메뉴 건너뛰기




Volumn 20, Issue 11, 2014, Pages 1655-1665

Databases for lncRNAs: A comparative evaluation of emerging tools

Author keywords

Databases; LncRNAs; Noncoding RNAs

Indexed keywords

LONG UNTRANSLATED RNA; TRANSCRIPTOME;

EID: 84908123944     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.044040.113     Document Type: Review
Times cited : (90)

References (75)
  • 2
    • 0038360922 scopus 로고    scopus 로고
    • Epigenetic gene regulation by noncoding RNAs
    • Andersen AA, Panning B. 2003. Epigenetic gene regulation by noncoding RNAs. Curr Opin Cell Biol 15: 281-289.
    • (2003) Curr Opin Cell Biol , vol.15 , pp. 281-289
    • Andersen, A.A.1    Panning, B.2
  • 3
    • 84870669335 scopus 로고    scopus 로고
    • Polyadenylation-dependent control of long noncoding RNA expression by the poly(a)-binding protein nuclear 1
    • Beaulieu YB, Kleinman CL, Landry-Voyer A-M, Majewski J, Bachand F. 2012. Polyadenylation-dependent control of long noncoding RNA expression by the poly(A)-binding protein nuclear 1. PLoS Genet 8: E1003078.
    • (2012) PLoS Genet , vol.8 , pp. e1003078
    • Beaulieu, Y.B.1    Kleinman, C.L.2    Landry-Voyer, A.-M.3    Majewski, J.4    Bachand, F.5
  • 6
    • 0026489906 scopus 로고
    • The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus
    • Brockdorff N, Ashworth A, Kay GF, McCabe VM, Norris DP, Cooper PJ, Swift S, Rastan S. 1992. The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus. Cell 71: 515-526.
    • (1992) Cell , vol.71 , pp. 515-526
    • Brockdorff, N.1    Ashworth, A.2    Kay, G.F.3    Mccabe, V.M.4    Norris, D.P.5    Cooper, P.J.6    Swift, S.7    Rastan, S.8
  • 7
    • 0025961771 scopus 로고
    • A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome
    • Brown CJ, Ballabio A, Rupert JL, Lafreniere RG, Grompe M, Tonlorenzi R, Willard HF. 1991. A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome. Nature 349: 38-44.
    • (1991) Nature , vol.349 , pp. 38-44
    • Brown, C.J.1    Ballabio, A.2    Rupert, J.L.3    Lafreniere, R.G.4    Grompe, M.5    Tonlorenzi, R.6    Willard, H.F.7
  • 8
    • 0026456701 scopus 로고
    • The human XIST gene: Analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus
    • Brown CJ, Hendrich BD, Rupert JL, Lafrenière RG, Xing Y, Lawrence J, Willard HF. 1992. The human XIST gene: Analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell 71: 527-542.
    • (1992) Cell , vol.71 , pp. 527-542
    • Brown, C.J.1    Hendrich, B.D.2    Rupert, J.L.3    Lafrenière, R.G.4    Xing, Y.5    Lawrence, J.6    Willard, H.F.7
  • 10
    • 80052978224 scopus 로고    scopus 로고
    • Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
    • Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL. 2011. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 25: 1915-1927.
    • (2011) Genes Dev , vol.25 , pp. 1915-1927
    • Cabili, M.N.1    Trapnell, C.2    Goff, L.3    Koziol, M.4    Tazon-Vega, B.5    Regev, A.6    Rinn, J.L.7
  • 11
    • 84861063896 scopus 로고    scopus 로고
    • SNPedia: A wiki supporting personal genome annotation, interpretation and analysis
    • Cariaso M, Lennon G. 2012. SNPedia: A wiki supporting personal genome annotation, interpretation and analysis. Nucleic Acids Res 40: D1308-D1312.
    • (2012) Nucleic Acids Res , vol.40 , pp. D1308-D1312
    • Cariaso, M.1    Lennon, G.2
  • 13
    • 84902279606 scopus 로고    scopus 로고
    • LncRNAMap: A map of putative regulatory functions in the long non-coding transcriptome
    • in press
    • Chan W-L, Huang H-D, Chang J-G. 2014. lncRNAMap: A map of putative regulatory functions in the long non-coding transcriptome. Comput Biol Chem (in press).
