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Volumn 35, Issue 1, 2010, Pages 105-118

Flanking region sequence information to refine microRNA target predictions

Author keywords

Bioinformatics; Genome; MicroRNA; Non coding; RNA

Indexed keywords

INSULIN; MICRORNA; TOLL LIKE RECEPTOR;

EID: 77951704878     PISSN: 02505991     EISSN: 02505991     Source Type: Journal    
DOI: 10.1007/s12038-010-0013-7     Document Type: Article
Times cited : (29)

References (51)
  • 1
  • 3
    • 11844254846 scopus 로고    scopus 로고
    • Secondary structure prediction of interacting RNA molecules
    • DOI 10.1016/j.jmb.2004.10.082, PII S0022283604014032
    • M. Andronescu Z. C. Zhang A. Condon 2005 Secondary structure prediction of interacting RNA molecules J. Mol. Biol. 4 987 1001 10.1016/j.jmb.2004.10.082 (Pubitemid 40092219)
    • (2005) Journal of Molecular Biology , vol.345 , Issue.5 , pp. 987-1001
    • Andronescu, M.1    Zhang, Z.C.2    Condon, A.3
  • 4
    • 18044377963 scopus 로고    scopus 로고
    • Principles of microRNA-target recognition
    • DOI 10.1371/journal.pbio.0030085, e85
    • J. Brennecke A. Stark R.B. Russell S. M. Cohen 2005 Principles of microRNA-target recognition PLoS Biol. 3 e85 10.1371/journal.pbio.0030085 15723116 (Pubitemid 40605291)
    • (2005) PLoS Biology , vol.3 , Issue.3 , pp. 0404-0418
    • Brennecke, J.1    Stark, A.2    Russell, R.B.3    Cohen, S.M.4
  • 6
    • 14844364472 scopus 로고    scopus 로고
    • Antisense inhibition of human miRNAs and indications for an involvement of miRNA in cell growth and apoptosis
    • DOI 10.1093/nar/gki200
    • A. M. Cheng M. W. Byrom J. Shelton L. P. Ford 2005 Antisense inhibition of human miRNAs and indications for an involvement of miRNA in cell growth and apoptosis Nucleic Acids Res. 33 1290 1297 10.1093/nar/gki200 15741182 (Pubitemid 41439922)
    • (2005) Nucleic Acids Research , vol.33 , Issue.4 , pp. 1290-1297
    • Cheng, A.M.1    Byrom, M.W.2    Shelton, J.3    Ford, L.P.4
  • 7
    • 10944254152 scopus 로고    scopus 로고
    • Transcription and processing of human microRNA precursors
    • DOI 10.1016/j.molcel.2004.12.002, PII S1097276504007567
    • B. R. Cullen 2004 Transcription and processing of human microRNA precursors Mol. Cell 16 861 865 10.1016/j.molcel.2004.12.002 15610730 (Pubitemid 40018397)
    • (2004) Molecular Cell , vol.16 , Issue.6 , pp. 861-865
    • Cullen, B.R.1
  • 8
    • 45749154794 scopus 로고    scopus 로고
    • Molecular architecture of a miRNA-regulated 3′ UTR
    • DOI 10.1261/rna.1082708
    • D. Didiano O. Hobert 2008 Molecular architecture of a miRNA-regulated 3' UTR RNA 14 1297 1317 10.1261/rna.1082708 18463285 (Pubitemid 351872188)
    • (2008) RNA , vol.14 , Issue.7 , pp. 1297-1317
    • Didiano, D.1    Hobert, O.2
  • 9
    • 1642374097 scopus 로고    scopus 로고
    • Specificity of microRNA target selection in translational repression
    • DOI 10.1101/gad.1184404
    • J. G. Doench P. A. Sharp 2004 Specificity of microRNA target selection in translational repression Genes Dev. 18 504 511 10.1101/gad.1184404 15014042 (Pubitemid 38372808)
    • (2004) Genes and Development , vol.18 , Issue.5 , pp. 504-511
    • Doench, J.G.1    Sharp, P.A.2
  • 11
    • 13344262673 scopus 로고    scopus 로고
    • A comprehensive comparison of comparative RNA structure prediction approaches
    • DOI 10.1186/1471-2105-5-140
