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Volumn 45, Issue 2, 2017, Pages 556-566

Prediction of human miRNA target genes using computationally reconstructed ancestral mammalian sequences

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; MESSENGER RNA;

EID: 85014036168     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw1085     Document Type: Article
Times cited : (32)

References (63)
  • 1
    • 0024963695 scopus 로고
    • A hierarchy of regulatory genes controls a larva-to-adult developmental switch in C. elegans
    • Ambros,V. (1989) A hierarchy of regulatory genes controls a larva-to-adult developmental switch in C. elegans. Cell, 57, 49-57.
    • (1989) Cell , vol.57 , pp. 49-57
    • Ambros, V.1
  • 2
    • 0035955406 scopus 로고    scopus 로고
    • Molecular biology: Glimpses of a tiny RNA world
    • Ruvkun,G. (2001) Molecular biology: glimpses of a tiny RNA world. Science, 294, 797-799
    • (2001) Science , vol.294 , pp. 797-799
    • Ruvkun, G.1
  • 3
    • 77249117641 scopus 로고    scopus 로고
    • Small RNAS: An epigenetic silencing influence
    • Swami,M. (2010) Small RNAS: An epigenetic silencing influence. Nat. Rev. Genet., 11, 172-173.
    • (2010) Nat. Rev. Genet. , vol.11 , pp. 172-173
    • Swami, M.1
  • 4
    • 84899005497 scopus 로고    scopus 로고
    • Concise review: MicroRNAs as modulators of stem cells and angiogenesis
    • Kane,N.M., Thrasher,A.J., Angelini,G.D. and Emanueli,C. (2014) Concise review: MicroRNAs as modulators of stem cells and angiogenesis. Stem Cells, 32, 1059-1066.
    • (2014) Stem Cells , vol.32 , pp. 1059-1066
    • Kane, N.M.1    Thrasher, A.J.2    Angelini, G.D.3    Emanueli, C.4
  • 5
    • 84863688212 scopus 로고    scopus 로고
    • MicroRNAs in health and disease-basic science and clinical applications
    • Osman,A. (2012) MicroRNAs in health and disease-basic science and clinical applications. Clin. Lab., 58, 393-402.
    • (2012) Clin. Lab. , vol.58 , pp. 393-402
    • Osman, A.1
  • 8
  • 9
    • 84857972182 scopus 로고    scopus 로고
    • Novel techniques and targets in cardiovascular microRNA research
    • Dangwal,S., Bang,C. and Thum,T. (2012) Novel techniques and targets in cardiovascular microRNA research. Cardiovasc. Res., 93, 545-554.
    • (2012) Cardiovasc. Res. , vol.93 , pp. 545-554
    • Dangwal, S.1    Bang, C.2    Thum, T.3
  • 11
    • 84937250562 scopus 로고    scopus 로고
    • An overview of microRNAs
    • Hammond,S.M. (2015) An overview of microRNAs. Adv. Drug Deliv. Rev., 87, 3-14.
    • (2015) Adv. Drug Deliv. Rev. , vol.87 , pp. 3-14
    • Hammond, S.M.1
  • 12
    • 58249088751 scopus 로고    scopus 로고
    • MicroRNAs: Target recognition and regulatory functions
    • Bartel,D.P. (2009) MicroRNAs: target recognition and regulatory functions. Cell, 136, 215-233.
    • (2009) Cell , vol.136 , pp. 215-233
    • Bartel, D.P.1
  • 13
    • 84906313950 scopus 로고    scopus 로고
    • Identification and consequences of miRNA-target interactions - Beyond repression of gene expression
    • Hausser,J. and Zavolan,M. (2014) Identification and consequences of miRNA-target interactions - beyond repression of gene expression. Nat. Rev. Genet., 15, 599-612.
