메뉴 건너뛰기




Volumn 5, Issue 3, 2014, Pages 671-683

Computational methods for microRNA target prediction

Author keywords

Bioinformatics; Computational methods; Gene expression regulation; MiRNA; Target prediction

Indexed keywords

MICRORNA;

EID: 84920067895     PISSN: None     EISSN: 20734425     Source Type: Journal    
DOI: 10.3390/genes5030671     Document Type: Review
Times cited : (79)

References (72)
  • 1
    • 0027751663 scopus 로고
    • The C. elegans heterochronic gene lin 4 encodes small RNAs with antisense complementarity to lin 14
    • Lee, R.C.; Feinbaum, R.L.; Ambros, V. The C. elegans heterochronic gene lin 4 encodes small RNAs with antisense complementarity to lin 14. Cell 1993, 75, 843–854.
    • (1993) Cell , vol.75 , pp. 843-854
    • Lee, R.C.1    Feinbaum, R.L.2    Ambros, V.3
  • 2
    • 0031767514 scopus 로고    scopus 로고
    • TheK box, a conserved 3' UTR sequence motif, negatively regulates accumulation of Enhancer of split complex transcripts
    • Lai, E.C.; Burks, C.; Posakony, J.W. The K box, a conserved 3' UTR sequence motif, negatively regulates accumulation of Enhancer of split complex transcripts. Development1998, 125, 4077–4088.
    • (1998) Development , vol.125 , pp. 4077-4088
    • Lai, E.C.1    Burks, C.2    Posakony, J.W.3
  • 3
    • 0036544755 scopus 로고    scopus 로고
    • MicroRNAs are complementary to 3' UTR sequence motifs that mediate negative post-transcriptional regulation
    • Lai, E.C. MicroRNAs are complementary to 3' UTR sequence motifs that mediate negative post-transcriptional regulation. Nat. Genet. 2002, 30, 363–364.
    • (2002) Nat. Genet , vol.30 , pp. 363-364
    • Lai, E.C.1
  • 5
    • 54149095553 scopus 로고    scopus 로고
    • Biological principles of microRNA-mediated regulation: Shared themes amid diversity
    • Flynt, A.S.; Lai, E.C. Biological principles of microRNA-mediated regulation: Shared themes amid diversity. Nat. Rev. Genet. 2008, 9, 831–842.
    • (2008) Nat. Rev. Genet , vol.9 , pp. 831-842
    • Flynt, A.S.1    Lai, E.C.2
  • 7
    • 77956645422 scopus 로고    scopus 로고
    • The therapeutic potential of microRNA modulation
    • Jackson, A.; Linsley, P.S. The therapeutic potential of microRNA modulation. Discov. Med. 2010, 9, 311–318.
    • (2010) Discov. Med , vol.9 , pp. 311-318
    • Jackson, A.1    Linsley, P.S.2
  • 8
    • 58249088751 scopus 로고    scopus 로고
    • MicroRNAs: Target recognition and regulatory functions
    • Bartel, D.P. MicroRNAs: Target recognition and regulatory functions. Cell2009, 136, 215–233.
    • (2009) Cell , vol.136 , pp. 215-233
    • Bartel, D.P.1
  • 9
    • 84858446579 scopus 로고    scopus 로고
    • MicroRNAs and their targets: Recognition, regulation and an emerging reciprocal relationship
    • Pasquinelli, A.E. MicroRNAs and their targets: Recognition, regulation and an emerging reciprocal relationship. Nat. Rev. Gen. 2012, 13, 271–282.
    • (2012) Nat. Rev. Gen , vol.13 , pp. 271-282
    • Pasquinelli, A.E.1
  • 10
    • 9344235449 scopus 로고    scopus 로고
    • Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs
    • Cai, X.; Hagedorn, C.H.; Cullen, B.R. Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA 2004, 10, 1957–1966.
    • (2004) RNA , vol.10 , pp. 1957-1966
    • Cai, X.1    Hagedorn, C.H.2    Cullen, B.R.3
  • 12
    • 0033598989 scopus 로고    scopus 로고
    • Transport of proteins and RNAs in and out of the nucleus
    • Nakielny, S.; Dreyfuss, G. Transport of proteins and RNAs in and out of the nucleus. Cell1999, 99, 677–690.
