메뉴 건너뛰기




Volumn 53, Issue 5, 2010, Pages 548-562

Computational RNomics: Structure identification and functional prediction of non-coding RNAs in silico

Author keywords

Computational RNomics; Eukaryote; Non coding RNA

Indexed keywords

UNTRANSLATED RNA;

EID: 77953712744     PISSN: 16747305     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11427-010-0101-9     Document Type: Review
Times cited : (7)

References (86)
  • 1
    • 34250305146 scopus 로고    scopus 로고
    • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    • Birney E, Stamatoyannopoulos J A, Dutta A, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 2007, 447: 799-816.
    • (2007) Nature , vol.447 , pp. 799-816
    • Birney, E.1    Stamatoyannopoulos, J.A.2    Dutta, A.3
  • 3
    • 33646490270 scopus 로고    scopus 로고
    • Transcript annotation in FANTOM3: Mouse gene catalog based on physical cDNAs
    • Maeda N, Kasukawa T, Oyama R, et al. Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. PLoS Genet, 2006, 2: e62.
    • (2006) PLoS Genet , vol.2
    • Maeda, N.1    Kasukawa, T.2    Oyama, R.3
  • 4
    • 63049126626 scopus 로고    scopus 로고
    • RNomics: The new frontier in the post-genomic era
    • Qu L H. RNomics: The new frontier in the post-genomic era. Sci China C Life Sci, 2009, 52: 193-194.
    • (2009) Sci China C Life Sci , vol.52 , pp. 193-194
    • Qu, L.H.1
  • 5
    • 13444293342 scopus 로고    scopus 로고
    • RNAdb-a comprehensive mammalian noncoding RNA database
    • Pang K C, Stephen S, Engstrom P G, et al. RNAdb-a comprehensive mammalian noncoding RNA database. Nucl Acids Res, 2005, 33: D125-130.
    • (2005) Nucl Acids Res , vol.33
    • Pang, K.C.1    Stephen, S.2    Engstrom, P.G.3
  • 6
    • 13444267841 scopus 로고    scopus 로고
    • NONCODE: An integrated knowledge database of non-coding RNAs
    • Liu C, Bai B, Skogerbo G, et al. NONCODE: An integrated knowledge database of non-coding RNAs. Nucl Acids Res, 2005, 33: D112-115.
    • (2005) Nucl Acids Res , vol.33
    • Liu, C.1    Bai, B.2    Skogerbo, G.3
  • 7
    • 58149191274 scopus 로고    scopus 로고
    • Rfam: Updates to the RNA families database
    • Gardner P P, Daub J, Tate J G, et al. Rfam: Updates to the RNA families database. Nucl Acids Res, 2009, 37: D136-140.
    • (2009) Nucl Acids Res , vol.37
    • Gardner, P.P.1    Daub, J.2    Tate, J.G.3
  • 8
    • 33846056835 scopus 로고    scopus 로고
    • FRNAdb: A platform for mining/annotating functional RNA candidates from non-coding RNA sequences
    • Kin T, Yamada K, Terai G, et al. fRNAdb: A platform for mining/annotating functional RNA candidates from non-coding RNA sequences. Nucl Acids Res, 2007, 35: D145-148.
    • (2007) Nucl Acids Res , vol.35
    • Kin, T.1    Yamada, K.2    Terai, G.3
  • 11
    • 33644875300 scopus 로고    scopus 로고
    • SnoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs
    • Lestrade L, Weber M J. snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nucleic Acids Res, 2006, 34: D158-162.
    • (2006) Nucleic Acids Res , vol.34
    • Lestrade, L.1    Weber, M.J.2
  • 12
    • 38549124383 scopus 로고    scopus 로고
    • The microRNA.org resource: Targets and expression
    • Betel D, Wilson M, Gabow A, et al. The microRNA. org resource: Targets and expression. Nucleic Acids Res, 2008, 36: D149-153.