    • (2014) Nat. Rev. Genet. , vol.15 , pp. 599-612
    • Hausser, J.1    Zavolan, M.2
  • 14
    • 34547441263 scopus 로고    scopus 로고
    • Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5′ UTR as in the 3′ UTR
    • Lytle,J.R., Yario,T.A. and Steitz,J.A. (2007) Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5′ UTR as in the 3′ UTR. Proc. Natl. Acad. Sci. U.S.A., 104, 9667-9672.
    • (2007) Proc. Natl. Acad. Sci. U.S.A. , vol.104 , pp. 9667-9672
    • Lytle, J.R.1    Yario, T.A.2    Steitz, J.A.3
  • 16
    • 80052451056 scopus 로고    scopus 로고
    • Experimental strategies for microRNA target identification
    • Thomson,D.W., Bracken,C.P. and Goodall,G.J. (2011) Experimental strategies for microRNA target identification. Nucleic Acids Res., 39, 6845-6853.
    • (2011) Nucleic Acids Res. , vol.39 , pp. 6845-6853
    • Thomson, D.W.1    Bracken, C.P.2    Goodall, G.J.3
  • 20
    • 84938384133 scopus 로고    scopus 로고
    • miRWalk2.0: A comprehensive atlas of microRNA-target interactions
    • Dweep,H. and Gretz,N. (2015) miRWalk2.0: a comprehensive atlas of microRNA-target interactions. Nat. Methods, 12, 697.
    • (2015) Nat. Methods , vol.12 , pp. 697
    • Dweep, H.1    Gretz, N.2
  • 23
    • 34748821761 scopus 로고    scopus 로고
    • The role of site accessibility in microRNA target recognition
    • Kertesz,M., Iovino,N., Unnerstall,U., Gaul,U. and Segal,E. (2007) The role of site accessibility in microRNA target recognition. Nat. Genet., 39, 1278-1284.
    • (2007) Nat. Genet. , vol.39 , pp. 1278-1284
    • Kertesz, M.1    Iovino, N.2    Unnerstall, U.3    Gaul, U.4    Segal, E.5
  • 24
    • 44149083586 scopus 로고    scopus 로고
    • miRDB: A microRNA target prediction and functional annotation database with a wiki interface
    • Wang,X. (2008) miRDB: a microRNA target prediction and functional annotation database with a wiki interface. RNA, 14, 1012-1017.
    • (2008) RNA , vol.14 , pp. 1012-1017
    • Wang, X.1
  • 25
    • 38849145861 scopus 로고    scopus 로고
    • Prediction of both conserved and nonconserved microRNA targets in animals
    • Wang,X. and El Naqa,I.M. (2008) Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics, 24, 325-332.
    • (2008) Bioinformatics , vol.24 , pp. 325-332
    • Wang, X.1    El Naqa, I.M.2
  • 26
    • 70350000602 scopus 로고    scopus 로고
    • TargetMiner: MicroRNA target prediction with systematic identification of tissue-specific negative examples
    • Bandyopadhyay,S. and Mitra,R. (2009) TargetMiner: MicroRNA target prediction with systematic identification of tissue-specific negative examples. Bioinformatics, 25, 2625-2631.
    • (2009) Bioinformatics , vol.25 , pp. 2625-2631
    • Bandyopadhyay, S.1    Mitra, R.2
  • 27
    • 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. and Jiang,S.-W. (2013) Advances in the techniques for the Prediction of microRNA Targets. Int. J. Mol. Sci., 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
  • 28
    • 85003365400 scopus 로고    scopus 로고
    • mirMark: A site-level and UTR-level classifier for miRNA target prediction
    • Menor,M., Ching,T., Zhu,X., Garmire,D. and Garmire,L.X. (2014) mirMark: a site-level and UTR-level classifier for miRNA target prediction. Genome Biol., 15, 500.
    • (2014) Genome Biol. , vol.15 , pp. 500
    • Menor, M.1    Ching, T.2    Zhu, X.3    Garmire, D.4    Garmire, L.X.5
  • 30
    • 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, e05005.
