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

한국정보과학회 (Korean Institute of Information Scientists and Engineers)
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Non-coding RNAs에 대한 생물정보학 접근

  • 발행 : 2013.08.16
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참고문헌

  1. Rinn J. L., Chang H. Y., "Genome regulation by long noncoding RNAs", Annu Rev Biochem, Vol. 81, pp. 145-166, 2012 https://doi.org/10.1146/annurev-biochem-051410-092902
  2. Michalak P., "RNA world-the dark matter of evolutionary genomics", J Evol Biol, Vol. 19, No. 6, pp. 1768-1774, 2006 https://doi.org/10.1111/j.1420-9101.2006.01141.x
  3. Dinger M. E., Amaral P. P., Mercer T. R., Mattick J. S., "Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications", Brief Funct Genomic Proteomic, Vol. 8, pp. 407-423, 2009 https://doi.org/10.1093/bfgp/elp038
  4. Kapranov P., St Laurent G., Raz T., Ozsolak F., and et al., "The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA", BMC Biol, Vol. 8, pp.149, 2010 https://doi.org/10.1186/1741-7007-8-149
  5. Zamore P. D., Haley B., "Ribo-gnome: the big world of small RNAs", Science, Vol. 309, pp. 1519-1524, 2005 https://doi.org/10.1126/science.1111444
  6. Bartel D. P., "MicroRNAs: genomics, biogenesis, mechanism, and function", Cell, Vol. 116, No. 2, pp. 281-297, 2004 https://doi.org/10.1016/S0092-8674(04)00045-5
  7. Baker M., "Long noncoding RNAs: the search for function", Nature Methods, Vol. 8, pp. 379-383, 2011 https://doi.org/10.1038/nmeth0511-379
  8. Chowdhury D., Choi Y. E., Brault M. E., "Charity begins at home: non-coding RNA functions in DNA repair", Nat Rev Mol Cell Biol, Vol. 10, No. 3, pp. 155-159, 2009
  9. Wahlestedt C., "Targeting long non-coding RNA to therapeutically upregulate gene expression", Nat Rev Drug Discov, Vol. 12, No. 6, pp. 433-446, 2013 https://doi.org/10.1038/nrd4018
  10. Bhartiya D. Pal K., ghosh S., Kapoor S. and et al., "lncRNome: a comprehensive knowledgebase of human long noncoding RNAs", Database(Oxford), article ID: bat034, 2013
  11. Amaral P. P., Clark M. B., Gascoigne D. K., Dinger M. E., and et al., "lncRNAdb: a reference database for long noncoding RNAs", Nucleic Acids Res, Vol. 39, pp. D146-D151, 2011 https://doi.org/10.1093/nar/gkq1138
  12. Yang J. H., Li J. H., Jiang S., Zhou H. and et al., "ChIPBase: A database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data", Nucleic Acids Res, Vol. 41, pp. D177-D187, 2013 https://doi.org/10.1093/nar/gks1060
  13. Niazi F., Valadkhan S., "Computational analysis of functional long noncoding RNAs reveals lack of peptide-coding capacity and parallels with 3'UTRs", RNA, Vol. 18, pp. 825-843, 2012 https://doi.org/10.1261/rna.029520.111
  14. Volders P. J., Helsens K., Wang X., Menten B., and et al., "LNCipedia: a database for annotated human lnc-RNA transcript sequences and structures", Nucleic Acids Res, Vol. 41, pp. D246-D251, 2013 https://doi.org/10.1093/nar/gks915
  15. Chen G., Wang Z., Wang D., Qiu C., and et al., "LncRNADisease: a database for long-non-coding RNA-associated diseases", Nucleic Acids Res, Vol. 41, pp. D983-D986, 2013 https://doi.org/10.1093/nar/gks1099
  16. Paraskevopoulou M. D., Georgakilas G., Kostoulas N., Reczko M., and et al., "DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs", Nucleic Acids Res, Vol. 41, pp. D239-D245, 2013 https://doi.org/10.1093/nar/gks1246
