메뉴 건너뛰기




Volumn 42, Issue 4, 2010, Pages 233-244

Got target?: Computational methods for microRNA target prediction and their extension

Author keywords

Algorithms; Computational biology; Micrornas; RNA; RNA interference; RNA induced silencing complex; Small interfering

Indexed keywords

MESSENGER RNA; MICRORNA;

EID: 77951953262     PISSN: 12263613     EISSN: 20926413     Source Type: Journal    
DOI: 10.3858/emm.2010.42.4.032     Document Type: Review
Times cited : (150)

References (56)
  • 1
    • 74049088856 scopus 로고    scopus 로고
    • Lost in translation: An assessment and perspective for computational microRNA target identification
    • Alexiou P, Maragkakis M, Papadopoulos GL, Reczko M, Hatzigeorgiou AG. Lost in translation: an assessment and perspective for computational microRNA target identification. Bioinformatics 2009;25:3049-55
    • (2009) Bioinformatics , vol.25 , pp. 3049-3055
    • Alexiou, P.1    Maragkakis, M.2    Papadopoulos, G.L.3    Reczko, M.4    Hatzigeorgiou, A.G.5
  • 2
    • 43449091567 scopus 로고    scopus 로고
    • Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome
    • Addo-Quaye C, Eshoo TW, Bartel DP, Axtell MJ. Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr Biol 2008;18:758-62
    • (2008) Curr Biol , vol.18 , pp. 758-762
    • Addo-Quaye, C.1    Eshoo, T.W.2    Bartel, D.P.3    Axtell, M.J.4
  • 4
    • 0347444723 scopus 로고    scopus 로고
    • MicroRNAs: Genomics, biogenesis, mechanism, and function
    • Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004;116:281-97
    • (2004) Cell , vol.116 , pp. 281-297
    • Bartel, D.P.1
  • 5
    • 26944498633 scopus 로고    scopus 로고
    • Prediction and validation of microRNAs and their targets
    • Bentwich I. Prediction and validation of microRNAs and their targets. FEBS Lett 2005;579:5904-10
    • (2005) FEBS Lett , vol.579 , pp. 5904-5910
    • Bentwich, I.1
  • 9
    • 34347398567 scopus 로고    scopus 로고
    • Inference of miRNA targets using evolutionary conservation and pathway analysis
    • Gaidatzis D, van Nimwegen E, Hausser J, Zavolan M. Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC Bioinformatics 2007;8:69
    • (2007) BMC Bioinformatics , vol.8 , pp. 69
    • Gaidatzis, D.1    van Nimwegen, E.2    Hausser, J.3    Zavolan, M.4
  • 10
    • 33645103560 scopus 로고    scopus 로고
    • GUUGle: A utility for fast exact matching under RNA complementary rules including G-U base pairing
    • Gerlach W, Giegerich R. GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing. Bioinformatics 2006;22:762-4
    • (2006) Bioinformatics , vol.22 , pp. 762-764
    • Gerlach, W.1    Giegerich, R.2
  • 14
    • 27344456287 scopus 로고    scopus 로고
    • MicroRNA target predictions across seven Drosophila species and comparison to mammalian targets
    • Grun D, Wang YL, Langenberger D, Gunsalus KC, Rajewsky N. MicroRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Comput Biol 2005;1:e13
    • (2005) PLoS Comput Biol , vol.1
    • Grun, D.1    Wang, Y.L.2    Langenberger, D.3    Gunsalus, K.C.4    Rajewsky, N.5
  • 16
    • 0043123153 scopus 로고    scopus 로고
    • Vienna RNA secondary structure server
    • Hofacker IL. Vienna RNA secondary structure server. Nucleic Acids Res 2003;31:3429-31
    • (2003) Nucleic Acids Res , vol.31 , pp. 3429-3431
    • Hofacker, I.L.1
  • 18
    • 38349097919 scopus 로고    scopus 로고
    • Zhao SH. miRFinder: An improved approach and software implementation for genome-wide fast micro RNA precursor scans
    • Huang TH, Fan B, Rothschild, MF, Hu ZL, Li K, Zhao SH. miRFinder: an improved approach and software implementation for genome-wide fast micro RNA precursor scans. BMC Bioinformatics 2007;8:341
