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Volumn 44, Issue D1, 2016, Pages D196-D202

deepBase v2.0: Identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data

Author keywords

[No Author keywords available]

Indexed keywords

CIRCULAR RNA; LONG UNTRANSLATED RNA; MICRORNA; RNA; SMALL NUCLEOLAR RNA; SMALL RNA; UNCLASSIFIED DRUG; RNA, CIRCULAR; SMALL UNTRANSLATED RNA;

EID: 84976909135     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv1273     Document Type: Article
Times cited : (199)

References (60)
  • 1
    • 84857066786 scopus 로고    scopus 로고
    • Modular regulatory principles of large non-coding RNAs
    • Guttman, M. and Rinn, J. L. (2012) Modular regulatory principles of large non-coding RNAs. Nature, 482, 339-346.
    • (2012) Nature , vol.482 , pp. 339-346
    • Guttman, M.1    Rinn, J.L.2
  • 2
    • 84879987789 scopus 로고    scopus 로고
    • LincRNAs: Genomics, evolution, and mechanisms
    • Ulitsky, I. and Bartel, D. P. (2013) lincRNAs: genomics, evolution, and mechanisms. Cell, 154, 26-46.
    • (2013) Cell , vol.154 , pp. 26-46
    • Ulitsky, I.1    Bartel, D.P.2
  • 3
    • 58249088751 scopus 로고    scopus 로고
    • MicroRNAs: Target recognition and regulatory functions
    • Bartel, D. P. (2009) MicroRNAs: target recognition and regulatory functions. Cell, 136, 215-233.
    • (2009) Cell , vol.136 , pp. 215-233
    • Bartel, D.P.1
  • 4
    • 84900322651 scopus 로고    scopus 로고
    • Detecting and characterizing circular RNAs
    • Jeck, W. R. and Sharpless, N. E. (2014) Detecting and characterizing circular RNAs. Nat. Biotechnol., 32, 453-461.
    • (2014) Nat. Biotechnol. , vol.32 , pp. 453-461
    • Jeck, W.R.1    Sharpless, N.E.2
  • 7
    • 84907032373 scopus 로고    scopus 로고
    • LncRNAtor: A comprehensive resource for functional investigation of long non-coding RNAs
    • Park, C., Yu, N., Choi, I., Kim, W. and Lee, S. (2014) lncRNAtor: a comprehensive resource for functional investigation of long non-coding RNAs. Bioinformatics, 30, 2480-2485.
    • (2014) Bioinformatics , vol.30 , pp. 2480-2485
    • Park, C.1    Yu, N.2    Choi, I.3    Kim, W.4    Lee, S.5
  • 8
    • 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. and Qu, L. H. (2013) 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
  • 10
    • 78651293534 scopus 로고    scopus 로고
    • MiRBase: Integrating microRNA annotation and deep-sequencing data
    • Kozomara, A. and Griffiths-Jones, S. (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res., 39, D152-D157.
    • (2011) Nucleic Acids Res. , vol.39 , pp. D152-D157
    • Kozomara, A.1    Griffiths-Jones, S.2
  • 11
    • 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
  • 12
    • 84908128765 scopus 로고    scopus 로고
    • CircBase: A database for circular RNAs
    • Glazar, P., Papavasileiou, P. and Rajewsky, N. (2014) circBase: a database for circular RNAs. RNA, 20, 1666-1670.
    • (2014) RNA , vol.20 , pp. 1666-1670
    • Glazar, P.1    Papavasileiou, P.2    Rajewsky, N.3
  • 14
    • 84898747543 scopus 로고    scopus 로고
    • Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals
    • Washietl, S., Kellis, M. and Garber, M. (2014) Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals. Genome Res., 24, 616-628.
    • (2014) Genome Res. , vol.24 , pp. 616-628
    • Washietl, S.1    Kellis, M.2    Garber, M.3
  • 15
    • 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
  • 19
    • 84864098110 scopus 로고    scopus 로고
    • Identification and properties of 1, 119 candidate lincRNA loci in the Drosophila melanogaster genome
    • Young, R. S., Marques, A. C., Tibbit, C., Haerty, W., Bassett, A. R., Liu, J. L. and Ponting, C. P. (2012) Identification and properties of 1, 119 candidate lincRNA loci in the Drosophila melanogaster genome. Genome Biol. Evol., 4, 427-442.
    • (2012) Genome Biol. Evol. , vol.4 , pp. 427-442
    • Young, R.S.1    Marques, A.C.2    Tibbit, C.3    Haerty, W.4    Bassett, A.R.5    Liu, J.L.6    Ponting, C.P.7
  • 20
    • 84870566023 scopus 로고    scopus 로고
    • Long noncoding RNAs in C. Elegans
    • Nam, J. W. and Bartel, D. P. (2012) Long noncoding RNAs in C. elegans. Genome Res., 22, 2529-2540.