    • (2014) Comput Biol Chem
    • Chan, W.-L.1    Huang, H.-D.2    Chang, J.-G.3
  • 16
    • 84878865619 scopus 로고    scopus 로고
    • Ribosome profiling reveals resemblance between long non-coding RNAs and 5′ leaders of coding RNAs
    • Chew G-L, Pauli A, Rinn JL, Regev A, Schier AF, Valen E. 2013. Ribosome profiling reveals resemblance between long non-coding RNAs and 5′ leaders of coding RNAs. Development 140: 2828-2834.
    • (2013) Development , vol.140 , pp. 2828-2834
    • Chew, G.-L.1    Pauli, A.2    Rinn, J.L.3    Regev, A.4    Schier, A.F.5    Valen, E.6
  • 22
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • The ENCODE Project Consortium
    • The ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74.
    • (2012) Nature , vol.489 , pp. 57-74
  • 23
    • 77954853506 scopus 로고    scopus 로고
    • Research resource: Expression profiling reveals unexpected targets and functions of the human steroid receptor RNA activator (SRA) gene
    • Foulds CE, Tsimelzon A, Long W, Le A, Tsai SY, Tsai M-J, O'Malley BW. 2010. Research resource: Expression profiling reveals unexpected targets and functions of the human steroid receptor RNA activator (SRA) gene. Mol Endocrinol 24: 1090-1105.
    • (2010) Mol Endocrinol , vol.24 , pp. 1090-1105
    • Foulds, C.E.1    Tsimelzon, A.2    Long, W.3    Le, A.4    Tsai, S.Y.5    Tsai, M.-J.6    O'malley, B.W.7
  • 24
    • 79953888460 scopus 로고    scopus 로고
    • The functional role of long noncoding RNA in human carcinomas
    • Gibb EA, Brown CJ, Lam WL. 2011. The functional role of long noncoding RNA in human carcinomas. Mol Cancer 10: 38.
    • (2011) Mol Cancer , vol.10 , pp. 38
    • Gibb, E.A.1    Brown, C.J.2    Lam, W.L.3
  • 25
    • 84866402694 scopus 로고    scopus 로고
    • Computational prediction of polycomb-associated long non-coding RNAs
    • GlazkoGV, Zybailov BL, Rogozin IB. 2012. Computational prediction of polycomb-associated long non-coding RNAs. PLoS One 7: E44878.
    • (2012) PLoS One , vol.7 , pp. e44878
    • Glazko, G.V.1    Zybailov, B.L.2    Rogozin, I.B.3
  • 26
  • 27
    • 84857066786 scopus 로고    scopus 로고
    • Modular regulatory principles of large noncoding RNAs
    • Guttman M, Rinn JL. 2012. Modular regulatory principles of large noncoding RNAs. Nature 482: 339-346.
    • (2012) Nature , vol.482 , pp. 339-346
    • Guttman, M.1    Rinn, J.L.2
  • 29
    • 84879969127 scopus 로고    scopus 로고
    • Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins
    • Guttman M, Russell P, Ingolia NT, Weissman JS, Lander ES. 2013. Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins. Cell 154: 240-251.
    • (2013) Cell , vol.154 , pp. 240-251
    • Guttman, M.1    Russell, P.2    Ingolia, N.T.3    Weissman, J.S.4    Lander, E.S.5
  • 30
    • 0031001346 scopus 로고    scopus 로고
    • Xist has properties of the X-chromosome inactivation centre
    • Herzing LB, Romer JT, Horn JM, Ashworth A. 1997. Xist has properties of the X-chromosome inactivation centre. Nature 386: 272-275.
    • (1997) Nature , vol.386 , pp. 272-275
    • Herzing, L.B.1    Romer, J.T.2    Horn, J.M.3    Ashworth, A.4
  • 31
    • 7244245762 scopus 로고    scopus 로고
    • Finishing the euchromatic sequence of the human genome
    • Human Genome Sequencing Consortium International
    • Human Genome Sequencing Consortium International. 2004. Finishing the euchromatic sequence of the human genome. Nature 431: 931-945.
    • (2004) Nature , vol.431 , pp. 931-945
  • 32
    • 84864739324 scopus 로고    scopus 로고
    • Integrative transcriptome analysis suggest processing of a subset of long non-coding RNAs to small RNAs
    • Jalali S, Jayaraj GG, Scaria V. 2012. Integrative transcriptome analysis suggest processing of a subset of long non-coding RNAs to small RNAs. Biol Direct 7: 25.