    • (2008) Nucleic Acids Res , vol.36
    • Betel, D.1    Wilson, M.2    Gabow, A.3
  • 13
    • 58149203235 scopus 로고    scopus 로고
    • The database of experimentally supported targets: A functional update of TarBase
    • Papadopoulos G L, Reczko M, Simossis V A, et al. The database of experimentally supported targets: A functional update of TarBase. Nucleic Acids Res, 2009, 37: D155-158.
    • (2009) Nucleic Acids Res , vol.37
    • Papadopoulos, G.L.1    Reczko, M.2    Simossis, V.A.3
  • 14
    • 75549084786 scopus 로고    scopus 로고
    • DeepBase: A database for deeply annotating and mining deep sequencing data
    • Yang J, Shao P, Zhou H, et al. deepBase: A database for deeply annotating and mining deep sequencing data. Nucleic Acids Res, 2010, 38: D123-130.
    • (2010) Nucleic Acids Res , vol.38
    • Yang, J.1    Shao, P.2    Zhou, H.3
  • 15
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res, 2003, 31: 3406-3415.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3406-3415
    • Zuker, M.1
  • 16
    • 0019876473 scopus 로고
    • Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
    • Zuker M, Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucl Acids Res, 1981, 9: 133-148.
    • (1981) Nucl Acids Res , vol.9 , pp. 133-148
    • Zuker, M.1    Stiegler, P.2
  • 17
    • 0043123153 scopus 로고    scopus 로고
    • Vienna RNA secondary structure server
    • Hofacker I L. Vienna RNA secondary structure server. Nucleic Acids Res, 2003, 31: 3429-3431.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3429-3431
    • Hofacker, I.L.1
  • 18
    • 27544437866 scopus 로고    scopus 로고
    • Structure clustering features on the Sfold web server
    • Chan C Y, Lawrence C E, Ding Y. Structure clustering features on the Sfold web server. Bioinformatics, 2005, 21: 3926-3928.
    • (2005) Bioinformatics , vol.21 , pp. 3926-3928
    • Chan, C.Y.1    Lawrence, C.E.2    Ding, Y.3
  • 19
    • 3242877996 scopus 로고    scopus 로고
    • Sfold web server for statistical folding and rational design of nucleic acids
    • Ding Y, Chan C Y, Lawrence C E. Sfold web server for statistical folding and rational design of nucleic acids. Nucl Acids Res, 2004, 32: W135-141.
    • (2004) Nucl Acids Res , vol.32
    • Ding, Y.1    Chan, C.Y.2    Lawrence, C.E.3
  • 20
    • 0346888665 scopus 로고    scopus 로고
    • A statistical sampling algorithm for RNA secondary structure prediction
    • Ding Y, Lawrence C E. A statistical sampling algorithm for RNA secondary structure prediction. Nucl Acids Res, 2003, 31: 7280-7301.
    • (2003) Nucl Acids Res , vol.31 , pp. 7280-7301
    • Ding, Y.1    Lawrence, C.E.2
  • 21
    • 0033765362 scopus 로고    scopus 로고
    • Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs
    • Rivas E, Eddy S R. Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs. Bioinformatics, 2000, 16: 583-605.
    • (2000) Bioinformatics , vol.16 , pp. 583-605
    • Rivas, E.1    Eddy, S.R.2
  • 22
    • 0003157183 scopus 로고    scopus 로고
    • Noncoding RNA gene detection using comparative sequence analysis
    • Rivas E, Eddy S R. Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics, 2001, 2: 8.
    • (2001) BMC Bioinformatics , vol.2 , pp. 8
    • Rivas, E.1    Eddy, S.R.2
  • 24
    • 33646272409 scopus 로고    scopus 로고
    • Identification and classification of conserved RNA secondary structures in the human genome
    • Pedersen J S, Bejerano G, Siepel A, et al. Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol, 2006, 2: e33.
    • (2006) PLoS Comput Biol , vol.2
    • Pedersen, J.S.1    Bejerano, G.2    Siepel, A.3
  • 25
    • 28544440092 scopus 로고    scopus 로고
    • Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs
    • Meyer I M, Miklos I. Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs. Nucl Acids Res, 2005, 33: 6338-6348.