    • (1999) Cell , vol.99 , pp. 677-690
    • Nakielny, S.1    Dreyfuss, G.2
  • 14
    • 0035929322 scopus 로고    scopus 로고
    • A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans
    • Knight, S.W.; Bass, B.L. A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science2001, 293, 2269–2271.
    • (2001) Science , vol.293 , pp. 2269-2271
    • Knight, S.W.1    Bass, B.L.2
  • 15
    • 28044455435 scopus 로고    scopus 로고
    • MicroPrimer: The biogenesis and function of microRNA
    • Du, T.; Zamore, P.D. MicroPrimer: The biogenesis and function of microRNA. Development2005, 132, 4645–4652.
    • (2005) Development , vol.132 , pp. 4645-4652
    • Du, T.1    Zamore, P.D.2
  • 16
    • 0142165224 scopus 로고    scopus 로고
    • Functional siRNAs and miRNAs exhibit strand bias
    • Khvorova, A.; Reynolds, A.; Jayasena, S.D. Functional siRNAs and miRNAs exhibit strand bias. Cell2003, 115, 209–216.
    • (2003) Cell , vol.115 , pp. 209-216
    • Khvorova, A.1    Reynolds, A.2    Jayasena, S.D.3
  • 17
    • 1642374097 scopus 로고    scopus 로고
    • Specificity of microRNA target selection in translational repression
    • Doench, J.G.; Sharp, P.A. Specificity of microRNA target selection in translational repression. Genes Dev. 2004, 18, 504–511.
    • (2004) Genes Dev , vol.18 , pp. 504-511
    • Doench, J.G.1    Sharp, P.A.2
  • 18
    • 0038343499 scopus 로고    scopus 로고
    • MicroRNA Pathways in Flies and Worms: Growth, Death, Fat, Stress, and Timing
    • Ambros, V. MicroRNA Pathways in Flies and Worms: Growth, Death, Fat, Stress, and Timing. Cell 2003, 6, 673–676.
    • (2003) Cell , vol.6 , pp. 673-676
    • Ambros, V.1
  • 19
    • 78751477191 scopus 로고    scopus 로고
    • Gene silencing by microRNAs: Contributions of translational repression and mRNA decay
    • Huntzinger, E.; Izaurralde, E. Gene silencing by microRNAs: Contributions of translational repression and mRNA decay. Nat. Rev. Genet. 2011, 12, 99–110.
    • (2011) Nat. Rev. Genet , vol.12 , pp. 99-110
    • Huntzinger, E.1    Izaurralde, E.2
  • 21
    • 0037144546 scopus 로고    scopus 로고
    • A microRNA in a multiple-turnover RNAi enzyme complex
    • Hutvágner, G.; Zamore, P.D. A microRNA in a multiple-turnover RNAi enzyme complex. Science2002, 297, 2056–2060.
    • (2002) Science , vol.297 , pp. 2056-2060
    • Hutvágner, G.1    Zamore, P.D.2
  • 25
    • 65949121645 scopus 로고    scopus 로고
    • New tricks for animal microRNAs: Targeting of amino acid coding regions at conserved and nonconserved sites
    • Rigoutsos, I. New tricks for animal microRNAs: Targeting of amino acid coding regions at conserved and nonconserved sites. Cancer Res. 2009, 69, 3245–3248.
    • (2009) Cancer Res , vol.69 , pp. 3245-3248
    • Rigoutsos, I.1
  • 26
    • 34447521718 scopus 로고    scopus 로고
    • Isolation of microRNA targets by miRNP immunopurification
    • Easow, G.; Teleman, A.A.; Cohen, S.M. Isolation of microRNA targets by miRNP immunopurification. RNA2007, 13, 1198–1204.
    • (2007) RNA , vol.13 , pp. 1198-1204
    • Easow, G.1    Teleman, A.A.2    Cohen, S.M.3
  • 28
    • 79952907985 scopus 로고    scopus 로고
    • The impact of miRNA target sites in coding sequences and in 3’ UTRs
    • Fang, Z.; Rajewsky, N. The impact of miRNA target sites in coding sequences and in 3' UTRs. PLoS One2011, 6, e18067.
    • (2011) Plos One , vol.6
    • Fang, Z.1    Rajewsky, N.2
  • 29
    • 80053197539 scopus 로고    scopus 로고
    • Argonaute protein identity and pairing geometry determine cooperativity in mammalian RNA silencing
    • Broderick, J.A.; Salomon, W.E.; Ryder, S.P.; Aronin, N.; Zamore, P.D. Argonaute protein identity and pairing geometry determine cooperativity in mammalian RNA silencing. RNA2011, 17, 1858–1869.