    • (2012) Biol Direct , vol.7 , pp. 25
    • Jalali, S.1    Jayaraj, G.G.2    Scaria, V.3
  • 33
    • 84861862859 scopus 로고    scopus 로고
    • The polymorphism rs944289 predisposes to papillary thyroid carcinoma through a large intergenic noncoding RNA gene of tumor suppressor type
    • Jendrzejewski J, He H, Radomska HS, Li W, Tomsic J, Liyanarachchi S, Davuluri RV, Nagy R, de la Chapelle A. 2012. The polymorphism rs944289 predisposes to papillary thyroid carcinoma through a large intergenic noncoding RNA gene of tumor suppressor type. Proc Natl Acad Sci 109: 8646-8651.
    • (2012) Proc Natl Acad Sci , vol.109 , pp. 8646-8651
    • Jendrzejewski, J.1    He, H.2    Radomska, H.S.3    Li, W.4    Tomsic, J.5    Liyanarachchi, S.6    Davuluri, R.V.7    Nagy, R.8    De, L.C.A.9
  • 34
    • 77955110979 scopus 로고    scopus 로고
    • Genome-wide computational identification and manual annotation of human long noncoding RNA genes
    • Jia H, Osak M, Bogu GK, Stanton LW, Johnson R, Lipovich L. 2010. Genome-wide computational identification and manual annotation of human long noncoding RNA genes. RNA 16: 1478-1487.
    • (2010) RNA , vol.16 , pp. 1478-1487
    • Jia, H.1    Osak, M.2    Bogu, G.K.3    Stanton, L.W.4    Johnson, R.5    Lipovich, L.6
  • 37
    • 84890852686 scopus 로고    scopus 로고
    • Evolutionary conservation of long non-coding RNAs; sequence, structure, function
    • Johnsson P, Lipovich L, Grandér D, Morris KV. 2014. Evolutionary conservation of long non-coding RNAs; sequence, structure, function. Biochim Biophys Acta 1840: 1063-1071.
    • (2014) Biochim Biophys Acta , vol.1840 , pp. 1063-1071
    • Johnsson, P.1    Lipovich, L.2    Grandér, D.3    Morris, K.V.4
  • 39
    • 22244442468 scopus 로고    scopus 로고
    • Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays
    • Kapranov P, Drenkow J, Cheng J, Long J, Helt G, Dike S, Gingeras TR. 2005. Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Res 15: 987-997.
    • (2005) Genome Res , vol.15 , pp. 987-997
    • Kapranov, P.1    Drenkow, J.2    Cheng, J.3    Long, J.4    Helt, G.5    Dike, S.6    Gingeras, T.R.7
  • 43
    • 34547582418 scopus 로고    scopus 로고
    • CPC: Assess the protein-coding potential of transcripts using sequence features and support vector machine
    • Kong L, Zhang Y, Ye Z-Q, Liu X-Q, Zhao S-Q, Wei L, Gao G. 2007. CPC: Assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res 35: W345-W349.
    • (2007) Nucleic Acids Res , vol.35 , pp. W345-W349
    • Kong, L.1    Zhang, Y.2    Ye, Z.-Q.3    Liu, X.-Q.4    Zhao, S.-Q.5    Wei, L.6    Gao, G.7
  • 44
    • 84886047908 scopus 로고    scopus 로고
    • TINCR, staufen1, and cellular differentiation
    • Kretz M. 2013. TINCR, staufen1, and cellular differentiation. RNA Biol 10: 1597-1601.
    • (2013) RNA Biol , vol.10 , pp. 1597-1601
    • Kretz, M.1
  • 45
    • 84875177348 scopus 로고    scopus 로고
    • X-inactivation, imprinting, and long noncoding RNAs in health and disease
    • Lee JT, Bartolomei MS. 2013. X-inactivation, imprinting, and long noncoding RNAs in health and disease. Cell 152: 1308-1323.
    • (2013) Cell , vol.152 , pp. 1308-1323
    • Lee, J.T.1    Bartolomei, M.S.2
  • 47
    • 84891818924 scopus 로고    scopus 로고
    • StarBase v2.0: Decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data
    • Li J-H, Liu S, Zhou H, Qu L-H, Yang J-H. 2014. starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res 42: D92-D97.
