메뉴 건너뛰기




Volumn 42, Issue 18, 2014, Pages

SPARTA: A parallelized pipeline for integrated analysis of plant miRNA and cleaved mRNA data sets, including new miRNA target-identification software

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICRORNA; PLANT RNA;

EID: 84922394706     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku693     Document Type: Article
Times cited : (59)

References (44)
  • 1
    • 0035984059 scopus 로고    scopus 로고
    • Endogenous and silencing-associated small RNAs in plants
    • Llave, C., Kasschau, K. D., Rector, M. A. And Carrington, J. C. (2002) Endogenous and silencing-associated small RNAs in plantS. Plant Cell, 14, 1605-1619.
    • (2002) Plant Cell , vol.14 , pp. 1605-1619
    • Llave, C.1    Kasschau, K.D.2    Rector, M.A.3    Carrington, J.C.4
  • 4
    • 63849207321 scopus 로고    scopus 로고
    • Construction of parallel analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome
    • German, M. A., Luo, S., Schroth, G., Meyers, B. C. And Green, P. J. (2009) Construction of parallel analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome. Nat. Protoc., 4, 356-362.
    • (2009) Nat. Protoc. , vol.4 , pp. 356-362
    • German, M.A.1    Luo, S.2    Schroth, G.3    Meyers, B.C.4    Green, P.J.5
  • 6
    • 43449091567 scopus 로고    scopus 로고
    • Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome
    • Addo-Quaye, C., Eshoo, T. W., Bartel, D. P. And Axtell, M. J. (2008) Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr. Biol., 18, 758-762.
    • (2008) Curr. Biol. , vol.18 , pp. 758-762
    • Addo-Quaye, C.1    Eshoo, T.W.2    Bartel, D.P.3    Axtell, M.J.4
  • 7
    • 58049220318 scopus 로고    scopus 로고
    • CleaveLand: A pipeline for using degradome data to find cleaved small RNA targets
    • Addo-Quaye, C., Miller, W. And Axtell, M. J. (2009) CleaveLand: A pipeline for using degradome data to find cleaved small RNA targets. Bioinformatics, 25, 130-131.
    • (2009) Bioinformatics , vol.25 , pp. 130-131
    • Addo-Quaye, C.1    Miller, W.2    Axtell, M.J.3
  • 9
    • 84863238628 scopus 로고    scopus 로고
    • SeqTar: An effective method for identifying microRNA guided cleavage sites from degradome of polyadenylated transcripts in plants
    • Zheng, Y., Li, Y.-F., Sunkar, R. And Zhang, W. (2012) SeqTar: An effective method for identifying microRNA guided cleavage sites from degradome of polyadenylated transcripts in plants. Nucleic Acids Res., 40, e28.
    • (2012) Nucleic Acids Res. , vol.40 , pp. e28
    • Zheng, Y.1    Li, Y.-F.2    Sunkar, R.3    Zhang, W.4
  • 11
    • 84864459173 scopus 로고    scopus 로고
    • PAREsnip: A tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing
    • Folkes, L., Moxon, S., Woolfenden, H. C., Stocks, M. B., Szittya, G., Dalmay, T. And Moulton, V. (2012) PAREsnip: A tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing. Nucleic Acids Res., 40, e103.
    • (2012) Nucleic Acids Res. , vol.40 , pp. e103
    • Folkes, L.1    Moxon, S.2    Woolfenden, H.C.3    Stocks, M.B.4    Szittya, G.5    Dalmay, T.6    Moulton, V.7
  • 12
    • 84878572794 scopus 로고    scopus 로고
    • Biogenesis and function of rice small RNAs from non-coding RNA precursors
    • Arikit, S., Zhai, J. And Meyers, B. C. (2013) Biogenesis and function of rice small RNAs from non-coding RNA precursors. Curr. Opin. Plant Biol., 16, 170-179.
    • (2013) Curr. Opin. Plant Biol. , vol.16 , pp. 170-179
    • Arikit, S.1    Zhai, J.2    Meyers, B.C.3
  • 17
    • 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
  • 19
    • 58149186499 scopus 로고    scopus 로고
    • MiRecords: An integrated resource for microRNA-target interactions
    • Xiao, F., Zuo, Z., Cai, G., Kang, S., Gao, X. And Li, T. (2009) miRecords: An integrated resource for microRNA-target interactions. Nucleic Acids Res., 37, D105-D110.
    • (2009) Nucleic Acids Res. , vol.37 , pp. D105-D110
    • Xiao, F.1    Zuo, Z.2    Cai, G.3    Kang, S.4    Gao, X.5    Li, T.6
  • 21
    • 77954238055 scopus 로고    scopus 로고
    • Efficient construction of an assembly string graph using the FM-index
