., et al., Many human large intergenic non-coding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci USA, 2009. 106(28): p. 11667-11672. https://doi.org/10.1073/pnas.0904715106
  4. Garber, M, et al., Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Methods, 2011. 8(6): p. 469-477. https://doi.org/10.1038/nmeth.1613
  5. Ponting, C.P., et al., Evolution and functions of long noncoding RNAs. Cell, 2009. 136(4): p. 629-641. https://doi.org/10.1016/j.cell.2009.02.006
  6. Guttman, M., et al., Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature, 2009. 458: p. 223-227. https://doi.org/10.1038/nature07672
  7. Mattick, lS., et al., The genetic signatures of noncoding RNAs. PLoS Genet, 2009. 5: p. e1000459. https://doi.org/10.1371/journal.pgen.1000459
  8. Mattick, lS., et al., Non-coding RNA. Hum. Mol. Genet, 2006. 15: p. R17-29. https://doi.org/10.1093/hmg/ddl046
  9. Qureshi, I.A., et al., Long non-coding RNAs in nervous system function and disease. Brain Res, 2010. 1338: p. 20-35. https://doi.org/10.1016/j.brainres.2010.03.110
  10. Wilusz, J.E., et al., Long noncoding RNAs: functional surprises from the RNA world. Genes Dev, 2009. 23: p. 1494-1504. https://doi.org/10.1101/gad.1800909
  11. Kunej, T., et al., The decalog of long non-coding RNA involvement in cancer diagnosis and monitoring. Clit Rev Clin Lav Sci, 2014. 15: p. 1-14.
  12. Kawai, J., et al., Functional annotation ofa full-length mouse cDNA collection. Nature, 2001. 409(6821): p. 685-690. https://doi.org/10.1038/35055500
  13. De Santa, F., et al., A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers. PLoS Biol, 2010. 8(5): p. e1000384. https://doi.org/10.1371/journal.pbio.1000384
  14. Garmire, L.X., et al., A global clustering algorithm to identify long intergenic non-coding RNA-with applications in mouse macrophages. PLoS ONE, 2011. 6(9): p. e24051. https://doi.org/10.1371/journal.pone.0024051
  15. Sun, H., et al., Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq. Nucleic Acids Res, 2011. 39(1): p. 190-201. https://doi.org/10.1093/nar/gkq775
  16. Kong, L., et al., CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res, 2007. 35: p. W345-W349. https://doi.org/10.1093/nar/gkm391
  17. Lin, M.F., et al., PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics, 2011. 27: p. i275-i282. https://doi.org/10.1093/bioinformatics/btr209
  18. Liu, J., et al., Distinguishing Protein-Coding from Non-Coding RNAs through Support Vector Machines. PLoS Genet, 2006. 2(4): p. e29. https://doi.org/10.1371/journal.pgen.0020029
  19. Sun, K., et al., iSeeRNA: identification of long intergenic non-coding RNA transcripts from transcriptome sequencing data. BMC Genomics, 2013. 14_Suppl2: p. S7.
  20. Sun, L., et al., Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. Nucleic Acids Res, 2013. 41(17): p. e166. https://doi.org/10.1093/nar/gkt646
  21. Wang, Y, et al., Computational identification of human long intergenic non-coding RNAs using a GA-SVM algorithm. Gene, 2014. 533(1): p. 94-99. https://doi.org/10.1016/j.gene.2013.09.118
  22. Chew, G.L., et al., Ribosome profiling reveals resemblance between long non-coding RNAs and 5' leaders of coding RNAs. Development, 2013. 140(13): p. 2828-2834. https://doi.org/10.1242/dev.098343
  23. Wang, L., et al., CPAT: Coding-Potenial Assessment Tool using an alignement-free logistic regression model. Nucleic Acids Res, 2013. 41(6): p. e74. https://doi.org/10.1093/nar/gkt006
  24. Ingolia, NT, et al., Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science, 2009. 324(5924): p. 218-223. https://doi.org/10.1126/science.1168978
  25. Ingolia, NT, et al., Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell, 2011. 147(4): p.789-802. https://doi.org/10.1016/j.cell.2011.10.002
  26. Guttman, M., et al., Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins. Cell, 2013. 154: p. 240-251. https://doi.org/10.1016/j.cell.2013.06.009
  27. Bazzini, A.A., et al., Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation. The EMBO journal, 2014. 33(9): p. 981-993. https://doi.org/10.1002/embj.201488411
  28. Guo, H., et al., Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature, 2010. 466(7308): p. 835-840. https://doi.org/10.1038/nature09267
  29. Tupy, J.L., et al., Identification of putative noncoding polyadenylated transcripts in Drosophila melanogaster. Proc Natl. Acad. Sci. USA, 2005. 102: p. 5495-5500. https://doi.org/10.1073/pnas.0501422102
  30. Kondo, T., et al., Small peptides switch the transcriptional activity of Shaven baby during Drosophila embryogenesis. Science, 2010. 329: p. 336-339. https://doi.org/10.1126/science.1188158
  31. Wapinski, O., et al. , Long noncoding RNAs and human disease. Trends Cell Biol, 2011. 21(6): p. 354-361. https://doi.org/10.1016/j.tcb.2011.04.001
  32. Nam, J.W., et al., Long noncoding RNAs in C. elegans. Genome Res, 2012. 22: p. 2529-2540. https://doi.org/10.1101/gr.140475.112