    • (2011) RNA , vol.17 , pp. 1858-1869
    • Broderick, J.A.1    Salomon, W.E.2    Ryder, S.P.3    Aronin, N.4    Zamore, P.D.5
  • 30
    • 34249856066 scopus 로고    scopus 로고
    • Distance constraints between microRNA target sites dictate efficacy and cooperativity
    • Saetrom, P.; Heale, B.S.; Snøve, O., Jr.; Aagaard, L.; Alluin, J.; Rossi, J.J. Distance constraints between microRNA target sites dictate efficacy and cooperativity. Nucleic Acids Res. 2007, 35, 2333–2342.
    • (2007) Nucleic Acids Res , vol.35 , pp. 2333-2342
    • Saetrom, P.1    Heale, B.S.2    Snøve, O.3    Aagaard, L.4    Alluin, J.5    Rossi, J.J.6
  • 31
    • 80052451056 scopus 로고    scopus 로고
    • Experimental strategies for microRNA target identification
    • Thomson, D.W.; Bracken, C.P.; Goodall, G.J. Experimental strategies for microRNA target identification. Nucleic Acids Res. 2011, 39, 6845–6853.
    • (2011) Nucleic Acids Res , vol.39 , pp. 6845-6853
    • Thomson, D.W.1    Bracken, C.P.2    Goodall, G.J.3
  • 32
    • 37649021046 scopus 로고    scopus 로고
    • Identification of human microRNA targets from isolatedargonaute protein complexes
    • Beitzinger, M.; Peters, L.; Zhu, J.Y.; Kremmer, E.; Meister, G. Identification of human microRNA targets from isolated argonaute protein complexes. RNA Biol. 2007, 4, 76–84.
    • (2007) RNA , vol.4 , pp. 76-84
    • Beitzinger, M.1    Peters, L.2    Zhu, J.Y.3    Kremmer, E.4    Meister, G.5
  • 33
    • 67749132423 scopus 로고    scopus 로고
    • Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps
    • Chi, S.W.; Zang, J.B.; Mele, A.; Darnell, R.B. Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature2009, 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
  • 35
  • 39
    • 42949131237 scopus 로고    scopus 로고
    • Computational methods for microRNA Target Prediction
    • Watanabe, Y.; Tomita, M.; Kanai, A. Computational methods for microRNA Target Prediction. Methods Enzymol. 2007, 427, 65–86.
    • (2007) Methods Enzymol , vol.427 , pp. 65-86
    • Watanabe, Y.1    Tomita, M.2    Kanai, A.3
  • 41
    • 11844278458 scopus 로고    scopus 로고
    • Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
    • Lewis, B.P.; Burge, C.B.; Bartel, D.P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell2005, 120, 15–20.
    • (2005) Cell , vol.120 , pp. 15-20
    • Lewis, B.P.1    Burge, C.B.2    Bartel, D.P.3
  • 42
    • 60149095444 scopus 로고    scopus 로고
    • Most mammalian mRNAs are conserved targets of microRNAs
    • Friedman, R.C.; Farh, K.K.; Burge, C.B.; Bartel, D.P. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 2009, 19, 92–105.
    • (2009) Genome Res , vol.19 , pp. 92-105
    • Friedman, R.C.1    Farh, K.K.2    Burge, C.B.3    Bartel, D.P.4
  • 43
    • 80455154984 scopus 로고    scopus 로고
    • Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs
    • Garcia, D.M.; Baek, D.; Shin, D.; Bell, G.W.; Grimson, A.; Bartel, D.P. Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nat. Struct. Mol. Biol. 2011, 18, 1139–1146.
    • (2011) Nat. Struct , vol.18 , pp. 1139-1146
    • Garcia, D.M.1    Baek, D.2    Shin, D.3    Bell, G.W.4    Grimson, A.5    Bartel, D.P.6
  • 49
    • 0024477261 scopus 로고
    • On finding all suboptimalfoldings of an RNA molecule
    • Zuker, M. On finding all suboptimal foldings of an RNA molecule. Science1989, 244, 48–52.