    • Simpson, J. T. And Durbin, R. (2010) Efficient construction of an assembly string graph using the FM-index. Bioinformatics, 26, i367-i373.
    • (2010) Bioinformatics , vol.26 , pp. i367-i373
    • Simpson, J.T.1    Durbin, R.2
  • 22
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead, B. And Salzberg, S. L. (2012) Fast gapped-read alignment with Bowtie 2. Nat. Methods, 9, 357-359.
    • (2012) Nat. Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 23
    • 84883492771 scopus 로고    scopus 로고
    • Kraken: A set of tools for quality control and analysis of high-throughput sequence data
    • Davis, M. P. A., 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.A.1    Van Dongen, S.2    Abreu-Goodger, C.3    Bartonicek, N.4    Enright, A.J.5
  • 24
    • 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
  • 25
    • 0029801668 scopus 로고    scopus 로고
    • A bulged lin-4/lin-14 RNA duplex is sufficient for Caenorhabditis elegans lin-14 temporal gradient formation
    • Ha, I., Wightman, B. And Ruvkun, G. (1996) A bulged lin-4/lin-14 RNA duplex is sufficient for Caenorhabditis elegans lin-14 temporal gradient formation. Genes Dev., 10, 3041-3050.
    • (1996) Genes Dev. , vol.10 , pp. 3041-3050
    • Ha, I.1    Wightman, B.2    Ruvkun, G.3
  • 26
    • 0027730383 scopus 로고
    • Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C
    • Wightman, B., Ha, I. And Ruvkun, G. (1993) Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. Elegans. Cell, 75, 855-862.
    • (1993) Elegans. Cell , vol.75 , pp. 855-862
    • Wightman, B.1    Ha, I.2    Ruvkun, G.3
  • 27
    • 33748346026 scopus 로고    scopus 로고
    • Perfect seed pairing is not a generally reliable predictor for miRNA-target interactions
    • Didiano, D. And Hobert, O. (2006) Perfect seed pairing is not a generally reliable predictor for miRNA-target interactions. Nat. Struct. Mol. Biol., 13, 849-851.
    • (2006) Nat. Struct. Mol. Biol. , vol.13 , pp. 849-851
    • Didiano, D.1    Hobert, O.2
  • 28
    • 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
  • 29
    • 84857955708 scopus 로고    scopus 로고
    • An alternative mode of microRNA target recognition
    • Chi, S. W., Hannon, G. J. And Darnell, R. B. (2012) An alternative mode of microRNA target recognition. Nat. Struct. Mol. Biol., 19, 321-327.
    • (2012) Nat. Struct. Mol. Biol. , vol.19 , pp. 321-327
    • Chi, S.W.1    Hannon, G.J.2    Darnell, R.B.3
  • 30
    • 84866096126 scopus 로고    scopus 로고
    • Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible "seed-less" targets
    • Xia, Z., Clark, P., Huynh, T., Loher, P., Zhao, Y., Chen, H.-W., Rigoutsos, I. And Zhou, R. (2012) Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible "seed-less" targets. Sci. Rep., 2, 569.
    • (2012) Sci. Rep. , vol.2 , pp. 569
    • Xia, Z.1    Clark, P.2    Huynh, T.3    Loher, P.4    Zhao, Y.5    Chen, H.-W.6    Rigoutsos, I.7    Zhou, R.8
  • 31
    • 84874646362 scopus 로고    scopus 로고
    • A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets
    • Khorshid, M., Hausser, J., Zavolan, M. And van Nimwegen, E. (2013) A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets. Nat. Methods, 10, 253-255.
    • (2013) Nat. Methods , vol.10 , pp. 253-255
    • Khorshid, M.1    Hausser, J.2    Zavolan, M.3    Van Nimwegen, E.4
  • 32
    • 17444430392 scopus 로고    scopus 로고
    • MicroRNA-directed phasing during trans-acting siRNA biogenesis in plants
    • Allen, E., Xie, Z., Gustafson, A. M. And Carrington, J. C. (2005) microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell, 121, 207-221.
    • (2005) Cell , vol.121 , pp. 207-221
    • Allen, E.1    Xie, Z.2    Gustafson, A.M.3    Carrington, J.C.4
  • 34
    • 33644876658 scopus 로고    scopus 로고
    • Plant MPSS databases: Signature-based transcriptional resources for analyses of mRNA and small RNA
    • Nakano, M., Nobuta, K., Vemaraju, K., Tej, S. S., Skogen, J. W. And Meyers, B. C. (2006) Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA. Nucleic Acids Res., 34, D731-D735.
    • (2006) Nucleic Acids Res. , vol.34 , pp. D731-D735