    • (2012) Genome Res. , vol.22 , pp. 2529-2540
    • Nam, J.W.1    Bartel, D.P.2
  • 21
    • 84455206362 scopus 로고    scopus 로고
    • Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution
    • Ulitsky, I., Shkumatava, A., Jan, C. H., Sive, H. and Bartel, D. P. (2011) Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell, 147, 1537-1550.
    • (2011) Cell , vol.147 , pp. 1537-1550
    • Ulitsky, I.1    Shkumatava, A.2    Jan, C.H.3    Sive, H.4    Bartel, D.P.5
  • 23
    • 75549084786 scopus 로고    scopus 로고
    • DeepBase: A database for deeply annotating and mining deep sequencing data
    • Yang, J. H., Shao, P., Zhou, H., Chen, Y. Q. and Qu, L. H. (2010) deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res., 38, D123-D130.
    • (2010) Nucleic Acids Res. , vol.38 , pp. D123-D130
    • Yang, J.H.1    Shao, P.2    Zhou, H.3    Chen, Y.Q.4    Qu, L.H.5
  • 25
    • 84859436530 scopus 로고    scopus 로고
    • NCBI Reference Sequences (RefSeq): Current status, new features and genome annotation policy
    • Pruitt, K. D., Tatusova, T., Brown, G. R. and Maglott, D. R. (2012) NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res., 40, D130-D135.
    • (2012) Nucleic Acids Res. , vol.40 , pp. D130-D135
    • Pruitt, K.D.1    Tatusova, T.2    Brown, G.R.3    Maglott, D.R.4
  • 30
    • 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
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R. and Salzberg, S. L. (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol., 14, R36.
    • (2013) Genome Biol. , vol.14 , pp. R36
    • Kim, D.1    Pertea, G.2    Trapnell, C.3    Pimentel, H.4    Kelley, R.5    Salzberg, S.L.6
  • 33
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: The European molecular biology open software suite
    • Rice, P., Longden, I. and Bleasby, A. (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet., 16, 276-277.
    • (2000) Trends Genet. , vol.16 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 36
    • 79959931985 scopus 로고    scopus 로고
    • HMMER web server: Interactive sequence similarity searching
    • Finn, R. D., Clements, J. and Eddy, S. R. (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res., 39, W29-W37.
    • (2011) Nucleic Acids Res. , vol.39 , pp. W29-W37
    • Finn, R.D.1    Clements, J.2    Eddy, S.R.3
  • 38
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders, S. and Huber, W. (2010) Differential expression analysis for sequence count data. Genome Biol., 11, R106.
    • (2010) Genome Biol. , vol.11 , pp. R106
    • Anders, S.1    Huber, W.2
  • 39
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • Quinlan, A. R. and Hall, I. M. (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26, 841-842.
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 40
    • 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. Ser. B (Methodological), 57, 289-300.
    • (1995) J. R. Stat. Soc. Ser. B (Methodological) , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 42
    • 77951953494 scopus 로고    scopus 로고
    • Ultra-high throughput sequencing-based small RNA discovery and discrete statistical biomarker analysis in a collection of cervical tumours and matched controls
    • Witten, D., Tibshirani, R., Gu, S. G., Fire, A. and Lui, W. O. (2010) Ultra-high throughput sequencing-based small RNA discovery and discrete statistical biomarker analysis in a collection of cervical tumours and matched controls. BMC Biol., 8, 58.
    • (2010) BMC Biol. , vol.8 , pp. 58
    • Witten, D.1    Tibshirani, R.2    Gu, S.G.3    Fire, A.4    Lui, W.O.5
  • 43
    • 84871436996 scopus 로고    scopus 로고
    • Evolutionary dynamics of gene and isoform regulation in Mammalian tissues
    • Merkin, J., Russell, C., Chen, P. and Burge, C. B. (2012) Evolutionary dynamics of gene and isoform regulation in Mammalian tissues. Science, 338, 1593-1599.
    • (2012) Science , vol.338 , pp. 1593-1599
    • Merkin, J.1    Russell, C.2    Chen, P.3    Burge, C.B.4
  • 44
    • 0025762971 scopus 로고
    • Ectopic expression of the H19 gene in mice causes prenatal lethality
    • Brunkow, M. E. and Tilghman, S. M. (1991) Ectopic expression of the H19 gene in mice causes prenatal lethality. Genes Dev., 5, 1092-1101.
