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Volumn 11, Issue SUPPLL.1, 2010, Pages

MTar: A computational microRNA target prediction architecture for human transcriptome

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL ARCHITECTURE; GENE REGULATORY NETWORKS; LEARNING ARCHITECTURES; MACHINE LEARNING MODELS; MICRORNA TARGET PREDICTIONS; MIRNA TARGET PREDICTIONS; STRUCTURAL PARAMETER; THERMODYNAMIC MODEL;

EID: 75149129669     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-S1-S2     Document Type: Article
Times cited : (53)

References (45)
  • 1
    • 33645294070 scopus 로고    scopus 로고
    • Oncomirs microRNAs with a role in Cancer
    • 10.1038/nrc1840, 16557279
    • Esquek KA, Slack FJ. Oncomirs microRNAs with a role in Cancer. Nature Reviews Cancer 2006, 6:259-269. 10.1038/nrc1840, 16557279.
    • (2006) Nature Reviews Cancer , vol.6 , pp. 259-269
    • Esquek, K.A.1    Slack, F.J.2
  • 3
    • 0347444723 scopus 로고    scopus 로고
    • MicroRNAs: genomics, biogenesis, mechanism, and function
    • 10.1016/S0092-8674(04)00045-5, 14744438
    • Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116:281-297. 10.1016/S0092-8674(04)00045-5, 14744438.
    • (2004) Cell , vol.116 , pp. 281-297
    • Bartel, D.P.1
  • 4
    • 18344369543 scopus 로고    scopus 로고
    • MicroRNA biogenesis:coordinated cropping and dicing
    • 10.1038/nrm1644, 15852042
    • Kim VN. MicroRNA biogenesis:coordinated cropping and dicing. Nat Rev Mol Cell Biol 2005, 6:376-385. 10.1038/nrm1644, 15852042.
    • (2005) Nat Rev Mol Cell Biol , vol.6 , pp. 376-385
    • Kim, V.N.1
  • 5
    • 27744537851 scopus 로고    scopus 로고
    • Human RISC couples microRNA biogenesis and posttranscriptional gene silencing
    • 10.1016/j.cell.2005.10.022, 16271387
    • Gregory R, Chendrimada T, Shiekhattar R. Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell 2005, 123:631-640. 10.1016/j.cell.2005.10.022, 16271387.
    • (2005) Cell , vol.123 , pp. 631-640
    • Gregory, R.1    Chendrimada, T.2    Shiekhattar, R.3
  • 6
    • 0035905766 scopus 로고    scopus 로고
    • Roll for a bidentate ribonuclease in the initiation step of RNA interface
    • 10.1038/35053110, 11201747
    • Bernstein E, Caudy A, Hammond S, Hannon G. Roll for a bidentate ribonuclease in the initiation step of RNA interface. Nature 2001, 409:363-366. 10.1038/35053110, 11201747.
    • (2001) Nature , vol.409 , pp. 363-366
    • Bernstein, E.1    Caudy, A.2    Hammond, S.3    Hannon, G.4
  • 7
    • 0037144546 scopus 로고    scopus 로고
    • A microRNA in a multiple turnover RANi enzyme complex
    • 10.1126/science.1073827, 12154197
    • Hutvagner G, Zamore PD. A microRNA in a multiple turnover RANi enzyme complex. Science 2002, 297:2056-2060. 10.1126/science.1073827, 12154197.
    • (2002) Science , vol.297 , pp. 2056-2060
    • Hutvagner, G.1    Zamore, P.D.2
  • 9
    • 0037162702 scopus 로고    scopus 로고
    • Prediction of Plant microRNA Targets
    • 10.1016/S0092-8674(02)00863-2, 12202040
    • Rhoades B, Reinhart B, Bartel B, Bartel DP. Prediction of Plant microRNA Targets. Cell 2002, 110:513-520. 10.1016/S0092-8674(02)00863-2, 12202040.
