메뉴 건너뛰기




Volumn 44, Issue D1, 2016, Pages D231-D238

DIANA-LncBase v2: Indexing microRNA targets on non-coding transcripts

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; UNTRANSLATED RNA; LONG UNTRANSLATED RNA;

EID: 84976875164     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv1270     Document Type: Article
Times cited : (603)

References (45)
  • 1
    • 78751477191 scopus 로고    scopus 로고
    • Gene silencing by microRNAs: Contributions of translational repression and mRNA decay
    • Huntzinger, E. and Izaurralde, E. (2011) Gene silencing by microRNAs: contributions of translational repression and mRNA decay. Nat. Rev. Genet., 12, 99-110.
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 99-110
    • Huntzinger, E.1    Izaurralde, E.2
  • 2
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • Consortium, E. P. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.
    • (2012) Nature , vol.489 , pp. 57-74
    • Consortium, E.P.1
  • 3
    • 84890852686 scopus 로고    scopus 로고
    • Evolutionary conservation of long non-coding RNAs; sequence, structure, function
    • Johnsson, P., Lipovich, L., Grander, D. and Morris, K. V. (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    Grander, D.3    Morris, K.V.4
  • 4
    • 84861904178 scopus 로고    scopus 로고
    • Genome regulation by long noncoding RNAs
    • Rinn, J. L. and Chang, H. Y. (2012) Genome regulation by long noncoding RNAs. Annu. Rev. Biochem., 81, 145-166.
    • (2012) Annu. Rev. Biochem. , vol.81 , pp. 145-166
    • Rinn, J.L.1    Chang, H.Y.2
  • 5
    • 84863495094 scopus 로고    scopus 로고
    • The hallmarks of cancer: A long non-coding RNA point of view
    • Gutschner, T. and Diederichs, S. (2012) The hallmarks of cancer: a long non-coding RNA point of view. RNA Biol., 9, 703-719.
    • (2012) RNA Biol. , vol.9 , pp. 703-719
    • Gutschner, T.1    Diederichs, S.2
  • 6
    • 80455143733 scopus 로고    scopus 로고
    • MiRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA
    • Hansen, T. B., Wiklund, E. D., Bramsen, J. B., Villadsen, S. B., Statham, A. L., Clark, S. J. and Kjems, J. (2011) miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA. EMBO J., 30, 4414-4422.
    • (2011) EMBO J. , vol.30 , pp. 4414-4422
    • Hansen, T.B.1    Wiklund, E.D.2    Bramsen, J.B.3    Villadsen, S.B.4    Statham, A.L.5    Clark, S.J.6    Kjems, J.7
  • 8
    • 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, W. J. and Pandolfi, P. P. (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
  • 10
    • 84874789694 scopus 로고    scopus 로고
    • Epigenetic activation of the MiR-200 family contributes to H19-mediated metastasis suppression in hepatocellular carcinoma
    • Zhang, L., Yang, F., Yuan, J. H., Yuan, S. X., Zhou, W. P., Huo, X. S., Xu, D., Bi, H. S., Wang, F. and Sun, S. H. (2013) Epigenetic activation of the MiR-200 family contributes to H19-mediated metastasis suppression in hepatocellular carcinoma. Carcinogenesis, 34, 577-586.
    • (2013) Carcinogenesis , vol.34 , pp. 577-586
    • Zhang, L.1    Yang, F.2    Yuan, J.H.3    Yuan, S.X.4    Zhou, W.P.5    Huo, X.S.6    Xu, D.7    Bi, H.S.8    Wang, F.9    Sun, S.H.10
  • 11
    • 84899808514 scopus 로고    scopus 로고
    • Long non-coding RNA H19 promotes glioma cell invasion by deriving miR-675
    • Shi, Y., Wang, Y., Luan, W., Wang, P., Tao, T., Zhang, J., Qian, J., Liu, N. and You, Y. (2014) Long non-coding RNA H19 promotes glioma cell invasion by deriving miR-675. PLoS one, 9, e86295.
    • (2014) PLoS One , vol.9 , pp. e86295
    • Shi, Y.1    Wang, Y.2    Luan, W.3    Wang, P.4    Tao, T.5    Zhang, J.6    Qian, J.7    Liu, N.8    You, Y.9
  • 12
    • 77956542998 scopus 로고    scopus 로고
    • CREB up-regulates long non-coding RNA, HULC expression through interaction with microRNA-372 in liver cancer
    • Wang, J., Liu, X., Wu, H., Ni, P., Gu, Z., Qiao, Y., Chen, N., Sun, F. and Fan, Q. (2010) CREB up-regulates long non-coding RNA, HULC expression through interaction with microRNA-372 in liver cancer. Nucleic Acids Res., 38, 5366-5383.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 5366-5383
    • Wang, J.1    Liu, X.2    Wu, H.3    Ni, P.4    Gu, Z.5    Qiao, Y.6    Chen, N.7    Sun, F.8    Fan, Q.9
  • 14
    • 79961170994 scopus 로고    scopus 로고
    • A ceRNA hypothesis: The Rosetta Stone of a hidden RNA language?
    • Salmena, L., Poliseno, L., Tay, Y., Kats, L. and Pandolfi, P. P. (2011) A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell, 146, 353-358.
    • (2011) Cell , vol.146 , pp. 353-358
    • Salmena, L.1    Poliseno, L.2    Tay, Y.3    Kats, L.4    Pandolfi, P.P.5