    • (2005) Nucl Acids Res , vol.33 , pp. 6338-6348
    • Meyer, I.M.1    Miklos, I.2
  • 26
    • 69249110138 scopus 로고    scopus 로고
    • An Ariadne's thread to the identification and annotation of noncoding RNAs in eukaryotes
    • Solda G, Makunin I V, Sezerman O U, et al. An Ariadne's thread to the identification and annotation of noncoding RNAs in eukaryotes. Brief Bioinform, 2009, 10: 475-489.
    • (2009) Brief Bioinform , vol.10 , pp. 475-489
    • Solda, G.1    Makunin, I.V.2    Sezerman, O.U.3
  • 27
    • 10244243802 scopus 로고    scopus 로고
    • Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences
    • Bonnet E, Wuyts J, Rouze P, et al. Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics, 2004, 20: 2911-2917.
    • (2004) Bioinformatics , vol.20 , pp. 2911-2917
    • Bonnet, E.1    Wuyts, J.2    Rouze, P.3
  • 28
    • 34250783658 scopus 로고    scopus 로고
    • RNAstrand: Reading direction of structured RNAs in multiple sequence alignments
    • Reiche K, Stadler P. RNAstrand: Reading direction of structured RNAs in multiple sequence alignments. Algori Mol Biol, 2007, 2: 6.
    • (2007) Algori Mol Biol , vol.2 , pp. 6
    • Reiche, K.1    Stadler, P.2
  • 29
    • 33646483032 scopus 로고    scopus 로고
    • The abundance of short proteins in the mammalian proteome
    • Frith M C, Forrest A R, Nourbakhsh E, et al. The abundance of short proteins in the mammalian proteome. PLoS Genet, 2006, 2: e52.
    • (2006) PLoS Genet , vol.2
    • Frith, M.C.1    Forrest, A.R.2    Nourbakhsh, E.3
  • 30
    • 57149107578 scopus 로고    scopus 로고
    • Differentiating protein-coding and noncoding RNA: Challenges and ambiguities
    • Dinger M E, Pang K C, Mercer T R, et al. Differentiating protein-coding and noncoding RNA: challenges and ambiguities. PLoS Comput Biol, 2008, 4: e1000176.
    • (2008) PLoS Comput Biol , vol.4
    • Dinger, M.E.1    Pang, K.C.2    Mercer, T.R.3
  • 31
    • 17244364714 scopus 로고    scopus 로고
    • Identification of putative noncoding polyadenylated transcripts in Drosophila melanogaster
    • Tupy J L, Bailey A M, Dailey G, et al. Identification of putative noncoding polyadenylated transcripts in Drosophila melanogaster. Proc Natl Acad Sci USA, 2005, 102: 5495-5500.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 5495-5500
    • Tupy, J.L.1    Bailey, A.M.2    Dailey, G.3
  • 32
    • 10944264765 scopus 로고    scopus 로고
    • Modeling sequencing errors by combining Hidden Markov models
    • Lottaz C, Iseli C, Jongeneel C V, et al. Modeling sequencing errors by combining Hidden Markov models. Bioinformatics, 2003, 19: ii103-112.
    • (2003) Bioinformatics , vol.19
    • Lottaz, C.1    Iseli, C.2    Jongeneel, C.V.3
  • 33
    • 3242878575 scopus 로고    scopus 로고
    • CSTminer: A web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison
    • Castrignanò T, Canali A, Grillo G, et al. CSTminer: A web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison. Nucleic Acids Res, 2004, 32: W624-627.
    • (2004) Nucleic Acids Res , vol.32
    • Castrignanò, T.1    Canali, A.2    Grillo, G.3
  • 34
    • 0032900737 scopus 로고    scopus 로고
    • CRITICA: Coding region identification tool invoking comparative analysis
    • Badger J H, Olsen G J. CRITICA: Coding region identification tool invoking comparative analysis. Mol Biol Evol, 1999, 16: 512-524.
    • (1999) Mol Biol Evol , vol.16 , pp. 512-524
    • Badger, J.H.1    Olsen, G.J.2
  • 35
    • 33646478817 scopus 로고    scopus 로고
    • Discrimination of non-protein-coding transcripts from protein-coding mRNA
    • Frith M C, Bailey T L, Kasukawa T, et al. Discrimination of non-protein-coding transcripts from protein-coding mRNA. RNA Biol, 2006, 3: 40-48.