    • (2002) Cell , vol.110 , pp. 513-520
    • Rhoades, B.1    Reinhart, B.2    Bartel, B.3    Bartel, D.P.4
  • 10
    • 11844278458 scopus 로고    scopus 로고
    • Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are microRNA Targets
    • 10.1016/j.cell.2004.12.035, 15652477
    • Lewis B, Burge C, Bartel DP. Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are microRNA Targets. Cell 2005, 120:15-20. 10.1016/j.cell.2004.12.035, 15652477.
    • (2005) Cell , vol.120 , pp. 15-20
    • Lewis, B.1    Burge, C.2    Bartel, D.P.3
  • 11
    • 4644237189 scopus 로고    scopus 로고
    • Fast and Effective prediction of microRNA/target duplexes
    • 10.1261/rna.5248604, 1370637, 15383676
    • Rehmsmeier M, Steffen P, Hochsmann M, Giegrich R. Fast and Effective prediction of microRNA/target duplexes. RNA 2004, 10:1507-1517. 10.1261/rna.5248604, 1370637, 15383676.
    • (2004) RNA , vol.10 , pp. 1507-1517
    • Rehmsmeier, M.1    Steffen, P.2    Hochsmann, M.3    Giegrich, R.4
  • 13
    • 4043110802 scopus 로고    scopus 로고
    • Binding Matrix a novel approach for binding site recognition
    • 10.1142/S0219720004000569, 15297983
    • Kim JT, Gewehr JE, Martinetz T. Binding Matrix a novel approach for binding site recognition. J Bioinform Comput Biol 2004, 2:289-307. 10.1142/S0219720004000569, 15297983.
    • (2004) J Bioinform Comput Biol , vol.2 , pp. 289-307
    • Kim, J.T.1    Gewehr, J.E.2    Martinetz, T.3
  • 14
    • 43449136789 scopus 로고    scopus 로고
    • A scoring matrix approach to detecting miRNA target sites
    • 10.1186/1748-7188-3-3, 2365947, 18377655
    • Moxon S, Moulton V, Kim JT. A scoring matrix approach to detecting miRNA target sites. Algorithms Mol Biol 2008, 3:3. 10.1186/1748-7188-3-3, 2365947, 18377655.
    • (2008) Algorithms Mol Biol , vol.3 , pp. 3
    • Moxon, S.1    Moulton, V.2    Kim, J.T.3
  • 15
    • 18044377963 scopus 로고    scopus 로고
    • Principles of microRNA-target recognition
    • 10.1371/journal.pbio.0030085, 1043860, 15723116
    • Brennecke J, Stark A, Russell RB, Cohen SM. Principles of microRNA-target recognition. PLoS Biol 2005, 3:e85. 10.1371/journal.pbio.0030085, 1043860, 15723116.
    • (2005) PLoS Biol , vol.3
    • Brennecke, J.1    Stark, A.2    Russell, R.B.3    Cohen, S.M.4
  • 16
    • 34250805982 scopus 로고    scopus 로고
    • Micro RNA targeting specificity in mammals: determinants beyond seed pairing
    • 10.1016/j.molcel.2007.06.017, 17612493
    • Grimson A, Farh K, Johnston W, Engele PG, Lim L, Bartel DP. Micro RNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 2007, 27:91-105. 10.1016/j.molcel.2007.06.017, 17612493.
    • (2007) Mol Cell , vol.27 , pp. 91-105
    • Grimson, A.1    Farh, K.2    Johnston, W.3    Engele, P.G.4    Lim, L.5    Bartel, D.P.6
  • 17
    • 31044444975 scopus 로고    scopus 로고
    • TarBase: A comprehensive database of experimentally supported animal microRNA targets
    • 10.1261/rna.2239606, 1370898, 16373484
    • Sethupathy P, Corda B, Hatzigeorgiou AG. TarBase: A comprehensive database of experimentally supported animal microRNA targets. RNA 2006, 12:192-197. 10.1261/rna.2239606, 1370898, 16373484.