  17. Bono H., Yagi K., Kasukawa T., Nikaido I. and et al., "Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays", Genome Res, Vol. 13, pp. 1318-1323, 2003 https://doi.org/10.1101/gr.1075103
  18. Bu D., Yu K., Sun S., Xie C., and et al., "NONCODE v3.0: integrative annotation of long noncoding RNAs", Nucleic Acids Res, Vol. 40, pp. D210-D215, 2012 https://doi.org/10.1093/nar/gkr1175
  19. Dinger M. E., Pang K. C., Mercer T. R., Crowe M. L., and et al., "NRED: a database of long noncoding RNA expression", Nucleic Acids Res, Vol. 37, pp. D122-D126, 2009 https://doi.org/10.1093/nar/gkn617
  20. Belinky F., Bahir I., Stelzer G., Zimmerman S., and et al., "Non-redundant compendium of human ncRNA genes in GeneCards", Vol. 29, No. 2, pp. 255-261, 2012
  21. Jin J., Liu J., Wang H., Wong L., and et al., "PLncDB: Plant Long noncoding RNA Database", Bioinformatics, Vol. 29, No. 8, pp. 1068-1071, 2013 https://doi.org/10.1093/bioinformatics/btt107
  22. Salmena L., Poliseno L., Tay Y., Kats L., and et al., "A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language?", Cell, Vol. 146, No. 3, pp. 353-358, 2011 https://doi.org/10.1016/j.cell.2011.07.014
  23. Barrett T., Suzek T.O., Troup D. B., Wilhite S. E., and et al., "NCBI GEO: mining millions of expression profiles-database and tools", Nucleic Acids Res, Vol. 33, pp. D562-D563, 2005
  24. Liao Q., Xiao H., Bu D., Xie C., and et al., "ncFANs: a web server for functional annotation of long non-coding RNAs", Nucleic Acids Res, Vol. 39, pp. W118-W124, 2011 https://doi.org/10.1093/nar/gkr432
  25. Liu K., Yan Z., Li Y., Sun Z., "Linc2GO: a human Linc-RNA function annotation resource based on ceRNA hypothesis", Bioinformatics, Epub ahead of print, 2013
  26. Asai K., Kiryu H., Hamada M., Tabei Y., "Software. ncrna.org: web servers for analyses of RNA sequences", Nucleic Acids Res, Vol. 36, pp. W75-W78, 2008 https://doi.org/10.1093/nar/gkn222
  27. Sun K., Chen X., Jiang P., Song X., and et al., "iSee-RNA: identification of long intergenic non-coding RNA transcripts from transcriptome sequencing data", BMC Genomics, Vol. 14, pp. Suppl 2:S7, 2013
  28. Gellert P., Ponomareva Y., Braun T., Uchida S., "Noncoder: a web interface for exon array-based detection of long non-coding RNAs", Nucleic Acids Res, Vol. 41, No. 1, pp. e20, 2013 https://doi.org/10.1093/nar/gks877
  29. Chen C. J., Servant N., Toedling J., Sarazin A., and et al., "ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data", Bioinformatics, Vol. 28, pp. 3147-3149, 2012 https://doi.org/10.1093/bioinformatics/bts587
  30. Sun L., Zhang Z., Bailey T. L., Perkins A. C., and et al., "Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study", BMC Bioinformatics, Vol. 13, pp. 331, 2012 https://doi.org/10.1186/1471-2105-13-331
  31. Lin M. F., Jungreis I., Kellis M., "PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions", Bioinformatics, Vol. 27, No. 13, pp. i275-i282, 2011 https://doi.org/10.1093/bioinformatics/btr209
  32. Jeggari A., Marks D. S., Larsson E., "miRcode: a map of putative microRNA target sites in the long non-coding transcriptome", Bioinformatics, Vol. 28, No. 15, pp. 2062-2063, 2012 https://doi.org/10.1093/bioinformatics/bts344
  33. Leung Y. Y., Ryvkin P., Ungar L. H., Gregory B. D., and et al., "CoRAL: predicting non-coding RNAs from small RNA-sequencing data", Nucleic Acids Res, Epub ahead of print, 2013