    • P. P. Gardner R. Giegerich 2004 A comprehensive comparison of comparative RNA structure prediction approaches BMC Bioinformatics 5 140 10.1186/1471-2105-5-140 15458580 (Pubitemid 40198135)
    • (2004) BMC Bioinformatics , vol.5 , pp. 140
    • Gardner, P.P.1    Giegerich, R.2
  • 12
    • 0347755643 scopus 로고    scopus 로고
    • The microRNA registry
    • 10.1093/nar/gkh023 14681370
    • S. Griffiths-Jones 2004 The microRNA registry Nucleic Acids Res. 32 D109 D111 10.1093/nar/gkh023 14681370
    • (2004) Nucleic Acids Res. , vol.32
    • Griffiths-Jones, S.1
  • 15
    • 34250805982 scopus 로고    scopus 로고
    • MicroRNA Targeting Specificity in Mammals: Determinants beyond Seed Pairing
    • DOI 10.1016/j.molcel.2007.06.017, PII S1097276507004078
    • A. Grimson K. K. Farh W. K. Johnston P. Garrett-Engele L. P. Lim D. P. Bartel 2007 MicroRNA targeting specificity in mammals: determinants beyond seed pairing Mol. Cell 6 91 105 10.1016/j.molcel.2007.06.017 (Pubitemid 46991392)
    • (2007) Molecular Cell , vol.27 , Issue.1 , pp. 91-105
    • Grimson, A.1    Farh, K.K.-H.2    Johnston, W.K.3    Garrett-Engele, P.4    Lim, L.P.5    Bartel, D.P.6
  • 16
    • 50849141708 scopus 로고    scopus 로고
    • MirWIP: MicroRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts
    • 10.1038/nmeth.1247 19160516
    • M. Hammell D. Long L. Zhang A. Lee C. S. Carmack M. Han Y. Ding V. Ambros 2008 mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts Nat. Methods 5 813 819 10.1038/nmeth.1247 19160516
    • (2008) Nat. Methods , vol.5 , pp. 813-819
    • Hammell, M.1    Long, D.2    Zhang, L.3    Lee, A.4    Carmack, C.S.5    Han, M.6    Ding, Y.7    Ambros, V.8
  • 18
    • 4344677175 scopus 로고    scopus 로고
    • Common logic of transcription factor and microRNA action
    • DOI 10.1016/j.tibs.2004.07.001, PII S0968000404001562
    • O. Hobert 2004 Common logic of transcription factor and microRNA action Trends Biochem. Sci. 29 462 468 10.1016/j.tibs.2004.07.001 15337119 (Pubitemid 39158869)
    • (2004) Trends in Biochemical Sciences , vol.29 , Issue.9 , pp. 462-468
    • Hobert, O.1
  • 20
    • 33646867882 scopus 로고    scopus 로고
    • Memory efficient folding algorithms for circular RNA secondary structures
    • DOI 10.1093/bioinformatics/btl023
    • I. L. Hofacker P. F. Stadler 2006 Memory efficient folding algorithms for circular RNA secondary structures Bioinformatics 22 1172 1176 10.1093/bioinformatics/btl023 16452114 (Pubitemid 43779007)
    • (2006) Bioinformatics , vol.22 , Issue.10 , pp. 1172-1176
    • Hofacker, I.L.1    Stadler, P.F.2
  • 22
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • 10.1093/nar/28.1.27 10592173
    • M. Kanehisa S. Goto 2000 KEGG: Kyoto encyclopedia of genes and genomes Nucleic Acids Res. 28 27 30 10.1093/nar/28.1.27 10592173
    • (2000) Nucleic Acids Res. , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 23
    • 0041853625 scopus 로고    scopus 로고
    • MATCH™: A tool for searching transcription factor binding sites in DNA sequences
    • DOI 10.1093/nar/gkg585
    • A. E. Kel E. Gössling I. Reuter E. Cheremushkin O. V. Kel-Margoulis E. Wingender 2003 MATCH: a tool for searching transcription factor binding sites in DNA sequences Nucleic Acids Res. 31 3576 3579 10.1093/nar/gkg585 12824369 (Pubitemid 37442201)
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3576-3579
    • Kel, A.E.1    Gossling, E.2    Reuter, I.3    Cheremushkin, E.4    Kel-Margoulis, O.V.5    Wingender, E.6
  • 24
    • 19844367341 scopus 로고    scopus 로고