    • (2006) RNA , vol.12 , pp. 192-197
    • Sethupathy, P.1    Corda, B.2    Hatzigeorgiou, A.G.3
  • 18
    • 28944439309 scopus 로고    scopus 로고
    • Animal MicroRNAsconfer robustness to gene expression and have a significant impact on 3'UTR evolution
    • 10.1016/j.cell.2005.11.023, 16337999
    • Stark A, Brennecke J, Bushati N, Russell RB, Cohen SM. Animal MicroRNAsconfer robustness to gene expression and have a significant impact on 3'UTR evolution. Cell 2005, 123:1133-1146. 10.1016/j.cell.2005.11.023, 16337999.
    • (2005) Cell , vol.123 , pp. 1133-1146
    • Stark, A.1    Brennecke, J.2    Bushati, N.3    Russell, R.B.4    Cohen, S.M.5
  • 20
    • 2942672580 scopus 로고    scopus 로고
    • Computational identification of Plant microRNAs and their targets, inducing a stress-induced miRNA
    • 10.1016/j.molcel.2004.05.027, 15200956
    • Johnes-Rahoades MW, Bartel DP. Computational identification of Plant microRNAs and their targets, inducing a stress-induced miRNA. Mol Cell 2004, 14:787-799. 10.1016/j.molcel.2004.05.027, 15200956.
    • (2004) Mol Cell , vol.14 , pp. 787-799
    • Johnes-Rahoades, M.W.1    Bartel, D.P.2
  • 22
    • 23144458275 scopus 로고    scopus 로고
    • MiRU: an automated plant miRNA target prediction server
    • 10.1093/nar/gki383, 1160144, 15980567
    • Zhang Y. miRU: an automated plant miRNA target prediction server. Nucleic Acids Res 2005, 33:W701-W704. 10.1093/nar/gki383, 1160144, 15980567.
    • (2005) Nucleic Acids Res , vol.33
    • Zhang, Y.1
  • 23
    • 27344456287 scopus 로고    scopus 로고
    • MicroRNA target predictions across seven Drosophila species and comparison to mammalian targets
    • 10.1371/journal.pcbi.0010013, 1183519, 16103902
    • 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. 10.1371/journal.pcbi.0010013, 1183519, 16103902.
    • (2005) PLoS Comput Biol , vol.1
    • Grun, D.1    Wang, Y.L.2    Langenberger, D.3    Gunsalus, K.C.4    Rajewsky, N.5
  • 26
    • 0346094457 scopus 로고    scopus 로고
    • Prediction of mammalian microRNA targets
    • 10.1016/S0092-8674(03)01018-3, 14697198
    • Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB. Prediction of mammalian microRNA targets. Cell 2003, 115:787-798. 10.1016/S0092-8674(03)01018-3, 14697198.
    • (2003) Cell , vol.115 , pp. 787-798
    • Lewis, B.P.1    Shih, I.H.2    Jones-Rhoades, M.W.3    Bartel, D.P.4    Burge, C.B.5
  • 28
    • 38549124383 scopus 로고    scopus 로고
    • The microRNA.org resource: targets and expression
    • 10.1093/nar/gkm995, 2238905, 18158296
    • Betel D, Wilson M, Gabow A, Marks DS, Sander C. The microRNA.org resource: targets and expression. Nucleic Acids Res 2008, 36:D149-D153. 10.1093/nar/gkm995, 2238905, 18158296.
    • (2008) Nucleic Acids Res , vol.36
    • Betel, D.1    Wilson, M.2    Gabow, A.3    Marks, D.S.4    Sander, C.5
  • 29
  • 30
    • 75149141414 scopus 로고    scopus 로고
    • MiTarget: miRNA target gene prediction using an SVM
    • 10.1186/1471-2105-7-441, 1618407, 17032452
    • Kim S, Nam J, Rhee J, Lee W, Zhang B. MiTarget: miRNA target gene prediction using an SVM. BMC Bioinformatics 2006, 7:441. 10.1186/1471-2105-7-441, 1618407, 17032452.