    • (2006) RNA Biol , vol.3 , pp. 40-48
    • Frith, M.C.1    Bailey, T.L.2    Kasukawa, T.3
  • 36
    • 33646488342 scopus 로고    scopus 로고
    • Distinguishing protein-coding from non-coding RNAs through support vector machines
    • Liu J, Gough J, Rost B. Distinguishing protein-coding from non-coding RNAs through support vector machines. PLoS Genet, 2006, 2: e29.
    • (2006) PLoS Genet , vol.2
    • Liu, J.1    Gough, J.2    Rost, B.3
  • 37
    • 34547582418 scopus 로고    scopus 로고
    • CPC: Assess the protein-coding potential of transcripts using sequence features and support vector machine
    • Kong L, Zhang Y, Ye Z, et al. CPC: Assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res, 2007, 35: W345-349.
    • (2007) Nucleic Acids Res , vol.35
    • Kong, L.1    Zhang, Y.2    Ye, Z.3
  • 38
    • 24644476482 scopus 로고    scopus 로고
    • MicroRNA identification based on sequence and structure alignment
    • Wang X, Zhang J, Li F, et al. microRNA identification based on sequence and structure alignment. Bioinformatics, 2005, 21: 3610-3614.
    • (2005) Bioinformatics , vol.21 , pp. 3610-3614
    • Wang, X.1    Zhang, J.2    Li, F.3
  • 39
    • 34547596338 scopus 로고    scopus 로고
    • MiPred: Classification of real and pseudo microRNA precursors using random forest prediction model with combined features
    • Jiang P, Wu H, Wang W, et al. MiPred: Classification of real and pseudo microRNA precursors using random forest prediction model with combined features. Nucleic Acids Res, 2007, 35: W339-344.
    • (2007) Nucleic Acids Res , vol.35
    • Jiang, P.1    Wu, H.2    Wang, W.3
  • 40
    • 38349097919 scopus 로고    scopus 로고
    • MiRFinder: An improved approach and software implementation for genome-wide fast microRNA precursor scans
    • Huang T, Fan B, Rothschild M F, et al. MiRFinder: An improved approach and software implementation for genome-wide fast microRNA precursor scans. BMC Bioinformatics, 2007, 8: 341.
    • (2007) BMC Bioinformatics , vol.8 , pp. 341
    • Huang, T.1    Fan, B.2    Rothschild, M.F.3
  • 41
    • 0033582628 scopus 로고    scopus 로고
    • A computational screen for methylation guide snoRNAs in yeast
    • Lowe T M, Eddy S R. A computational screen for methylation guide snoRNAs in yeast. Science, 1999, 283: 1168-1171.
    • (1999) Science , vol.283 , pp. 1168-1171
    • Lowe, T.M.1    Eddy, S.R.2
  • 42
    • 29844435528 scopus 로고    scopus 로고
    • A computational screen for mammalian pseudouridylation guide H/ACA RNAs
    • Schattner P, Barberan-Soler S, Lowe T M. A computational screen for mammalian pseudouridylation guide H/ACA RNAs. RNA, 2006, 12: 15-25.
    • (2006) Rna , vol.12 , pp. 15-25
    • Schattner, P.1    Barberan-Soler, S.2    Lowe, T.M.3
  • 43
    • 33751009398 scopus 로고    scopus 로고
    • SnoSeeker: An advanced computational package for screening of guide and orphan snoRNA genes in the human genome
    • Yang J, Zhang X, Huang Z, et al. snoSeeker: An advanced computational package for screening of guide and orphan snoRNA genes in the human genome. Nucl Acids Res, 2006, 34: 5112-5123.
    • (2006) Nucl Acids Res , vol.34 , pp. 5112-5123
    • Yang, J.1    Zhang, X.2    Huang, Z.3
  • 44
    • 38449092636 scopus 로고    scopus 로고
    • SnoReport: Computational identification of snoRNAs with unknown targets
    • Hertel J, Hofacker I L, Stadler P F. SnoReport: Computational identification of snoRNAs with unknown targets. Bioinformatics, 2008, 24: 158-164.