    • (2014) Nucleic Acids Res , vol.42 , pp. D92-D97
    • Li, J.-H.1    Liu, S.2    Zhou, H.3    Qu, L.-H.4    Yang, J.-H.5
  • 48
    • 79956010263 scopus 로고    scopus 로고
    • Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network
    • 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-non-coding gene co-expression network. Nucleic Acids Res 39: 3864-3878.
    • (2011) Nucleic Acids Res , vol.39 , pp. 3864-3878
    • Liao, Q.1    Liu, C.2    Yuan, X.3    Kang, S.4    Miao, R.5    Xiao, H.6    Zhao, G.7    Luo, H.8    Bu, D.9    Zhao, H.10
  • 49
    • 84882643385 scopus 로고    scopus 로고
    • Linc2GO: A human LincRNA function annotation resource based on ceRNA hypothesis
    • Liu K, Yan Z, Li Y, Sun Z. 2013. Linc2GO: A human LincRNA function annotation resource based on ceRNA hypothesis. Bioinformatics 29: 2221-2222.
    • (2013) Bioinformatics , vol.29 , pp. 2221-2222
    • Liu, K.1    Yan, Z.2    Li, Y.3    Sun, Z.4
  • 50
    • 84890415138 scopus 로고    scopus 로고
    • Long non-coding RNA identification over mouse brain development by integrative modeling of chromatin and genomic features
    • Lv J, Liu H, Huang Z, Su J, He H, Xiu Y, Zhang Y, Wu Q. 2013. Long non-coding RNA identification over mouse brain development by integrative modeling of chromatin and genomic features. Nucleic Acids Res 41: 10044-10061.
    • (2013) Nucleic Acids Res , vol.41 , pp. 10044-10061
    • Lv, J.1    Liu, H.2    Huang, Z.3    Su, J.4    He, H.5    Xiu, Y.6    Zhang, Y.7    Wu, Q.8
  • 51
    • 84875183056 scopus 로고    scopus 로고
    • Structure and function of long noncoding RNAs in epigenetic regulation
    • Mercer TR, Mattick JS. 2013. Structure and function of long noncoding RNAs in epigenetic regulation. Nat Struct Mol Biol 20: 300-307.
    • (2013) Nat Struct Mol Biol , vol.20 , pp. 300-307
    • Mercer, T.R.1    Mattick, J.S.2
  • 54
    • 84858692231 scopus 로고    scopus 로고
    • Computational analysis of functional long noncoding RNAs reveals lack of peptide-coding capacity and parallels with 3′ UTRs
    • Niazi F, Valadkhan S. 2012. Computational analysis of functional long noncoding RNAs reveals lack of peptide-coding capacity and parallels with 3′ UTRs. RNA 18: 825-843.
    • (2012) RNA , vol.18 , pp. 825-843
    • Niazi, F.1    Valadkhan, S.2
  • 57
    • 84907032373 scopus 로고    scopus 로고
    • LncRNAtor: A comprehensive resource for functional investigation of long noncoding RNAs
    • in press
    • Park C, Yu N, Choi I, KimW, Lee S. 2014. lncRNAtor: A comprehensive resource for functional investigation of long noncoding RNAs. Bioinformatics (in press).
    • (2014) Bioinformatics
    • Park, C.1    Yu, N.2    Choi, I.3    Kim, W.4    Lee, S.5
  • 58
    • 84896073446 scopus 로고    scopus 로고
    • Non-coding RNAs turn up the heat: An emerging layer of novel regulators in the mammalian heat shock response
    • Place RF, Noonan EJ. 2013. Non-coding RNAs turn up the heat: An emerging layer of novel regulators in the mammalian heat shock response. Cell Stress Chaperones 19: 159-172.
    • (2013) Cell Stress Chaperones , vol.19 , pp. 159-172
    • Place, R.F.1    Noonan, E.J.2
  • 59
    • 77953957633 scopus 로고    scopus 로고
    • A coding-independent function of gene and pseudogene mRNAs regulates tumour biology
    • Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ, Pandolfi PP. 2010. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 465: 1033-1038.
    • (2010) Nature , vol.465 , pp. 1033-1038
    • Poliseno, L.1    Salmena, L.2    Zhang, J.3    Carver, B.4    Haveman, W.J.5    Pandolfi, P.P.6
  • 60
    • 60149099385 scopus 로고    scopus 로고
    • Evolution and functions of long noncoding RNAs
    • Ponting CP, Oliver PL, Reik W. 2009. Evolution and functions of long noncoding RNAs. Cell 136: 629-641.