    • Nakano, M.1    Nobuta, K.2    Vemaraju, K.3    Tej, S.S.4    Skogen, J.W.5    Meyers, B.C.6
  • 35
    • 82955207556 scopus 로고    scopus 로고
    • MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs
    • Zhai, J., Jeong, D. H., De Paoli, E., Park, S., Rosen, B. D., Li, Y., González, A. J., Yan, Z., Kitto, S. L., Grusak, M. A. et al. (2011) MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs. Genes Dev., 25, 2540-2553.
    • (2011) Genes Dev. , vol.25 , pp. 2540-2553
    • Zhai, J.1    Jeong, D.H.2    De Paoli, E.3    Park, S.4    Rosen, B.D.5    Li, Y.6    González, A.J.7    Yan, Z.8    Kitto, S.L.9    Grusak, M.A.10
  • 36
    • 84872205293 scopus 로고    scopus 로고
    • R: A Language and Environment for Statistical Computing
    • R Development Core Team, R.
    • R Development Core Team, R. (2011) R: A Language and Environment for Statistical Computing. R Found. Stat. Comput., 1, 409.
    • (2011) R Found. Stat. Comput. , vol.1 , pp. 409
  • 37
    • 84892526727 scopus 로고    scopus 로고
    • Composition and expression of conserved microRNA genes in diploid cotton (Gossypium) species
    • Gong, L., Kakrana, A., Arikit, S., Meyers, B. C. And Wendel, J. F. (2013) Composition and expression of conserved microRNA genes in diploid cotton (Gossypium) species. Genome Biol. Evol., 5, 2449-2459.
    • (2013) Genome Biol. Evol. , vol.5 , pp. 2449-2459
    • Gong, L.1    Kakrana, A.2    Arikit, S.3    Meyers, B.C.4    Wendel, J.F.5
  • 38
    • 79951527525 scopus 로고    scopus 로고
    • Evidence that XRN4, an Arabidopsis homolog of exoribonuclease XRN1, preferentially impacts transcripts with certain sequences or in particular functional categories
    • Rymarquis, L. A., Souret, F. F. And Green, P. J. (2011) Evidence that XRN4, an Arabidopsis homolog of exoribonuclease XRN1, preferentially impacts transcripts with certain sequences or in particular functional categories. RNA, 17, 501-511.
    • (2011) RNA , vol.17 , pp. 501-511
    • Rymarquis, L.A.1    Souret, F.F.2    Green, P.J.3
  • 39
    • 33750440526 scopus 로고    scopus 로고
    • A two-hit trigger for siRNA biogenesis in plants
    • Axtell, M. J., Jan, C., Rajagopalan, R. And Bartel, D. P. (2006) A two-hit trigger for siRNA biogenesis in plants. Cell, 127, 565-577.
    • (2006) Cell , vol.127 , pp. 565-577
    • Axtell, M.J.1    Jan, C.2    Rajagopalan, R.3    Bartel, D.P.4
  • 41
    • 84857497803 scopus 로고    scopus 로고
    • Functional specialization of the plant miR396 regulatory network through distinct microRNA-target interactions
    • Debernardi, J. M., Rodriguez, R. E., Mecchia, M. A. And Palatnik, J. F. (2012) Functional specialization of the plant miR396 regulatory network through distinct microRNA-target interactionS. PLoS Genet., 8.
    • (2012) PLoS Genet. , pp. 8
    • Debernardi, J.M.1    Rodriguez, R.E.2    Mecchia, M.A.3    Palatnik, J.F.4
  • 43
    • 79955524820 scopus 로고    scopus 로고
    • Implementation of a de novo genome-wide computational approach for updating Brachypodium miRNAs
    • Baev, V., Milev, I., Naydenov, M., Apostolova, E., Minkov, G., Minkov, I. And Yahubyan, G. (2011) Implementation of a de novo genome-wide computational approach for updating Brachypodium miRNAs. Genomics, 97, 282-293.
    • (2011) Genomics , vol.97 , pp. 282-293
    • Baev, V.1    Milev, I.2    Naydenov, M.3    Apostolova, E.4    Minkov, G.5    Minkov, I.6    Yahubyan, G.7
  • 44
    • 84879704714 scopus 로고    scopus 로고
    • Comprehensive investigation of microRNAs enhanced by analysis of sequence variants, expression patterns, ARGONAUTE loading, and target cleavage
    • Jeong, D. H., Thatcher, S. R., Brown, R. S. H., Zhai, J., Park, S., Rymarquis, L. A., Meyers, B. C. And Green, P. J. (2013) Comprehensive investigation of microRNAs enhanced by analysis of sequence variants, expression patterns, ARGONAUTE loading, and target cleavage. Plant Physiol., 162, 1225-1245.
    • (2013) Plant Physiol. , vol.162 , pp. 1225-1245
    • Jeong, D.H.1    Thatcher, S.R.2    Brown, R.S.H.3    Zhai, J.4    Park, S.5    Rymarquis, L.A.6    Meyers, B.C.7    Green, P.J.8


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.