    • (2007) BMC Bioinformatics , vol.8 , pp. 341
    • Huang, T.H.1    Fan, B.2    Rothschild, M.F.3    Hu, Z.L.4    Li, K.5
  • 20
    • 34748821761 scopus 로고    scopus 로고
    • The role of site accessibility in miRNA target recognition
    • Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E. The role of site accessibility in miRNA target recognition. Nat Genet 2007;39:1278-84
    • (2007) Nat Genet , vol.39 , pp. 1278-1284
    • Kertesz, M.1    Iovino, N.2    Unnerstall, U.3    Gaul, U.4    Segal, E.5
  • 22
    • 40449085254 scopus 로고    scopus 로고
    • Nurr77 upregulates HIF-α by inhibiting pVHL-mediated degradation
    • Kim B-Y, Kim H, Cho E-J, Youn H-D. Nurr77 upregulates HIF-α by inhibiting pVHL-mediated degradation. Exp Mol Med 2008;40:71-83
    • (2008) Exp Mol Med , vol.40 , pp. 71-83
    • Kim, B.-Y.1    Kim, H.2    Cho, E.-J.3    Youn, H.-D.4
  • 27
    • 0027751663 scopus 로고
    • The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
    • Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993;75:843-54
    • (1993) Cell , vol.75 , pp. 843-854
    • Lee, R.C.1    Feinbaum, R.L.2    Ambros, V.3
  • 29
    • 11844278458 scopus 로고    scopus 로고
    • Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
    • Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005;120:15-20
    • (2005) Cell , vol.120 , pp. 15-20
    • Lewis, B.P.1    Burge, C.B.2    Bartel, D.P.3
  • 31
    • 38549095711 scopus 로고    scopus 로고
    • Micromanagement of the immune system by microRNAs
    • Lodish HF, Zhou B, Liu G, Chen CZ. Micromanagement of the immune system by microRNAs. Nat Rev Immunol 2008; 8:120-30
    • (2008) Nat Rev Immunol , vol.8 , pp. 120-130
    • Lodish, H.F.1    Zhou, B.2    Liu, G.3    Chen, C.Z.4
  • 35
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews DH, Sabina J, Zuker M, Turner DH. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 1999;288:911-40
    • (1999) J Mol Biol , vol.288 , pp. 911-940
    • Mathews, D.H.1    Sabina, J.2    Zuker, M.3    Turner, D.H.4
  • 37
    • 33748587841 scopus 로고    scopus 로고
    • A pattern-based method for the identification of microRNA binding sites and their corresponding heteroduplexes
    • Miranda KC, Huynh T, Tay Y, Ang YS, Tam WL, Thomson AM, Lim B, Rigoutsos I. A pattern-based method for the identification of microRNA binding sites and their corresponding heteroduplexes. Cell 2006;126:1203-17
    • (2006) Cell , vol.126 , pp. 1203-1217
    • Miranda, K.C.1    Huynh, T.2    Tay, Y.3    Ang, Y.S.4    Tam, W.L.5    Thomson, A.M.6    Lim, B.7    Rigoutsos, I.8
  • 38
    • 38549092089 scopus 로고    scopus 로고
    • Lee S. 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 Acid Res 2008;36:D159-64
    • (2008) Nucleic Acid Res , vol.36
    • Nam, S.1    Kim, B.2    Shin, S.3
  • 39
    • 67849101186 scopus 로고    scopus 로고
    • MicroRNA and mRNA integrated analysis (MMIA): A web tool for examining biological functions of microRNA expression
    • Web server issue
    • Nam S, Li M, Choi K, Balch C, Kim S, Nephew KP. MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression. Nucleic Acids Res 2009;37(Web server issue):W356-62
    • (2009) Nucleic Acids Res , vol.37
    • Nam, S.1    Li, M.2    Choi, K.3    Balch, C.4    Kim, S.5    Nephew, K.P.6
  • 41
    • 33745248430 scopus 로고    scopus 로고
    • microRNA target predictions in animals
    • Rajewsky N. microRNA target predictions in animals. Nat Genet 2006;38(Suppl.):S8-13
    • (2006) Nat Genet , vol.38 , Issue.SUPPL.
    • Rajewsky, N.1
  • 42
    • 4644237189 scopus 로고    scopus 로고
    • Fast and effective prediction of microRNA/target duplexes
    • Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R. Fast and effective prediction of microRNA/target duplexes. RNA 2004;10:1507-17