    • (2009) Cell , vol.136 , pp. 629-641
    • Ponting, C.P.1    Oliver, P.L.2    Reik, W.3
  • 64
    • 84887033381 scopus 로고    scopus 로고
    • A novel non-coding RNA lncRNA-JADE connects DNA damage signalling to histone H4 acetylation
    • Wan G, Hu X, Liu Y, Han C, Sood AK, Calin GA, Zhang X, Lu X. 2013. A novel non-coding RNA lncRNA-JADE connects DNA damage signalling to histone H4 acetylation. EMBO J 32: 2833-2847.
    • (2013) EMBO J , vol.32 , pp. 2833-2847
    • Wan, G.1    Hu, X.2    Liu, Y.3    Han, C.4    Sood, A.K.5    Calin, G.A.6    Zhang, X.7    Lu, X.8
  • 65
    • 84860723671 scopus 로고    scopus 로고
    • A novel hypoxic stress-responsive long non-coding RNA transcribed by RNA polymerase III in arabidopsis
    • Wu J, Okada T, Fukushima T, Tsudzuki T, Sugiura M, Yukawa Y. 2012. A novel hypoxic stress-responsive long non-coding RNA transcribed by RNA polymerase III in Arabidopsis. RNA Biol 9: 302-313.
    • (2012) RNA Biol , vol.9 , pp. 302-313
    • Wu, J.1    Okada, T.2    Fukushima, T.3    Tsudzuki, T.4    Sugiura, M.5    Yukawa, Y.6
  • 67
    • 84875810883 scopus 로고    scopus 로고
    • Repression of the long noncoding RNA-LET by histone deacetylase 3 contributes to hypoxia-mediated metastasis
    • Yang F, Huo X, Yuan S, Zhang L, Zhou W, Wang F, Sun S. 2013a. Repression of the long noncoding RNA-LET by histone deacetylase 3 contributes to hypoxia-mediated metastasis. Mol Cell 49: 1083- 1096.
    • (2013) Mol Cell , vol.49 , pp. 1083-1096
    • Yang, F.1    Huo, X.2    Yuan, S.3    Zhang, L.4    Zhou, W.5    Wang, F.6    Sun, S.7
  • 68
    • 84876566914 scopus 로고    scopus 로고
    • CHIPBase: A database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from Chip-Seq data
    • Yang J-H, Li J-H, Jiang S, Zhou H, Qu L-H. 2013b. ChIPBase: A database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. Nucleic Acids Res 41: D177-D187.
    • (2013) Nucleic Acids Res , vol.41 , pp. D177-D187
    • Yang, J.-H.1    Li, J.-H.2    Jiang, S.3    Zhou, H.4    Qu, L.-H.5
  • 71
    • 84883806117 scopus 로고    scopus 로고
    • Posttranscriptional gene regulation by long noncoding RNA
    • Yoon J-H, Abdelmohsen K, Gorospe M. 2013. Posttranscriptional gene regulation by long noncoding RNA. J Mol Biol 425: 3723- 3730.
    • (2013) J Mol Biol , vol.425 , pp. 3723-3730
    • Yoon, J.-H.1    Abdelmohsen, K.2    Gorospe, M.3
  • 74
    • 84861156701 scopus 로고    scopus 로고
    • MEG3 noncoding RNA: A tumor suppressor
    • Zhou Y, Zhang X, Klibanski A. 2012. MEG3 noncoding RNA: A tumor suppressor. J Mol Endocrinol 48: R45-R53.
    • (2012) J Mol Endocrinol , vol.48 , pp. R45-R53
    • Zhou, Y.1    Zhang, X.2    Klibanski, A.3
  • 75
    • 81255211626 scopus 로고    scopus 로고
    • RNA splicing control: Yet another gene regulatory role for long nuclear noncoding RNAs
    • Zong X, Tripathi V, Prasanth KV. 2011. RNA splicing control: yet another gene regulatory role for long nuclear noncoding RNAs. RNA Biol 8: 968-977.
    • (2011) RNA Biol , vol.8 , pp. 968-977
    • Zong, X.1    Tripathi, V.2    Prasanth, K.V.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.