    • (1989) Science , vol.244 , pp. 48-52
    • Zuker, M.1
  • 50
    • 0033080745 scopus 로고    scopus 로고
    • Complete suboptimal folding of RNA and the stability of secondary structures
    • Wuchty, S.; Fontana, W.; Hofacker, I.L.; Schuster, P. Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers1999, 49, 145–165.
    • (1999) Biopolymers , vol.49 , pp. 145-165
    • Wuchty, S.1    Fontana, W.2    Hofacker, I.L.3    Schuster, P.4
  • 54
    • 78651293534 scopus 로고    scopus 로고
    • MiRBase: Integrating microRNA annotation and deep-sequencing data
    • Kozomara, A.; Griffiths-Jones, S. MiRBase: Integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 2011, 39, D152–D157.
    • (2011) Nucleic Acids Res , vol.39 , pp. D152-D157
    • Kozomara, A.1    Griffiths-Jones, S.2
  • 55
    • 84877069189 scopus 로고    scopus 로고
    • Advances in the techniques for the prediction of microRNA targets
    • Zheng, H.; Fu, R.; Wang, J.T.; Liu, Q.; Chen, H.; Jiang, S.W. Advances in the techniques for the prediction of microRNA targets. Int. J. Mol. Sci. 2013, 14, 8179–8187.
    • (2013) Int. J. Mol. Sci , vol.14 , pp. 8179-8187
    • Zheng, H.1    Fu, R.2    Wang, J.T.3    Liu, Q.4    Chen, H.5    Jiang, S.W.6
  • 58
    • 78651271270 scopus 로고    scopus 로고
    • CLIPZ: A database and analysis environment for experimentally determined binding sites of RNA-binding proteins
    • Khorshid, M.; Rodak, C.; Zavolan, M. CLIPZ: A database and analysis environment for experimentally determined binding sites of RNA-binding proteins. Nucleic Acids Res. 2011, 39, D245–D252.
    • (2011) Nucleic Acids Res , vol.39 , pp. D245-D252
    • Khorshid, M.1    Rodak, C.2    Zavolan, M.3
  • 60
    • 79958250243 scopus 로고    scopus 로고
    • Computational prediction of intronic microRNA targets using host gene expression reveals novel regulatory mechanisms
    • Radfar, M.; Wong, W.; Morris, Q. Computational prediction of intronic microRNA targets using host gene expression reveals novel regulatory mechanisms. PLoS One2011, 6, e19312.
    • (2011) Plos One , vol.6
    • Radfar, M.1    Wong, W.2    Morris, Q.3
  • 61
    • 33846118697 scopus 로고    scopus 로고
    • PolymiRTS database: Linking polymorphisms in microRNA target sites with complex traits
    • Bao, L.; Zhou, M.; Wu, L.; Lu, L.; Goldowitz, D.; Williams, R.W.; Cui, Y. PolymiRTS database: linking polymorphisms in microRNA target sites with complex traits. Nucleic Acids Res. 2007, 35, D51–D54.
    • (2007) Nucleic Acids Res , vol.35 , pp. D51-D54
    • Bao, L.1    Zhou, M.2    Wu, L.3    Lu, L.4    Goldowitz, D.5    Williams, R.W.6    Cui, Y.7
  • 62
    • 75549088251 scopus 로고    scopus 로고
    • Patrocles: A database of polymorphic miRNA-mediated gene regulation in vertebrates
    • Hiard, S.; Charlier, C.; Coppieters, W.; Georges, M.; Baurain, D. Patrocles: A database of polymorphic miRNA-mediated gene regulation in vertebrates. Nucleic Acids Res. 2010, 38, D640–D651.
    • (2010) Nucleic Acids Res , vol.38 , pp. D640-D651
    • Hiard, S.1    Charlier, C.2    Coppieters, W.3    Georges, M.4    Baurain, D.5
  • 63
    • 84856105903 scopus 로고    scopus 로고
    • MiRdSNP: A database of disease-associated SNPs and microRNA target sites on 3'UTRs of human genes
    • Bruno, A.E.; Li, L.; Kalabus, J.L.; Pan, Y.; Yu, Y.; Hu, Z. miRdSNP: A database of disease-associated SNPs and microRNA target sites on 3'UTRs of human genes. BMC Genomics2012, 13, 44.