    • (2008) Bioinformatics , vol.24 , pp. 158-164
    • Hertel, J.1    Hofacker, I.L.2    Stadler, P.F.3
  • 45
    • 0033515637 scopus 로고    scopus 로고
    • A steroid receptor coactivator, SRA, functions as an RNA and is present in an SRC-1 complex
    • Lanz R B, McKenna N J, Onate S A, et al. A steroid receptor coactivator, SRA, functions as an RNA and is present in an SRC-1 complex. Cell, 1999, 97: 17-27.
    • (1999) Cell , vol.97 , pp. 17-27
    • Lanz, R.B.1    McKenna, N.J.2    Onate, S.A.3
  • 46
    • 30044434769 scopus 로고    scopus 로고
    • Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome
    • Ravasi T, Suzuki H, Pang K C, et al. Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. Genome Res, 2006, 16: 11-19.
    • (2006) Genome Res , vol.16 , pp. 11-19
    • Ravasi, T.1    Suzuki, H.2    Pang, K.C.3
  • 47
    • 41849084855 scopus 로고    scopus 로고
    • Discovering microRNAs from deep sequencing data using miRDeep
    • Friedlander M R, Chen W, Adamidi C, et al. Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotech, 2008, 26: 407-415.
    • (2008) Nat Biotech , vol.26 , pp. 407-415
    • Friedlander, M.R.1    Chen, W.2    Adamidi, C.3
  • 48
    • 67349157682 scopus 로고    scopus 로고
    • Tiny RNAs associated with transcription start sites in animals
    • Taft R J, Glazov E A, Cloonan N, et al. Tiny RNAs associated with transcription start sites in animals. Nat Genet, 2009, 41: 572-578.
    • (2009) Nat Genet , vol.41 , pp. 572-578
    • Taft, R.J.1    Glazov, E.A.2    Cloonan, N.3
  • 49
    • 67349173665 scopus 로고    scopus 로고
    • The regulated retrotrans-poson transcriptome of mammalian cells
    • Faulkner G J, Kimura Y, Daub C O, et al. The regulated retrotrans-poson transcriptome of mammalian cells. Nat Genet, 2009, 41: 563-571.
    • (2009) Nat Genet , vol.41 , pp. 563-571
    • Faulkner, G.J.1    Kimura, Y.2    Daub, C.O.3
  • 50
    • 67849114241 scopus 로고    scopus 로고
    • MiRanalyzer: A microRNA detection and analysis tool for next-generation sequencing experiments
    • Hackenberg M, Sturm M, Langenberger D, et al. miRanalyzer: A microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res, 2009, 37: W68-76.
    • (2009) Nucleic Acids Res , vol.37
    • Hackenberg, M.1    Sturm, M.2    Langenberger, D.3
  • 52
    • 0041941514 scopus 로고    scopus 로고
    • The small RNA profile during Drosophila melanogaster development
    • Aravin A A, Lagos-Quintana M, Yalcin A, et al. The small RNA profile during Drosophila melanogaster development. Dev Cell, 2003, 5: 337-350.
    • (2003) Dev Cell , vol.5 , pp. 337-350
    • Aravin, A.A.1    Lagos-Quintana, M.2    Yalcin, A.3
  • 53
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology
    • Ashburner M, Ball C A, Blake J A, et al. Gene ontology: Tool for the unification of biology. Nat Genet, 2000, 25: 25-29.
    • (2000) Nat Genet , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3
  • 54
    • 0346094457 scopus 로고    scopus 로고
    • Prediction of mammalian microRNA targets
    • Lewis B P, Shih I, Jones-Rhoades M W, et al. Prediction of mammalian microRNA targets. Cell, 2003, 115: 787-798.
    • (2003) Cell , vol.115 , pp. 787-798
    • Lewis, B.P.1    Shih, I.2    Jones-Rhoades, M.W.3
  • 55
    • 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. Cell, 2005, 120: 15-20.