    • Exploring relationships and mining data with the UCSC Gene Sorter
    • DOI 10.1101/gr.3694705
    • W. J. Kent F. Hsu D. Karolchik R. M. Kuhn H. Clawson H. Trumbower D. Haussler 2005 Exploring relationships and mining data with the UCSC gene sorter Genome Res. 15 737 741 10.1101/gr.3694705 15867434 (Pubitemid 41043644)
    • (2005) Genome Research , vol.15 , Issue.5 , pp. 737-741
    • Kent, W.J.1    Hsu, F.2    Karolchik, D.3    Kuhn, R.M.4    Clawson, H.5    Trumbower, H.6    Haussler, D.7
  • 25
    • 34748821761 scopus 로고    scopus 로고
    • The role of site accessibility in microRNA target recognition
    • DOI 10.1038/ng2135, PII NG2135
    • M. Kertesz N. Iovino U. Unnerstall U. Gaul E. Segal 2007 The role of site accessibility in microRNA target recognition Nat. Genet. 39 1278 1284 10.1038/ng2135 17893677 (Pubitemid 47482690)
    • (2007) Nature Genetics , vol.39 , Issue.10 , pp. 1278-1284
    • Kertesz, M.1    Iovino, N.2    Unnerstall, U.3    Gaul, U.4    Segal, E.5
  • 26
    • 33749645474 scopus 로고    scopus 로고
    • MiTarget: MicroRNA target gene prediction using a support vector machine
    • DOI 10.1186/1471-2105-7-411
    • S. K. Kim J. W. Nam J. K. Rhee W. J. Lee B. T. Zhang 2006 miTarget: microRNA target gene prediction using a support vector machine BMC Bioinformatics 7 411 10.1186/1471-2105-7-411 16978421 (Pubitemid 44540776)
    • (2006) BMC Bioinformatics , vol.7 , pp. 411
    • Kim, S.-K.1    Nam, J.-W.2    Rhee, J.-K.3    Lee, W.-J.4    Zhang, B.-T.5
  • 29
    • 0036544755 scopus 로고    scopus 로고
    • Micro RNAs are complementary to 3' UTR sequence motifs that mediate negative post-transcriptional regulation
    • 10.1038/ng865 11896390
    • E. C. Lai 2002 Micro RNAs are complementary to 3' UTR sequence motifs that mediate negative post-transcriptional regulation Nat. Genet. 30 363 374 10.1038/ng865 11896390
    • (2002) Nat. Genet. , vol.30 , pp. 363-374
    • Lai, E.C.1
  • 30
    • 19544390155 scopus 로고    scopus 로고
    • Predicting and validating microRNA targets
    • DOI 10.1186/gb-2004-5-9-115
    • E. C. Lai 2004 Predicting and validating microRNA targets Genome Biol. 5 115 10.1186/gb-2004-5-9-115 15345038 (Pubitemid 39335022)
    • (2004) Genome Biology , vol.5 , Issue.9 , pp. 115
    • Lai, E.C.1
  • 31
    • 0027751663 scopus 로고
    • The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
    • DOI 10.1016/0092-8674(93)90529-Y
    • R. C. Lee R. L. Feinbaum V. Ambros 1993 The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 Cell 75 843 854 10.1016/0092-8674(93)90529-Y 8252621 (Pubitemid 24014542)
    • (1993) Cell , vol.75 , Issue.5 , pp. 843-854
    • Lee, R.C.1    Feinbaum, R.L.2    Ambros, V.3
  • 32
    • 11844278458 scopus 로고    scopus 로고
    • Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
    • DOI 10.1016/j.cell.2004.12.035, PII S0092867404012607
    • B. P. Lewis C. B. Burge D. P. Bartel 2005 Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets Cell 120 15 20 10.1016/j.cell.2004.12.035 15652477 (Pubitemid 40094598)
    • (2005) Cell , vol.120 , Issue.1 , pp. 15-20
    • Lewis, B.P.1    Burge, C.B.2    Bartel, D.P.3
  • 33
    • 0346094457 scopus 로고    scopus 로고
    • Prediction of mammalian microRNA targets
    • DOI 10.1016/S0092-8674(03)01018-3
    • B. P. Lewis I. H. Shih M. W. Jones-Rhoades D. P. Bartel C. B. Burge 2003 Prediction of mammalian microRNA targets Cell 115 787 798 10.1016/S0092-8674(03) 01018-3 14697198 (Pubitemid 38058492)
