메뉴 건너뛰기




Volumn 45, Issue 15, 2017, Pages 8731-8744

Web-based NGS data analysis using miRMaster: A large-scale meta-analysis of human miRNAs

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; UNTRANSLATED RNA; TRANSCRIPTOME;

EID: 85032863592     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkx595     Document Type: Article
Times cited : (52)

References (65)
  • 1
    • 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
  • 2
    • 84876374428 scopus 로고    scopus 로고
    • Deep sequencing of small RNAs identifies canonical and non-canonical miRNA and endogenous siRNAs in mammalian somatic tissues
    • Castellano, L. and Stebbing, J. (2013) Deep sequencing of small RNAs identifies canonical and non-canonical miRNA and endogenous siRNAs in mammalian somatic tissues. Nucleic Acids Res., 41, 3339-3351.
    • (2013) Nucleic Acids Res , vol.41 , pp. 3339-3351
    • Castellano, L.1    Stebbing, J.2
  • 4
    • 84865423169 scopus 로고    scopus 로고
    • Conservation and divergence in plant microRNAs
    • Jones-Rhoades, M.W. (2012) Conservation and divergence in plant microRNAs. Plant Mol. Biol., 80, 3-16.
    • (2012) Plant Mol. Biol , vol.80 , pp. 3-16
    • Jones-Rhoades, M.W.1
  • 6
    • 84860762769 scopus 로고    scopus 로고
    • Are all the miRBase-registered microRNAs true? A structure- and expression-based re-examination in plants
    • Meng, Y., Shao, C., Wang, H. and Chen, M. (2012) Are all the miRBase-registered microRNAs true? A structure- and expression-based re-examination in plants. RNA Biol., 9, 249-253.
    • (2012) RNA Biol , vol.9 , pp. 249-253
    • Meng, Y.1    Shao, C.2    Wang, H.3    Chen, M.4
  • 7
    • 84866267741 scopus 로고    scopus 로고
    • Do miRNAs have a deep evolutionary history?
    • Tarver, J.E., Donoghue, P.C. and Peterson, K.J. (2012) Do miRNAs have a deep evolutionary history? Bioessays, 34, 857-866.
    • (2012) Bioessays , vol.34 , pp. 857-866
    • Tarver, J.E.1    Donoghue, P.C.2    Peterson, K.J.3
  • 9
    • 84871522891 scopus 로고    scopus 로고
    • Systematic curation of miRBase annotation using integrated small RNA high-throughput sequencing data for C. Elegans and Drosophila
    • Wang, X. and Liu, X.S. (2011) Systematic curation of miRBase annotation using integrated small RNA high-throughput sequencing data for C. elegans and Drosophila. Front. Genet., 2, 25.
    • (2011) Front. Genet , vol.2 , pp. 25
    • Wang, X.1    Liu, X.S.2
  • 16
    • 84855293838 scopus 로고    scopus 로고
    • MiRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades
    • Friedländer, M.R., Mackowiak, S.D., Li, N., Chen, W. and Rajewsky, N. (2011) miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res., 40, 37-52.
    • (2011) Nucleic Acids Res , vol.40 , pp. 37-52
    • Friedländer, M.R.1    Mackowiak, S.D.2    Li, N.3    Chen, W.4    Rajewsky, N.5
  • 17
    • 79959953839 scopus 로고    scopus 로고
    • MiRanalyzer: An update on the detection and analysis of microRNAs in high-throughput sequencing experiments
    • Hackenberg, M., Rodriguez-Ezpeleta, N. and Aransay, A.M. (2011) miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments. Nucleic Acids Res., 39, W132-W138.
    • (2011) Nucleic Acids Res , vol.39 , pp. W132-W138
    • Hackenberg, M.1    Rodriguez-Ezpeleta, N.2    Aransay, A.M.3
  • 19
    • 84961572745 scopus 로고    scopus 로고
    • MiR-isomiRExp: A web-server for the analysis of expression of miRNA at the miRNA/isomiR levels
    • Guo, L., Yu, J., Liang, T. and Zou, Q. (2016) miR-isomiRExp: a web-server for the analysis of expression of miRNA at the miRNA/isomiR levels. Sci. Rep., 6, 23700.
    • (2016) Sci. Rep , vol.6 , pp. 23700