    • (2012) BMC Genomics , vol.13 , pp. 44
    • Bruno, A.E.1    Li, L.2    Kalabus, J.L.3    Pan, Y.4    Yu, Y.5    Hu, Z.6
  • 64
    • 84892466713 scopus 로고    scopus 로고
    • MiRClassify: An advanced web server for miRNA family classification and annotation
    • Zou, Q.; Mao, Y.; Hu, L.; Wu, Y.; Ji, Z. MiRClassify: An advanced web server for miRNA family classification and annotation. Comput. Biol. Med. 2014, 45, 157–160.
    • (2014) Comput. Biol. Med , vol.45 , pp. 157-160
    • Zou, Q.1    Mao, Y.2    Hu, L.3    Wu, Y.4    Ji, Z.5
  • 65
    • 33750318273 scopus 로고    scopus 로고
    • A guide through present computational approaches for the identification of mammalian microRNA targets
    • Sethupathy, P.; Megraw, M.; Hatzigeorgiou, A.G. A guide through present computational approaches for the identification of mammalian microRNA targets. Nat. Methods2006, 3, 881–886.
    • (2006) Nat. Methods , vol.3 , pp. 881-886
    • Sethupathy, P.1    Megraw, M.2    Hatzigeorgiou, A.G.3
  • 66
    • 19544390155 scopus 로고    scopus 로고
    • Predicting and validating microRNA targets
    • Lai, E.C. Predicting and validating microRNA targets. Genome Biol. 2004, 5, 115.
    • (2004) Genome Biol , vol.5 , pp. 115
    • Lai, E.C.1
  • 67
    • 31044444975 scopus 로고    scopus 로고
    • TarBase: A comprehensive database of experimentally supported animal microRNA targets
    • Sethupathy, P.; Corda, B.; Hatzigeorgiou, A.G. TarBase: A comprehensive database of experimentally supported animal microRNA targets. RNA2006, 12, 192–197.
    • (2006) RNA , vol.12 , pp. 192-197
    • Sethupathy, P.1    Corda, B.2    Hatzigeorgiou, A.G.3
  • 68
    • 34249003938 scopus 로고    scopus 로고
    • Principles and limitations of computational microRNA gene and target finding
    • Lindow, M.; Gorodkin, J. Principles and limitations of computational microRNA gene and target finding. DNA Cell Biol. 2007, 26, 339–351.
    • (2007) DNA , vol.26 , pp. 339-351
    • Lindow, M.1    Gorodkin, J.2
  • 69
    • 84903957327 scopus 로고    scopus 로고
    • ComTAR: A web tool for the prediction and characterization of conserved microRNA targets in plants
    • Chorostecki, U.; Palatnik, J.F. ComTAR: A web tool for the prediction and characterization of conserved microRNA targets in plants. Bioinformatics2014, 30, 2066–2067.
    • (2014) Bioinformatics , vol.30 , pp. 2066-2067
    • Chorostecki, U.1    Palatnik, J.F.2
  • 70
    • 38549092089 scopus 로고    scopus 로고
    • MiRGator: An integrated system for functional annotation of microRNAs
    • Nam, S.; Kim, B.; Shin, S.; Lee, S. MiRGator: An integrated system for functional annotation of microRNAs. Nucleic Acids Res. 2008, 36, D159–D164.
    • (2008) Nucleic Acids Res , vol.36 , pp. D159-D164
    • Nam, S.1    Kim, B.2    Shin, S.3    Lee, S.4
  • 71
    • 55649091427 scopus 로고    scopus 로고
    • A bioinformatics tool for linking gene expression profiling results with public databases of microRNA target predictions
    • Creighton, C.J.; Nagaraja, A.K.; Hanash, S.M.; Matzuk, M.M.; Gunaratne, P.H. A bioinformatics tool for linking gene expression profiling results with public databases of microRNA target predictions. RNA2008, 14, 2290–2296.
    • (2008) RNA , vol.14 , pp. 2290-2296
    • Creighton, C.J.1    Nagaraja, A.K.2    Hanash, S.M.3    Matzuk, M.M.4    Gunaratne, P.H.5
  • 72
    • 62749123448 scopus 로고    scopus 로고
    • Integration of ranked lists via cross entropy Monte Carlo with applications to mRNA and microRNA studies
    • Lin, S.; Ding, J. Integration of ranked lists via cross entropy Monte Carlo with applications to mRNA and microRNA studies. Biometrics2009, 65, 9–18.
    • (2009) Biometrics , vol.65 , pp. 9-18
    • Lin, S.1    Ding, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.