    • (2003) Cell , vol.115 , Issue.7 , pp. 787-798
    • Lewis, B.P.1    Shih, I.-H.2    Jones-Rhoades, M.W.3    Bartel, D.P.4    Burge, C.B.5
  • 36
    • 11244251011 scopus 로고    scopus 로고
    • Plant and animal microRNAs: Similarities and differences
    • DOI 10.1007/s10142-005-0145-2
    • A. A. Miller P. Waterhouse 2005 Plant and animal microRNAs: similarities and differences Funct. Integr. Genomics 5 129 135 10.1007/s10142-005-0145-2 (Pubitemid 40823254)
    • (2005) Functional and Integrative Genomics , vol.5 , Issue.3 , pp. 129-135
    • Millar, A.A.1    Waterhouse, P.M.2
  • 37
    • 4644237189 scopus 로고    scopus 로고
    • Fast and effective prediction of microRNA/target duplexes
    • DOI 10.1261/rna.5248604
    • M. Rehmsmeier P. Steffen M. Hochsmann R. Giegerich 2004 Fast and effective prediction of microRNA/target duplexes RNA 10 1507 1517 10.1261/rna.5248604 15383676 (Pubitemid 39288185)
    • (2004) RNA , vol.10 , Issue.10 , pp. 1507-1517
    • Rehmsmeier, M.1    Steffen, P.2    Hochsmann, M.3    Giegerich, R.4
  • 39
    • 31044444975 scopus 로고    scopus 로고
    • TarBase: A comprehensive database of experimentally supported animal microRNA targets
    • DOI 10.1261/rna.2239606
    • P. Sethupathy B. Corda A. G. Hatzigeorgiou 2006 TarBase: a comprehensive database of experimentally supported animal microRNA targets RNA 12 192 197 10.1261/rna.2239606 16373484 (Pubitemid 43121923)
    • (2006) RNA , vol.12 , Issue.2 , pp. 192-197
    • Sethupathy, P.1    Corda, B.2    Hatzigeorgiou, A.G.3
  • 40
    • 33947368233 scopus 로고    scopus 로고
    • Non-random genomic divergence in repetitive sequences of human and chimpanzee in genes of different functional categories
    • DOI 10.1007/s00438-007-0210-8
    • R. Shankar A. Chaurasia B. Ghosh D. Chekmenev E. Cheremushkin A. Kel M. Mukerji 2007 Non-random genomic divergence in repetitive sequences of human and chimpanzee in genes of different functional categories Mol. Genet. Genomics 277 441 455 10.1007/s00438-007-0210-8 17375324 (Pubitemid 46452271)
    • (2007) Molecular Genetics and Genomics , vol.277 , Issue.4 , pp. 441-455
    • Shankar, R.1    Chaurasia, A.2    Ghosh, B.3    Chekmenev, D.4    Cheremushkin, E.5    Kel, A.6    Mukerji, M.7
  • 41
    • 0027987217 scopus 로고
    • A novel cysteine-rich sequence-specific DNA-binding protein interacts with the conserved X-box motif of the human major histocompatibility complex class II genes via a repeated cys-his domain and functions as a transcriptional repressor
    • DOI 10.1084/jem.180.5.1763
    • Z. Song S. Krishna D. Thanos J. L. Strominger S. J. Ono 1994 A novel cysteine-rich sequence-specific DNA-binding protein interacts with the conserved X-box motif of the human major histocompatibility complex class II genes via a repeated Cys-His domain and functions as a transcriptional repressor J. Exp. Med. 180 1763 1774 10.1084/jem.180.5.1763 7964459 (Pubitemid 24328567)
    • (1994) Journal of Experimental Medicine , vol.180 , Issue.5 , pp. 1763-1774
    • Song, Z.1    Krishna, S.2    Thanos, D.3    Strominger, J.L.4    Ono, S.J.5
  • 42
    • 33947424813 scopus 로고    scopus 로고
    • MicroTar: Predicting microRNA targets from RNA duplexes
    • R. Thadani M. T. Tammi 2006 MicroTar: predicting microRNA targets from RNA duplexes BMC Bioinformatics 18 7
    • (2006) BMC Bioinformatics , vol.18 , pp. 7
    • Thadani, R.1    Tammi, M.T.2
  • 43
    • 0043123063 scopus 로고    scopus 로고