    • (2004) RNA , vol.10 , pp. 1507-1517
    • Rehmsmeier, M.1    Steffen, P.2    Hochsmann, M.3    Giegerich, R.4
  • 44
    • 33744805399 scopus 로고    scopus 로고
    • Specific activation of microRNA-127 with downregulation of the proto-oncogene BCL6 by chromatin-modifying drugs in human cancer cells
    • Saito Y, Liang G, Egger G, Friedman JM, Chuang JC, Coetzee GA, Jones PA. Specific activation of microRNA-127 with downregulation of the proto-oncogene BCL6 by chromatin-modifying drugs in human cancer cells. Cancer Cell 2006;9:435-43
    • (2006) Cancer Cell , vol.9 , pp. 435-443
    • Saito, Y.1    Liang, G.2    Egger, G.3    Friedman, J.M.4    Chuang, J.C.5    Coetzee, G.A.6    Jones, P.A.7
  • 46
    • 31044444975 scopus 로고    scopus 로고
    • TarBase: A comprehensive database of experimentally supported animal micro RNA targets
    • Sethupathy P, Corda B, Hatzigeorgiou AG. TarBase: A comprehensive database of experimentally supported animal micro RNA targets. RNA 2006;12:192-7
    • (2006) RNA , vol.12 , pp. 192-197
    • Sethupathy, P.1    Corda, B.2    Hatzigeorgiou, A.G.3
  • 48
    • 28944439309 scopus 로고    scopus 로고
    • Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3'UTR evolution
    • Stark A, Brennecke J, Bushati N, Russell RB, Cohen SM. Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3'UTR evolution. Cell 2005;123:1133-46
    • (2005) Cell , vol.123 , pp. 1133-1146
    • Stark, A.1    Brennecke, J.2    Bushati, N.3    Russell, R.B.4    Cohen, S.M.5
  • 50
    • 44149083586 scopus 로고    scopus 로고
    • miRDB: A microRNA target prediction and functional annotation database with a wiki interface
    • Wang X. miRDB: A microRNA target prediction and functional annotation database with a wiki interface. RNA 2008;14:1012-7
    • (2008) RNA , vol.14 , pp. 1012-1017
    • Wang, X.1
  • 51
    • 38849145861 scopus 로고    scopus 로고
    • Prediction of both conserved and nonconserved microRNA targets in animals
    • Wang X, El Naqa IM. Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics 2008;24:325-32
    • (2008) Bioinformatics , vol.24 , pp. 325-332
    • Wang, X.1    El Naqa, I.M.2
  • 52
    • 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
  • 53
    • 0033080745 scopus 로고    scopus 로고
    • Complete suboptimal folding of RNA and the stability of secondary structures
    • Wuchty S, Fontana W, Hofacker IL, Schuster P. Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers 1999;49:145-65
    • (1999) Biopolymers , vol.49 , pp. 145-165
    • Wuchty, S.1    Fontana, W.2    Hofacker, I.L.3    Schuster, P.4
  • 54
    • 58149186499 scopus 로고    scopus 로고
    • MiRecords: An integrated resource for microRNA-target interactions
    • Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T. MiRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res 2009;37:D105-10
    • (2009) Nucleic Acids Res , vol.37
    • Xiao, F.1    Zuo, Z.2    Cai, G.3    Kang, S.4    Gao, X.5    Li, T.6
  • 55
    • 33747126827 scopus 로고    scopus 로고
    • Computational identification of microRNAs and their targets
    • Yoon S, De Micheli G. Computational identification of microRNAs and their targets. Birth Defects Res C Embryo Today 2006;78:118-28
    • (2006) Birth Defects Res C Embryo Today , vol.78 , pp. 118-128
    • Yoon, S.1    de Micheli, G.2
  • 56
    • 0019876473 scopus 로고
    • Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
    • Zuker, M. and Stiegler, P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res 1981;9:133-48
    • (1981) Nucleic Acids Res , vol.9 , pp. 133-148
    • Zuker, M.1    Stiegler, P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.