    • (2006) BMC Bioinformatics , vol.7 , pp. 441
    • Kim, S.1    Nam, J.2    Rhee, J.3    Lee, W.4    Zhang, B.5
  • 31
    • 25444461163 scopus 로고    scopus 로고
    • Prediction and verification of microRNA targets by Moving Targets, a highly adaptable prediction method
    • 10.1186/1471-2105-6-88, 1090555, 15817129
    • Burgler C, Macdonald PM. Prediction and verification of microRNA targets by Moving Targets, a highly adaptable prediction method. BMC Bioinformatics 2005, 6:88. 10.1186/1471-2105-6-88, 1090555, 15817129.
    • (2005) BMC Bioinformatics , vol.6 , pp. 88
    • Burgler, C.1    Macdonald, P.M.2
  • 32
    • 33947424813 scopus 로고    scopus 로고
    • MicroTar: Predicting microRNA targets from RNA duplexes
    • 10.1186/1471-2105-7-S5-S20, 1764477, 17254305
    • Thadani R, Tammi MT. MicroTar: Predicting microRNA targets from RNA duplexes. BMC Bioinformatics 2006, 7(Suppl 5):S20. 10.1186/1471-2105-7-S5-S20, 1764477, 17254305.
    • (2006) BMC Bioinformatics , vol.7 , Issue.SUPPL 5
    • Thadani, R.1    Tammi, M.T.2
  • 33
    • 33644750115 scopus 로고    scopus 로고
    • MiRBase: microRNA sequences, targets and gene nomenclature
    • 10.1093/nar/gkj112, 1347474, 16381832
    • Griffiths-Jones S, Russell JG, Stijn D V, Alex B, Anton E J. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 2006, 34:D140-D144. 10.1093/nar/gkj112, 1347474, 16381832.
    • (2006) Nucleic Acids Res , vol.34
    • Griffiths-Jones, S.1    Russell, J.G.2    Stijn D, V.3    Alex, B.4    Anton E, J.5
  • 34
    • 75149125707 scopus 로고    scopus 로고
    • A Pre-microRNA Classifier by Structural and Thermodynamic Motifs
    • Vinod C, Reshmi G. A Pre-microRNA Classifier by Structural and Thermodynamic Motifs. IEEE - NaBIC 2009, 2009:9-11.
    • (2009) IEEE - NaBIC , vol.2009 , pp. 9-11
    • Vinod, C.1    Reshmi, G.2
  • 35
    • 33748587841 scopus 로고    scopus 로고
    • A pattern-based method for the identification of microRNA-target sites and their corresponding RNA/RNA complexes
    • 10.1016/j.cell.2006.07.031, 16990141
    • Huynh T, Miranda K, Tay Y, Ang S, Tam L, Thomson AM, Lim B, Rigoutsos I. A pattern-based method for the identification of microRNA-target sites and their corresponding RNA/RNA complexes. Cell 2006, 126:1203-1217. 10.1016/j.cell.2006.07.031, 16990141.
    • (2006) Cell , vol.126 , pp. 1203-1217
    • Huynh, T.1    Miranda, K.2    Tay, Y.3    Ang, S.4    Tam, L.5    Thomson, A.M.6    Lim, B.7    Rigoutsos, I.8
  • 36
    • 34347398567 scopus 로고    scopus 로고
    • Inference of miRNA targets using evolutionary conservation and pathway analysis
    • 10.1186/1471-2105-8-69, 1838429, 17331257
    • Gaidatzis D, van Nimwegen E, Hausser J, Zavolan M. Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC Bioinformatics 2007, 8:69. 10.1186/1471-2105-8-69, 1838429, 17331257.