    • (2005) Cell , vol.120 , pp. 15-20
    • Lewis, B.P.1    Burge, C.B.2    Bartel, D.P.3
  • 56
    • 20944450160 scopus 로고    scopus 로고
    • Combinatorial microRNA target predictions
    • Krek A, Grun D, Poy M N, et al. Combinatorial microRNA target predictions. Nat Genet, 2005, 37: 495-500.
    • (2005) Nat Genet , vol.37 , pp. 495-500
    • Krek, A.1    Grun, D.2    Poy, M.N.3
  • 57
    • 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
  • 58
    • 27344456287 scopus 로고    scopus 로고
    • MicroRNA target predictions across seven Drosophila species and comparison to mammalian targets
    • Grün D, Wang Y, Langenberger D, et al. microRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Comput Biol, 2005, 1: e13.
    • (2005) PLoS Comput Biol , vol.1
    • Grün, D.1    Wang, Y.2    Langenberger, D.3
  • 59
    • 33644756532 scopus 로고    scopus 로고
    • A genome-wide map of conserved microRNA targets in C. elegans
    • Lall S, Grün D, Krek A, et al. A genome-wide map of conserved microRNA targets in C. elegans. Curr Biol, 2006, 16: 460-471.
    • (2006) Curr Biol , vol.16 , pp. 460-471
    • Lall, S.1    Grün, D.2    Krek, A.3
  • 60
    • 33751520430 scopus 로고    scopus 로고
    • Natural selection on human microRNA binding sites inferred from SNP data
    • Chen K, Rajewsky N. Natural selection on human microRNA binding sites inferred from SNP data. Nat Genet, 2006, 38: 1452-1456.
    • (2006) Nat Genet , vol.38 , pp. 1452-1456
    • Chen, K.1    Rajewsky, N.2
  • 61
    • 34250805982 scopus 로고    scopus 로고
    • MicroRNA targeting specificity in mammals: Determinants beyond seed pairing
    • Grimson A, Farh K K, Johnston W K, et al. microRNA targeting specificity in mammals: Determinants beyond seed pairing. Mol Cell, 2007, 27: 91-105.
    • (2007) Mol Cell , vol.27 , pp. 91-105
    • Grimson, A.1    Farh, K.K.2    Johnston, W.K.3
  • 62
    • 67650747402 scopus 로고    scopus 로고
    • DIANA-microT web server: Elucidating microRNA functions through target prediction
    • Maragkakis M, Reczko M, Simossis V A, et al. DIANA-microT web server: Elucidating microRNA functions through target prediction. Nucl Acids Res, 2009, 37: W273-276.
    • (2009) Nucl Acids Res , vol.37
    • Maragkakis, M.1    Reczko, M.2    Simossis, V.A.3
  • 63
    • 4644237189 scopus 로고    scopus 로고
    • Fast and effective prediction of microRNA/target duplexes
    • Rehmsmeier M, Steffen P, Höchsmann M, et al. Fast and effective prediction of microRNA/target duplexes. RNA, 2004, 10: 1507-1517.
    • (2004) Rna , vol.10 , pp. 1507-1517
    • Rehmsmeier, M.1    Steffen, P.2    Höchsmann, M.3
  • 64
    • 38849145861 scopus 로고    scopus 로고
    • Prediction of both conserved and nonconserved microRNA targets in animals
    • Wang X, El Naqa I M. Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics, 2008, 24: 325-332.
    • (2008) Bioinformatics , vol.24 , pp. 325-332
    • Wang, X.1    El Naqa, I.M.2
  • 65
    • 42949131237 scopus 로고    scopus 로고
    • Computational methods for microRNA target prediction
    • Watanabe Y, Tomita M, Kanai A. Computational methods for microRNA target prediction. Meth Enzymol 2007, 427: 65-86.