    • (1991) Genes Dev. , vol.5 , pp. 1092-1101
    • Brunkow, M.E.1    Tilghman, S.M.2
  • 45
    • 0031041908 scopus 로고    scopus 로고
    • Association of IGF2 and H19 imprinting with choriocarcinoma development
    • Arima, T., Matsuda, T., Takagi, N. and Wake, N. (1997) Association of IGF2 and H19 imprinting with choriocarcinoma development. Cancer Genet. Cytogenet., 93, 39-47.
    • (1997) Cancer Genet. Cytogenet. , vol.93 , pp. 39-47
    • Arima, T.1    Matsuda, T.2    Takagi, N.3    Wake, N.4
  • 49
    • 84876020023 scopus 로고    scopus 로고
    • CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model
    • Wang, L., Park, H. J., Dasari, S., Wang, S. Q., Kocher, J. P. and Li, W. (2013) CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model. Nucleic Acids Res., 41, e74.
    • (2013) Nucleic Acids Res. , vol.41 , pp. e74
    • Wang, L.1    Park, H.J.2    Dasari, S.3    Wang, S.Q.4    Kocher, J.P.5    Li, W.6
  • 50
    • 84884915826 scopus 로고    scopus 로고
    • Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts
    • Sun, L., Luo, H. T., Bu, D. C., Zhao, G. G., Yu, K. T., Zhang, C. H., Liu, Y. N., Chen, R. S. and Zhao, Y. (2013) Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. Nucleic Acids Res., 41, e166.
    • (2013) Nucleic Acids Res. , vol.41 , pp. e166
    • Sun, L.1    Luo, H.T.2    Bu, D.C.3    Zhao, G.G.4    Yu, K.T.5    Zhang, C.H.6    Liu, Y.N.7    Chen, R.S.8    Zhao, Y.9
  • 54
    • 84965186421 scopus 로고    scopus 로고
    • LncRNA2Function: A comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data
    • Jiang, Q., Ma, R., Wang, J., Wu, X., Jin, S., Peng, J., Tan, R., Zhang, T., Li, Y. and Wang, Y. (2015) LncRNA2Function: a comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data. BMC Genomics, 16(Suppl. 3), S2.
    • (2015) BMC Genomics , vol.16 , pp. S2
    • Jiang, Q.1    Ma, R.2    Wang, J.3    Wu, X.4    Jin, S.5    Peng, J.6    Tan, R.7    Zhang, T.8    Li, Y.9    Wang, Y.10
  • 55
    • 77956117850 scopus 로고    scopus 로고
    • Towards computational prediction of microRNA function and activity
    • Ulitsky, I., Laurent, L. C. and Shamir, R. (2010) Towards computational prediction of microRNA function and activity. Nucleic Acids Res., 38, e160.
    • (2010) Nucleic Acids Res. , vol.38 , pp. e160
    • Ulitsky, I.1    Laurent, L.C.2    Shamir, R.3
  • 57
    • 84876519505 scopus 로고    scopus 로고
    • MiRGator v3.0: A microRNA portal for deep sequencing, expression profiling and mRNA targeting
    • Cho, S., Jang, I., Jun, Y., Yoon, S., Ko, M., Kwon, Y., Choi, I., Chang, H., Ryu, D., Lee, B. et al. (2013) miRGator v3.0: a microRNA portal for deep sequencing, expression profiling and mRNA targeting. Nucleic Acids Res., 41, D252-D257.
    • (2013) Nucleic Acids Res. , vol.41 , pp. D252-D257
    • Cho, S.1    Jang, I.2    Jun, Y.3    Yoon, S.4    Ko, M.5    Kwon, Y.6    Choi, I.7    Chang, H.8    Ryu, D.9    Lee, B.10
  • 58
    • 84941100252 scopus 로고    scopus 로고
    • LncRNAWiki: Harnessing community knowledge in collaborative curation of human long non-coding RNAs
    • Ma, L. N., Li, A., Zou, D., Xu, X. J., Xia, L., Yu, J., Bajic, V. B. and Zhang, Z. (2015) LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs. Nucleic Acids Res., 43, D187-D192.
    • (2015) Nucleic Acids Res. , vol.43 , pp. D187-D192
    • Ma, L.N.1    Li, A.2    Zou, D.3    Xu, X.J.4    Xia, L.5    Yu, J.6    Bajic, V.B.7    Zhang, Z.8
  • 59
    • 84883496216 scopus 로고    scopus 로고
    • Predicting long non-coding RNAs using RNA sequencing
    • Ilott, N. E. and Ponting, C. P. (2013) Predicting long non-coding RNAs using RNA sequencing. Methods, 63, 50-59.
    • (2013) Methods , vol.63 , pp. 50-59
    • Ilott, N.E.1    Ponting, C.P.2
  • 60
    • 75549084786 scopus 로고    scopus 로고
    • DeepBase: A database for deeply annotating and mining deep sequencing data
    • Yang, J. H., Shao, P., Zhou, H., Chen, Y. Q. and Qu, L. H. (2010) deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res., 38, D123-D130.
    • (2010) Nucleic Acids Res. , vol.38 , pp. D123-D130
    • Yang, J.H.1    Shao, P.2    Zhou, H.3    Chen, Y.Q.4    Qu, L.H.5


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