    • (2007) BMC Bioinformatics , vol.8 , pp. 69
    • Gaidatzis, D.1    van Nimwegen, E.2    Hausser, J.3    Zavolan, M.4
  • 37
    • 34748821761 scopus 로고    scopus 로고
    • The role of site accessibility in microRNA target recognition
    • 10.1038/ng2135, 17893677
    • Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E. The role of site accessibility in microRNA target recognition. Nature Genetics 2007, 39:1278-1283. 10.1038/ng2135, 17893677.
    • (2007) Nature Genetics , vol.39 , pp. 1278-1283
    • Kertesz, M.1    Iovino, N.2    Unnerstall, U.3    Gaul, U.4    Segal, E.5
  • 38
    • 22244447130 scopus 로고    scopus 로고
    • Weighted Sequence motif as an improvd seed step in microRNA target prediction algorithms
    • Sactron O, Ola S, Saetrom P. Weighted Sequence motif as an improvd seed step in microRNA target prediction algorithms. RNA 2004, 11:995-1003.
    • (2004) RNA , vol.11 , pp. 995-1003
    • Sactron, O.1    Ola, S.2    Saetrom, P.3
  • 39
    • 0043123153 scopus 로고    scopus 로고
    • Vienna RNA secondary structure server
    • 10.1093/nar/gkg599, 169005, 12824340
    • Hofacker IL. Vienna RNA secondary structure server. Nucleic Acids Res 2003, 31:3429-3431. 10.1093/nar/gkg599, 169005, 12824340.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3429-3431
    • Hofacker, I.L.1
  • 40
    • 1642374097 scopus 로고    scopus 로고
    • Specificity of microRNA target selection in translational representation
    • Doench JG, Sharp PA. Specificity of microRNA target selection in translational representation. Genome Res 2004, 18:504-511.
    • (2004) Genome Res , vol.18 , pp. 504-511
    • Doench, J.G.1    Sharp, P.A.2
  • 41
    • 0019887799 scopus 로고
    • Identification of Common Molecular Subse-quences
    • 10.1016/0022-2836(81)90087-5, 7265238
    • Smith TF, Waterman MS. Identification of Common Molecular Subse-quences. J Mol Biol 1981, 147:195-197. 10.1016/0022-2836(81)90087-5, 7265238.
    • (1981) J Mol Biol , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 42
    • 0034954414 scopus 로고    scopus 로고
    • Classification and diagonostic prediction of cancers using gene expression profiling an Artificial Neural Networks
    • 10.1038/89044, 1282521, 11385503
    • Khan J, Wei JS, Ringner M, Saal LH, Laddnyi M, Antonescu CR, Peterson C, Melter PS. Classification and diagonostic prediction of cancers using gene expression profiling an Artificial Neural Networks. Nat Med 2001, 7:673-679. 10.1038/89044, 1282521, 11385503.
    • (2001) Nat Med , vol.7 , pp. 673-679
    • Khan, J.1    Wei, J.S.2    Ringner, M.3    Saal, L.H.4    Laddnyi, M.5    Antonescu, C.R.6    Peterson, C.7    Melter, P.S.8
  • 43
    • 19544377389 scopus 로고    scopus 로고
    • Classification of bacterial species from proteomic data using combinatorial approaches incorporating artificial neural networks, cluster analysis and principal components analysis
    • 10.1093/bioinformatics/bti368, 15746279
    • Lancashire L, Schmid O, Shah H, Ball G. Classification of bacterial species from proteomic data using combinatorial approaches incorporating artificial neural networks, cluster analysis and principal components analysis. Bioinformatics 2005, 21(10):2191-2199. 10.1093/bioinformatics/bti368, 15746279.
    • (2005) Bioinformatics , vol.21 , Issue.10 , pp. 2191-2199
    • Lancashire, L.1    Schmid, O.2    Shah, H.3    Ball, G.4


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