  • 18
    • 38849145861 scopus 로고    scopus 로고
    • Prediction of both conserved and nonconserved microRNA targets in animals
    • Wang, X. and El Naqa, I. M. (2008) Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics, 24, 325-332.
    • (2008) Bioinformatics , vol.24 , pp. 325-332
    • Wang, X.1    El Naqa, I.M.2
  • 19
    • 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. and 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
  • 20
    • 77955963884 scopus 로고    scopus 로고
    • Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites
    • Betel, D., Koppal, A., Agius, P., Sander, C. and Leslie, C. (2010) Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol., 11, R90.
    • (2010) Genome Biol. , vol.11 , pp. R90
    • Betel, D.1    Koppal, A.2    Agius, P.3    Sander, C.4    Leslie, C.5
  • 21
    • 84891773261 scopus 로고    scopus 로고
    • NPInter v2.0: An updated database of ncRNA interactions
    • Yuan, J., Wu, W., Xie, C., Zhao, G., Zhao, Y. and Chen, R. (2014) NPInter v2.0: an updated database of ncRNA interactions. Nucleic Acids Res., 42, D104-D108.
    • (2014) Nucleic Acids Res. , vol.42 , pp. D104-D108
    • Yuan, J.1    Wu, W.2    Xie, C.3    Zhao, G.4    Zhao, Y.5    Chen, R.6
  • 23
    • 84943165926 scopus 로고    scopus 로고
    • LncReg: A reference resource for lncRNA-associated regulatory networks
    • Zhou, Z., Shen, Y., Khan, M. R. and Li, A. (2015) LncReg: a reference resource for lncRNA-associated regulatory networks. Database (Oxford), 2015, doi:10.1093/database/bav083.
    • (2015) Database (Oxford) , vol.2015
    • Zhou, Z.1    Shen, Y.2    Khan, M.R.3    Li, A.4
  • 26
    • 67749132423 scopus 로고    scopus 로고
    • Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps
    • Chi, S. W., Zang, J. B., Mele, A. and Darnell, R. B. (2009) Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature, 460, 479-486.
    • (2009) Nature , vol.460 , pp. 479-486
    • Chi, S.W.1    Zang, J.B.2    Mele, A.3    Darnell, R.B.4
  • 28
    • 84876935138 scopus 로고    scopus 로고
    • Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding
    • Helwak, A., Kudla, G., Dudnakova, T. and Tollervey, D. (2013) Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell, 153, 654-665.
    • (2013) Cell , vol.153 , pp. 654-665
    • Helwak, A.1    Kudla, G.2    Dudnakova, T.3    Tollervey, D.4
  • 29
    • 84891818318 scopus 로고    scopus 로고
    • MiRBase: Annotating high confidence microRNAs using deep sequencing data
    • Kozomara, A. and Griffiths-Jones, S. (2014) miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res., 42, D68-D73.
    • (2014) Nucleic Acids Res. , vol.42 , pp. D68-D73
    • Kozomara, A.1    Griffiths-Jones, S.2
  • 31
    • 80052978224 scopus 로고    scopus 로고
    • Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
    • 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.
    • (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
  • 33
    • 84883492771 scopus 로고    scopus 로고
    • Kraken: A set of tools for quality control and analysis of high-throughput sequence data
    • Davis, M. P., Van Dongen, S., Abreu-Goodger, C., Bartonicek, N. and Enright, A. J. (2013) Kraken: a set of tools for quality control and analysis of high-throughput sequence data. Methods, 63, 41-49.
    • (2013) Methods , vol.63 , pp. 41-49
    • Davis, M.P.1    Van Dongen, S.2    Abreu-Goodger, C.3    Bartonicek, N.4    Enright, A.J.5
  • 35
    • 84905049901 scopus 로고    scopus 로고
    • Trimmomatic: A flexible trimmer for Illumina sequence data
    • Bolger, A. M., Lohse, M. and Usadel, B. (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30, 2114-2120.
    • (2014) Bioinformatics , vol.30 , pp. 2114-2120
    • Bolger, A.M.1    Lohse, M.2    Usadel, B.3
  • 41
    • 79961123152 scopus 로고    scopus 로고
    • RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome
    • Li, B. and Dewey, C. (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics, 12, 323.
    • (2011) BMC Bioinformatics , vol.12 , pp. 323
    • Li, B.1    Dewey, C.2
  • 43
    • 74949092081 scopus 로고    scopus 로고
    • Detection of nonneutral substitution rates on mammalian phylogenies
    • Pollard, K. S., Hubisz, M. J., Rosenbloom, K. R. and Siepel, A. (2010) Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res., 20, 110-121.
    • (2010) Genome Res. , vol.20 , pp. 110-121
    • Pollard, K.S.1    Hubisz, M.J.2    Rosenbloom, K.R.3    Siepel, A.4
  • 44
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B, 57, 289-300.
    • (1995) J. R. Stat. Soc. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.