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

한국정보과학회 (Korean Institute of Information Scientists and Engineers)
권호 표지

조절 Long Noncoding RNA의 생물정보학적 주석과 도전과제

  • 발행 : 2014.03.14
PDF 다운로드
⟨ 이전 논문 다음 논문 ⟩

초록

키워드

참고문헌

  1. Gerstein, M.B., et al., Architecture of the human regulatory network derived from ENCODE data. Nature, 2012. 489(7414): p. 91-100. https://doi.org/10.1038/nature11245
  2. Gerstein, M., Genomics: ENCODE leads the way on big data. Nature, 2012. 489(7415): p. 208.
  3. Lander, E.S., et al., Initial sequencing and analysis of the human genome. Nature, 2001. 409(6822): p. 860-921. https://doi.org/10.1038/35057062
  4. Khalil, A.M., et al., Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A, 2009. 106(28): p. 11667-72. https://doi.org/10.1073/pnas.0904715106
  5. Garber, M., et al., Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Methods, 2011. 8(6): p. 469-77. https://doi.org/10.1038/nmeth.1613
  6. Ulitsky, I., et al., Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell, 2011. 147(7): p. 1537-50. https://doi.org/10.1016/j.cell.2011.11.055
  7. Harrow, J., et al., GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res, 2012. 22(9): p. 1760-74. https://doi.org/10.1101/gr.135350.111
  8. Cabili, M.N., et al., Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev, 2011. 25(18): p. 1915-27. https://doi.org/10.1101/gad.17446611
  9. Nam, J.W. and D.P. Bartel, Long noncoding RNAs in C. elegans. Genome Res, 2012. 22(12): p. 2529-40. https://doi.org/10.1101/gr.140475.112
  10. Ingolia, N.T., et al., Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science, 2009. 324(5924): p. 218-23. https://doi.org/10.1126/science.1168978
  11. Tanaka, T., Y. Yamada, and M. Ikehara, Polymer support synthesis of oligodeoxyribonucleotide with an aminoethyl or aminohexyl group at the 5' end by the phosphite-triester approach. Chem Pharm Bull(Tokyo), 1988. 36(4): p. 1386-92. https://doi.org/10.1248/cpb.36.1386
  12. Ingolia, N.T., L.F. Lareau, and J.S. Weissman, 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
  13. Trapnell, C., et al., Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol, 2010. 28(5): p. 511-5. https://doi.org/10.1038/nbt.1621
  14. Kodzius, R., et al., CAGE: cap analysis of gene expression. Nat Methods, 2006. 3(3): p. 211-22. https://doi.org/10.1038/nmeth0306-211
  15. Jan, C.H., et al., Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs. Nature, 2011. 469(7328): p. 97-101. https://doi.org/10.1038/nature09616
  16. Sun, K., et al., iSeeRNA: identification of long intergenic non-coding RNA transcripts from transcriptome sequencing data. BMC Genomics, 2013. 14 Suppl 2: p.S7.
  17. Wang, Y., et al., Computational identification of human long intergenic non-coding RNAs using a GA-SVM algorithm. Gene, 2014. 533(1): p. 94-9. https://doi.org/10.1016/j.gene.2013.09.118
  18. 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.2828-34. https://doi.org/10.1242/dev.098343
  19. Wang, L., et al., CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model. Nucleic Acids Res, 2013. 41(6): p. e74. https://doi.org/10.1093/nar/gkt006