    • (2007) Meth Enzymol , vol.427 , pp. 65-86
    • Watanabe, Y.1    Tomita, M.2    Kanai, A.3
  • 66
    • 40349094597 scopus 로고    scopus 로고
    • MicroRNA-373 induces expression of genes with complementary promoter sequences
    • Place R F, Li L, Pookot D, et al. microRNA-373 induces expression of genes with complementary promoter sequences. Proc Natl Acad Sci USA, 2008, 105: 1608-1613.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 1608-1613
    • Place, R.F.1    Li, L.2    Pookot, D.3
  • 67
    • 42449086421 scopus 로고    scopus 로고
    • MiR-148 targets human DNMT3b protein coding region
    • Duursma A M, Kedde M, Schrier M, et al. miR-148 targets human DNMT3b protein coding region. RNA, 2008, 14: 872-877.
    • (2008) Rna , vol.14 , pp. 872-877
    • Duursma, A.M.1    Kedde, M.2    Schrier, M.3
  • 68
    • 67650087599 scopus 로고    scopus 로고
    • New class of microRNA targets containing simultaneous 5′-UTR and 3′-UTR interaction sites
    • Lee I, Ajay S S, Yook J I, et al. New class of microRNA targets containing simultaneous 5′-UTR and 3′-UTR interaction sites. Genome Res, 2009, 19: 1175-1183.
    • (2009) Genome Res , vol.19 , pp. 1175-1183
    • Lee, I.1    Ajay, S.S.2    Yook, J.I.3
  • 69
    • 54449097149 scopus 로고    scopus 로고
    • A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence
    • Forman J J, Legesse-Miller A, Coller H A. A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence. Proc Natl Acad Sci USA, 2008, 105: 14879-14884.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 14879-14884
    • Forman, J.J.1    Legesse-Miller, A.2    Coller, H.A.3
  • 70
    • 0036544755 scopus 로고    scopus 로고
    • Micro RNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation
    • Lai E C. Micro RNAs 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
  • 71
    • 4444363152 scopus 로고    scopus 로고
    • MicroRNA control of PHABULOSA in leaf development: Importance of pairing to the microRNA 5′ region
    • Mallory A C, Reinhart B J, Jones-Rhoades M W, et al. microRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5′ region. EMBO J, 2004, 23: 3356-3364.
    • (2004) EMBO J , vol.23 , pp. 3356-3364
    • Mallory, A.C.1    Reinhart, B.J.2    Jones-Rhoades, M.W.3
  • 72
    • 18044377963 scopus 로고    scopus 로고
    • Principles of microRNA-target recognition
    • Brennecke J, Stark A, Russell R B, et al. Principles of microRNA-target recognition. PLoS Biol, 2005, 3: e85.
    • (2005) PLoS Biol , vol.3
    • Brennecke, J.1    Stark, A.2    Russell, R.B.3
  • 73
    • 13944282215 scopus 로고    scopus 로고
    • Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs
    • Lim L P, Lau N C, Garrett-Engele P, et al. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature, 2005, 433: 769-773.
    • (2005) Nature , vol.433 , pp. 769-773
    • Lim, L.P.1    Lau, N.C.2    Garrett-Engele, P.3
  • 74
    • 49949117302 scopus 로고    scopus 로고
    • Widespread changes in protein synthesis induced by microRNAs
    • Selbach M, Schwanhäusser B, Thierfelder N, et al. Widespread changes in protein synthesis induced by microRNAs. Nature, 2008, 455: 58-63.
    • (2008) Nature , vol.455 , pp. 58-63
    • Selbach, M.1    Schwanhäusser, B.2    Thierfelder, N.3
  • 75
    • 49949116902 scopus 로고    scopus 로고
    • The impact of microRNAs on protein output
    • Baek D, Villén J, Shin C, et al. The impact of microRNAs on protein output. Nature, 2008, 455: 64-71.
    • (2008) Nature , vol.455 , pp. 64-71
    • Baek, D.1    Villén, J.2    Shin, C.3
  • 76
    • 0029801668 scopus 로고    scopus 로고
    • A bulged lin-4/lin-14 RNA duplex is sufficient for Caenorhabditis elegans lin-14 temporal gradient forma tion
    • Ha I, Wightman B, Ruvkun G. A bulged lin-4/lin-14 RNA duplex is sufficient for Caenorhabditis elegans lin-14 temporal gradient forma tion. Genes Dev, 1996, 10: 3041-3050.