    • Gibbs Recursive Sampler: Finding transcription factor binding sites
    • DOI 10.1093/nar/gkg608
    • W. Thompson E. C. Rouchka C. E. Lawrence 2003 Gibbs recursive sampler: finding transcription factor binding sites Nucleic Acids Res. 31 3580 3585 10.1093/nar/gkg608 12824370 (Pubitemid 37442202)
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3580-3585
    • Thompson, W.1    Rouchka, E.C.2    Lawrence, C.E.3
  • 45
    • 0037448607 scopus 로고    scopus 로고
    • A novel nuclear protein, Twa1, and Muskelin comprise a complex with RanBPM
    • DOI 10.1016/S0378-1119(02)01153-8
    • M. Umeda H. Nishitani T. Nishimoto 2003 A novel nuclear protein, Twa1, and Muskelin comprise a complex with RanBPM Gene 303 47 54 10.1016/S0378- 1119(02)01153-8 12559565 (Pubitemid 36151769)
    • (2003) Gene , vol.303 , Issue.1-2 , pp. 47-54
    • Umeda, M.1    Nishitani, H.2    Nishimoto, T.3
  • 46
    • 38849145861 scopus 로고    scopus 로고
    • Prediction of both conserved and nonconserved microRNA targets in animals
    • DOI 10.1093/bioinformatics/btm595
    • X. Wang I. M. El Naqa 2008 Prediction of both conserved and nonconserved microRNA targets in animals Bioinformatics 24 325 332 10.1093/bioinformatics/ btm595 18048393 (Pubitemid 351189007)
    • (2008) Bioinformatics , vol.24 , Issue.3 , pp. 325-332
    • Wang, X.1    El Naqa, I.M.2
  • 47
    • 34247598415 scopus 로고    scopus 로고
    • Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering
    • DOI 10.1371/journal.pcbi.0030065
    • S. Will K. Reiche I. L. Hofacker P. F. Stadler R. Backofen 2007 Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering PLoS Comput. Biol. 3 4 10.1371/journal.pcbi.0030065 (Pubitemid 46683450)
    • (2007) PLoS Computational Biology , vol.3 , Issue.4 , pp. 680-691
    • Will, S.1    Reiche, K.2    Hofacker, I.L.3    Stadler, P.F.4    Backofen, R.5
  • 49
    • 58149186499 scopus 로고    scopus 로고
    • MiRecords: An integrated resource for microRNA-target interactions
    • 10.1093/nar/gkn851 18996891
    • F. Xiao Z. Zuo G. Cai S. Kang X. Gao T. Li 2009 miRecords: an integrated resource for microRNA-target interactions Nucleic Acids Res. 37 D105 D110 10.1093/nar/gkn851 18996891
    • (2009) Nucleic Acids Res. , vol.37
    • Xiao, F.1    Zuo, Z.2    Cai, G.3    Kang, S.4    Gao, X.5    Li, T.6
  • 50
    • 57649174704 scopus 로고    scopus 로고
    • MirTif: A support vector machine-based microRNA target interaction filter
    • 10.1186/1471-2105-9-S12-S4 19091027
    • Y. Yang Y. Wang K. Li 2008 MirTif: a support vector machine-based microRNA target interaction filter BMC Bioinformatics 9 S4 10.1186/1471-2105-9- S12-S4 19091027
    • (2008) BMC Bioinformatics , vol.9 , pp. 4
    • Yang, Y.1    Wang, Y.2    Li, K.3
  • 51
    • 22544465244 scopus 로고    scopus 로고
    • JMJD2A is a novel N-CoR-interacting protein and is involved in repression of the human transcription factor achaete scute-like homologue 2 (ASCL2/Hash2)
    • DOI 10.1128/MCB.25.15.6404-6414.2005
    • D. Zhang H. G. Yoon J. Wong 2005 JMJD2A is a novel N-CoRinteracting protein and is involved in repression of the human transcription factor achaete scute-like homologue 2 (ASCL2/Hash2) Mol. Cell. Biol. 25 6404 6414 10.1128/MCB.25.15.6404-6414.2005 16024779 (Pubitemid 41023217)
    • (2005) Molecular and Cellular Biology , vol.25 , Issue.15 , pp. 6404-6414
    • Zhang, D.1    Yoon, H.-G.2    Wong, J.3


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