    • (2015) Elife , vol.4 , pp. e05005
    • Agarwal, V.1    Bell, G.W.2    Nam, J.-W.3    Bartel, D.P.4
  • 33
    • 84887479221 scopus 로고    scopus 로고
    • The evolution of evolvability in microRNA target sites in vertebrates
    • Xu,J., Zhang,R., Shen,Y., Liu,G., Lu,X. and Wu,C.-I. (2013) The evolution of evolvability in microRNA target sites in vertebrates. Genome Res., 23, 1810-1816.
    • (2013) Genome Res. , vol.23 , pp. 1810-1816
    • Xu, J.1    Zhang, R.2    Shen, Y.3    Liu, G.4    Lu, X.5    Wu, C.-I.6
  • 35
    • 15244358503 scopus 로고    scopus 로고
    • Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals
    • Xie,X., Lu,J., Kulbokas,E.J., Golub,T.R., Mootha,V., Lindblad-Toh,K., Lander,E.S. and Kellis,M. (2005) Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature, 434, 338-345.
    • (2005) Nature , vol.434 , pp. 338-345
    • Xie, X.1    Lu, J.2    Kulbokas, E.J.3    Golub, T.R.4    Mootha, V.5    Lindblad-Toh, K.6    Lander, E.S.7    Kellis, M.8
  • 36
    • 79952276786 scopus 로고    scopus 로고
    • Is transcription factor binding site turnover a sufficient explanation for cis-regulatory sequence divergence?
    • Venkataram,S. and Fay,J.C. (2010) Is transcription factor binding site turnover a sufficient explanation for cis-regulatory sequence divergence? Genome Biol. Evol., 2, 851-858.
    • (2010) Genome Biol. Evol. , vol.2 , pp. 851-858
    • Venkataram, S.1    Fay, J.C.2
  • 37
    • 84883167952 scopus 로고    scopus 로고
    • Biogenesis, turnover, and mode of action of plant microRNAs
    • Rogers,K. and Chen,X. (2013) Biogenesis, turnover, and mode of action of plant microRNAs. Plant Cell, 25, 2383-2399.
    • (2013) Plant Cell , vol.25 , pp. 2383-2399
    • Rogers, K.1    Chen, X.2
  • 40
    • 0035986888 scopus 로고    scopus 로고
    • Evolution of transcription factor binding sites in mammalian gene regulatory regions: Conservation and turnover
    • Dermitzakis,E.T. and Clark,A.G. (2002) Evolution of transcription factor binding sites in mammalian gene regulatory regions: Conservation and turnover. Mol. Biol. Evol., 19, 1114-1121.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 1114-1121
    • Dermitzakis, E.T.1    Clark, A.G.2
  • 41
    • 84878050299 scopus 로고    scopus 로고
    • Exploiting ancestral mammalian genomes for the prediction of human transcription factor binding sites
    • Blanchette,M. (2012) Exploiting ancestral mammalian genomes for the prediction of human transcription factor binding sites. BMC Bioinformatics, 13(Suppl. 1), S2.
    • (2012) BMC Bioinformatics , vol.13 , pp. S2
    • Blanchette, M.1
  • 42
    • 34249856066 scopus 로고    scopus 로고
    • Distance constraints between microRNA target sites dictate efficacy and cooperativity
    • Saetrom,P., Heale,B.S.E., Snøve,O., Aagaard,L., Alluin,J. and Rossi,J.J. (2007) Distance constraints between microRNA target sites dictate efficacy and cooperativity. Nucleic Acids Res., 35, 2333-2342.
    • (2007) Nucleic Acids Res. , vol.35 , pp. 2333-2342
    • Saetrom, P.1    Heale, B.S.E.2    Snøve, O.3    Aagaard, L.4    Alluin, J.5    Rossi, J.J.6
  • 43
    • 84903722927 scopus 로고    scopus 로고
    • Inferring the evolutionary history of primate microRNA binding sites: Overcoming motif counting biases
    • Simkin,A.T., Bailey,J.A., Gao,F.-B. and Jensen,J.D. (2014) Inferring the evolutionary history of primate microRNA binding sites: overcoming motif counting biases. Mol. Biol. Evol., 31, 1894-1901.