    • Guo, L.1    Yu, J.2    Liang, T.3    Zou, Q.4
  • 20
    • 84979227262 scopus 로고    scopus 로고
    • MiEAA: MicroRNA enrichment analysis and annotation
    • Backes, C., Khaleeq, Q.T., Meese, E. and Keller, A. (2016) miEAA: microRNA enrichment analysis and annotation. Nucleic Acids Res., 44, W110-W116.
    • (2016) Nucleic Acids Res , vol.44 , pp. W110-W116
    • Backes, C.1    Khaleeq, Q.T.2    Meese, E.3    Keller, A.4
  • 23
    • 84940502214 scopus 로고    scopus 로고
    • Predicting effective microRNA target sites in mammalian mRNAs
    • Agarwal, V., Bell, G.W., Nam, J.W. and Bartel, D.P. (2015) Predicting effective microRNA target sites in mammalian mRNAs. Elife, 4, doi:10.7554/eLife.05005.
    • (2015) Elife , vol.4
    • Agarwal, V.1    Bell, G.W.2    Nam, J.W.3    Bartel, D.P.4
  • 25
    • 84874086395 scopus 로고    scopus 로고
    • Beyond secondary structure: Primary-sequence determinants license pri-miRNA hairpins for processing
    • Auyeung, V.C., Ulitsky, I., McGeary, S.E. and Bartel, D.P. (2013) Beyond secondary structure: primary-sequence determinants license pri-miRNA hairpins for processing. Cell, 152, 844-858.
    • (2013) Cell , vol.152 , pp. 844-858
    • Auyeung, V.C.1    Ulitsky, I.2    McGeary, S.E.3    Bartel, D.P.4
  • 26
    • 84951994729 scopus 로고    scopus 로고
    • The menu of features that define primary microRNAs and enable de novo design of microRNA genes
    • Fang, W. and Bartel, D.P. (2015) The menu of features that define primary microRNAs and enable de novo design of microRNA genes. Mol. Cell, 60, 131-145.
    • (2015) Mol. Cell , vol.60 , pp. 131-145
    • Fang, W.1    Bartel, D.P.2
  • 27
    • 84925796024 scopus 로고    scopus 로고
    • N6-methyladenosine marks primary microRNAs for processing
    • Alarcon, C.R., Lee, H., Goodarzi, H., Halberg, N. and Tavazoie, S.F. (2015) N6-methyladenosine marks primary microRNAs for processing. Nature, 519, 482-485.
    • (2015) Nature , vol.519 , pp. 482-485
    • Alarcon, C.R.1    Lee, H.2    Goodarzi, H.3    Halberg, N.4    Tavazoie, S.F.5
  • 28
    • 84891822155 scopus 로고    scopus 로고
    • RefSeq microbial genomes database: New representation and annotation strategy
    • Tatusova, T., Ciufo, S., Fedorov, B., O'Neill, K. and Tolstoy, I. (2014) RefSeq microbial genomes database: new representation and annotation strategy. Nucleic Acids Res., 42, D553-D559.
    • (2014) Nucleic Acids Res , vol.42 , pp. D553-D559
    • Tatusova, T.1    Ciufo, S.2    Fedorov, B.3    O'Neill, K.4    Tolstoy, I.5
  • 32
    • 84984688359 scopus 로고    scopus 로고
    • A legion of potential regulatory sRNAs exists beyond the typical microRNAs microcosm
    • Jha, A., Panzade, G., Pandey, R. and Shankar, R. (2015) A legion of potential regulatory sRNAs exists beyond the typical microRNAs microcosm. Nucleic Acids Res., 43, 8713-8724.
    • (2015) Nucleic Acids Res , vol.43 , pp. 8713-8724
    • Jha, A.1    Panzade, G.2    Pandey, R.3    Shankar, R.4
  • 37
    • 84946492901 scopus 로고    scopus 로고
    • Next-generation sequencing identifies altered whole blood microRNAs in neuromyelitis optica spectrum disorder which may permit discrimination from multiple sclerosis
    • Keller, A., Leidinger, P., Meese, E., Haas, J., Backes, C., Rasche, L., Behrens, J.R., Pfuhl, C., Wakonig, K., Giess, R.M. et al. (2015) Next-generation sequencing identifies altered whole blood microRNAs in neuromyelitis optica spectrum disorder which may permit discrimination from multiple sclerosis. J. Neuroinflammation, 12, 196.
    • (2015) J. Neuroinflammation , vol.12 , pp. 196
    • Keller, A.1    Leidinger, P.2    Meese, E.3    Haas, J.4    Backes, C.5    Rasche, L.6    Behrens, J.R.7    Pfuhl, C.8    Wakonig, K.9    Giess, R.M.10