    • (1996) Genes Dev , vol.10 , pp. 3041-3050
    • Ha, I.1    Wightman, B.2    Ruvkun, G.3
  • 77
    • 45849107663 scopus 로고    scopus 로고
    • The effect of central loops in miRNA: MRE duplexes on the efficiency of miRNA-mediated gene regulation
    • Ye W, Lv Q, Wong C A, et al. The effect of central loops in miRNA: MRE duplexes on the efficiency of miRNA-mediated gene regulation. PLoS ONE, 2008, 3: e1719.
    • (2008) PLoS ONE , vol.3
    • Ye, W.1    Lv, Q.2    Wong, C.A.3
  • 78
    • 29144505309 scopus 로고    scopus 로고
    • The widespread impact of mammalian microRNAs on mRNA repression and evolution
    • Farh K K, Grimson A, Jan C, et al. The widespread impact of mammalian microRNAs on mRNA repression and evolution. Science, 2005, 310: 1817-1821.
    • (2005) Science , vol.310 , pp. 1817-1821
    • Farh, K.K.1    Grimson, A.2    Jan, C.3
  • 79
    • 33748587841 scopus 로고    scopus 로고
    • A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes
    • Miranda K C, Huynh T, Tay Y, et al. A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell, 2006, 126: 1203-1217.
    • (2006) Cell , vol.126 , pp. 1203-1217
    • Miranda, K.C.1    Huynh, T.2    Tay, Y.3
  • 80
    • 75649108609 scopus 로고    scopus 로고
    • Progress in miRNA target prediction and identification
    • Xia W, Cao G, Shao N. Progress in miRNA target prediction and identification. Sci China C Life Sci, 2009, 52: 1123-1130.
    • (2009) Sci China C Life Sci , vol.52 , pp. 1123-1130
    • Xia, W.1    Cao, G.2    Shao, N.3
  • 81
    • 54549108798 scopus 로고    scopus 로고
    • MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation
    • Tay Y, Zhang J, Thomson A M, et al. microRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation. Nature, 2008, 455: 1124-1128.
    • (2008) Nature , vol.455 , pp. 1124-1128
    • Tay, Y.1    Zhang, J.2    Thomson, A.M.3
  • 82
    • 33947424813 scopus 로고    scopus 로고
    • MicroTar: Predicting microRNA targets from RNA duplexes
    • Thadani R, Tammi M T. MicroTar: Predicting microRNA targets from RNA duplexes. BMC Bioinformatics, 2006, 7: S20.
    • (2006) BMC Bioinformatics , vol.7
    • Thadani, R.1    Tammi, M.T.2
  • 83
    • 34748821761 scopus 로고    scopus 로고
    • The role of site accessibility in microRNA target recognition
    • Kertesz M, Iovino N, Unnerstall U, et al. The role of site accessibility in microRNA target recognition. Nat Genet, 2007, 39: 1278-1284.
    • (2007) Nat Genet , vol.39 , pp. 1278-1284
    • Kertesz, M.1    Iovino, N.2    Unnerstall, U.3
  • 84
    • 34247258888 scopus 로고    scopus 로고
    • Potent effect of target structure on microRNA function
    • Long D, Lee R, Williams P, et al. Potent effect of target structure on microRNA function. Nat Struct Mol Biol, 2007, 14: 287-294.
    • (2007) Nat Struct Mol Biol , vol.14 , pp. 287-294
    • Long, D.1    Lee, R.2    Williams, P.3
  • 85
    • 36749005527 scopus 로고    scopus 로고
    • Using expression profiling data to identify human microRNA targets
    • Huang J C, Babak T, Corson T W, et al. Using expression profiling data to identify human microRNA targets. Nat Meth, 2007, 4: 1045-1049.
    • (2007) Nat Meth , vol.4 , pp. 1045-1049
    • Huang, J.C.1    Babak, T.2    Corson, T.W.3
  • 86
    • 33847647538 scopus 로고    scopus 로고
    • Same computational analysis, different miRNA target predictions
    • Xu X. Same computational analysis, different miRNA target predictions. Nat Methods, 2007, 4: 191.
    • (2007) Nat Methods , vol.4 , pp. 191
    • Xu, X.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.