    • (2014) Mol. Biol. Evol. , vol.31 , pp. 1894-1901
    • Simkin, A.T.1    Bailey, J.A.2    Gao, F.-B.3    Jensen, J.D.4
  • 44
    • 74949092081 scopus 로고    scopus 로고
    • Detection of nonneutral substitution rates on mammalian phylogenies
    • Pollard,K.S., Hubisz,M.J., Rosenbloom,K.R. and Siepel,A. (2010) Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res., 20, 110-121.
    • (2010) Genome Res. , vol.20 , pp. 110-121
    • Pollard, K.S.1    Hubisz, M.J.2    Rosenbloom, K.R.3    Siepel, A.4
  • 49
    • 33747849920 scopus 로고    scopus 로고
    • RNAhybrid: MicroRNA target prediction easy, fast and flexible
    • Krüger,J. and Rehmsmeier,M. (2006) RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Res., 34, W451-W454.
    • (2006) Nucleic Acids Res. , vol.34 , pp. W451-W454
    • Krüger, J.1    Rehmsmeier, M.2
  • 50
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews,D.H., Sabina,J., Zuker,M. and Turner,D.H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol., 288, 911-940.
    • (1999) J. Mol. Biol. , vol.288 , pp. 911-940
    • Mathews, D.H.1    Sabina, J.2    Zuker, M.3    Turner, D.H.4
  • 51
    • 75249091585 scopus 로고    scopus 로고
    • Ancestors 1.0: A web server for ancestral sequence reconstruction
    • Diallo,A.B., Makarenkov,V. and Blanchette,M. (2010) Ancestors 1.0: a web server for ancestral sequence reconstruction. Bioinformatics, 26, 130-131.
    • (2010) Bioinformatics , vol.26 , pp. 130-131
    • Diallo, A.B.1    Makarenkov, V.2    Blanchette, M.3
  • 58
    • 84860121995 scopus 로고    scopus 로고
    • miR-125b promotes early germ layer specification through Lin28/let-7d and preferential differentiation of mesoderm in human embryonic stem cells
    • Wong,S.S.Y., Ritner,C., Ramachandran,S., Aurigui,J., Pitt,C., Chandra,P., Ling,V.B., Yabut,O. and Bernstein,H.S. (2012) miR-125b promotes early germ layer specification through Lin28/let-7d and preferential differentiation of mesoderm in human embryonic stem cells. PLoS One, 7, e36121.
    • (2012) PLoS One , vol.7
    • Wong, S.S.Y.1    Ritner, C.2    Ramachandran, S.3    Aurigui, J.4    Pitt, C.5    Chandra, P.6    Ling, V.B.7    Yabut, O.8    Bernstein, H.S.9
  • 60
    • 77958117982 scopus 로고    scopus 로고
    • MiR-124a is important for migratory cell fate transition during gastrulation of human embryonic stem cells
    • Lee,M.R., Kim,J.S. and Kim,K.S. (2010) MiR-124a is important for migratory cell fate transition during gastrulation of human embryonic stem cells. Stem Cells, 28, 1550-1559.
    • (2010) Stem Cells , vol.28 , pp. 1550-1559
    • Lee, M.R.1    Kim, J.S.2    Kim, K.S.3
  • 63
    • 84923163752 scopus 로고    scopus 로고
    • The Genome 10K Project: A way forward
    • Koepfli,K., Paten,B., O'Brien,S.J. and Genome 10K Community of Scientists. (2015) The Genome 10K Project: a way forward. Annu. Rev. Anim. Biosci., 3, 57-111.
    • (2015) Annu. Rev. Anim. Biosci. , vol.3 , pp. 57-111
    • Koepfli, K.1    Paten, B.2    O'Brien, S.J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.