  • 41
    • 84891760538 scopus 로고    scopus 로고
    • Can MiRBase provide positive data for machine learning for the detection of MiRNA hairpins?
    • Sacar, M.D., Hamzeiy, H. and Allmer, J. (2013) Can MiRBase provide positive data for machine learning for the detection of MiRNA hairpins? J. Integr. Bioinform., 10, 215.
    • (2013) J. Integr. Bioinform , vol.10 , pp. 215
    • Sacar, M.D.1    Hamzeiy, H.2    Allmer, J.3
  • 44
    • 30344447264 scopus 로고    scopus 로고
    • Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine
    • Xue, C., Li, F., He, T., Liu, G.P., Li, Y. and Zhang, X. (2005) Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine. BMC Bioinformatics, 6, 310.
    • (2005) BMC Bioinformatics , vol.6 , pp. 310
    • Xue, C.1    Li, F.2    He, T.3    Liu, G.P.4    Li, Y.5    Zhang, X.6
  • 45
    • 54349104464 scopus 로고    scopus 로고
    • Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs
    • Babiarz, J.E., Ruby, J.G., Wang, Y., Bartel, D.P. and Blelloch, R. (2008) Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. Genes Dev., 22, 2773-2785.
    • (2008) Genes Dev , vol.22 , pp. 2773-2785
    • Babiarz, J.E.1    Ruby, J.G.2    Wang, Y.3    Bartel, D.P.4    Blelloch, R.5
  • 47
    • 34447309058 scopus 로고    scopus 로고
    • De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures
    • Ng, K.L. and Mishra, S.K. (2007) De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures. Bioinformatics, 23, 1321-1330.
    • (2007) Bioinformatics , vol.23 , pp. 1321-1330
    • Ng, K.L.1    Mishra, S.K.2
  • 48
    • 64549116289 scopus 로고    scopus 로고
    • MicroPred: Effective classification of pre-miRNAs for human miRNA gene prediction
    • Batuwita, R. and Palade, V. (2009) microPred: effective classification of pre-miRNAs for human miRNA gene prediction. Bioinformatics, 25, 989-995.
    • (2009) Bioinformatics , vol.25 , pp. 989-995
    • Batuwita, R.1    Palade, V.2
  • 50
    • 50949084360 scopus 로고    scopus 로고
    • Self containment, a property of modular RNA structures, distinguishes microRNAs
    • Lee, M.T. and Kim, J. (2008) Self containment, a property of modular RNA structures, distinguishes microRNAs. PLoS Comput. Biol., 4, e1000150.
    • (2008) PLoS Comput. Biol , vol.4 , pp. e1000150
    • Lee, M.T.1    Kim, J.2
  • 52
    • 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. Methodol., 57, 289-300.
    • (1995) J. R. Stat. Soc. B. Methodol , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 55
    • 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
  • 56
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead, B., Trapnell, C., Pop, M. and Salzberg, S.L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
    • (2009) Genome Biol , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 59
    • 84976870479 scopus 로고    scopus 로고
    • GtRNAdb 2.0: An expanded database of transfer RNA genes identified in complete and draft genomes
    • Chan, P.P. and Lowe, T.M. (2016) GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes. Nucleic Acids Res., 44, D184-D189.
    • (2016) Nucleic Acids Res , vol.44 , pp. D184-D189
    • Chan, P.P.1    Lowe, T.M.2
  • 65
    • 84992743701 scopus 로고    scopus 로고
    • Distribution of microRNA biomarker candidates in solid tissues and body fluids
    • Fehlmann, T., Ludwig, N., Backes, C., Meese, E. and Keller, A. (2016) Distribution of microRNA biomarker candidates in solid tissues and body fluids. RNA Biol., 13, 1084-1088.
    • (2016) RNA Biol , vol.13 , pp. 1084-1088
    • Fehlmann, T.1    Ludwig, N.2    Backes, C.3    Meese, E.4    Keller, A.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.