메뉴 건너뛰기




Volumn 10, Issue , 2009, Pages

Predicting functional upstream open reading frames in Saccharomyces cerevisiae

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL CONSERVATION; COMPUTATIONAL APPROACH; GENE ONTOLOGY ANNOTATIONS; HIGH SENSITIVITY; OPEN READING FRAME; YEAST SACCHAROMYCES CEREVISIAE;

EID: 75449118967     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-451     Document Type: Article
Times cited : (11)

References (55)
  • 1
    • 23944483135 scopus 로고    scopus 로고
    • Post-transcriptional control of gene expression: a genome-wide perspective
    • 10.1016/j.tibs.2005.07.005, 16054366
    • Mata J, Marguerat S, Bähler J. Post-transcriptional control of gene expression: a genome-wide perspective. Trends Biochem Sci 2005, 30(9):506-514. 10.1016/j.tibs.2005.07.005, 16054366.
    • (2005) Trends Biochem Sci , vol.30 , Issue.9 , pp. 506-514
    • Mata, J.1    Marguerat, S.2    Bähler, J.3
  • 2
    • 0035802386 scopus 로고    scopus 로고
    • Structural and functional features of eukaryotic mRNA untranslated regions
    • Pesole G, Mignone F, Gissi C, Grillo G, Licciulli F, Liuni S. Structural and functional features of eukaryotic mRNA untranslated regions. Gene 2001, 276:78-81.
    • (2001) Gene , vol.276 , pp. 78-81
    • Pesole, G.1    Mignone, F.2    Gissi, C.3    Grillo, G.4    Licciulli, F.5    Liuni, S.6
  • 3
    • 0035864389 scopus 로고    scopus 로고
    • Posttranscriptional Regulation of Human ADH5/FDH and Myf6 Gene Expression by Upstream AUG Codons
    • 10.1006/abbi.2000.2205, 11368338
    • Kwon HS, Lee DK, Lee JJ, Edenberg HJ, ho Ahn Y, Hur MW. Posttranscriptional Regulation of Human ADH5/FDH and Myf6 Gene Expression by Upstream AUG Codons. Arch Biochem Biophys 2001, 386(2):163-171. 10.1006/abbi.2000.2205, 11368338.
    • (2001) Arch Biochem Biophys , vol.386 , Issue.2 , pp. 163-171
    • Kwon, H.S.1    Lee, D.K.2    Lee, J.J.3    Edenberg, H.J.4    ho Ahn, Y.5    Hur, M.W.6
  • 4
    • 0042065288 scopus 로고    scopus 로고
    • Regulation of fungal gene expression via short open reading frames in the mRNA 5' untranslated region
    • 10.1046/j.1365-2958.2003.03622.x, 12890013
    • Vilela C, McCarthy JEG. Regulation of fungal gene expression via short open reading frames in the mRNA 5' untranslated region. Mol Microbiol 2003, 49(4):859-867. 10.1046/j.1365-2958.2003.03622.x, 12890013.
    • (2003) Mol Microbiol , vol.49 , Issue.4 , pp. 859-867
    • Vilela, C.1    McCarthy, J.E.G.2
  • 5
    • 0033153446 scopus 로고    scopus 로고
    • Post-termination ribosome interactions with the 5' UTR modulate yeast mRNA stability
    • 10.1093/emboj/18.11.3139, 1171395, 10357825
    • Vilela C, Ramirez CV, Linz B, Rodrigues-Pousada C, McCarthy JEG. Post-termination ribosome interactions with the 5' UTR modulate yeast mRNA stability. EMBO J 1999, 18(11):3139-3152. 10.1093/emboj/18.11.3139, 1171395, 10357825.
    • (1999) EMBO J , vol.18 , Issue.11 , pp. 3139-3152
    • Vilela, C.1    Ramirez, C.V.2    Linz, B.3    Rodrigues-Pousada, C.4    McCarthy, J.E.G.5
  • 6
    • 0030803256 scopus 로고    scopus 로고
    • Translational Regulation of Yeast GCN4. A Window on Factors that Control Initiator-tRNA Binding to the Ribosome
    • 10.1074/jbc.272.35.21661, 9268289
    • Hinnebusch AG. Translational Regulation of Yeast GCN4. A Window on Factors that Control Initiator-tRNA Binding to the Ribosome. J Biol Chem 1997, 272(35):21661-21664. 10.1074/jbc.272.35.21661, 9268289.
    • (1997) J Biol Chem , vol.272 , Issue.35 , pp. 21661-21664
    • Hinnebusch, A.G.1
  • 7
    • 0030667661 scopus 로고    scopus 로고
    • The 5'-untranslated region of the human muscle acylphosphatase mRNA has an inhibitory effect on protein expression
    • 10.1016/S0014-5793(97)01270-2, 9395090
    • Fiaschi T, Marzocchini R, Raugei G, Veggi D, Chiarugi P, Ramponi G. The 5'-untranslated region of the human muscle acylphosphatase mRNA has an inhibitory effect on protein expression. FEBS Lett 1997, 417:130-134. 10.1016/S0014-5793(97)01270-2, 9395090.
    • (1997) FEBS Lett , vol.417 , pp. 130-134
    • Fiaschi, T.1    Marzocchini, R.2    Raugei, G.3    Veggi, D.4    Chiarugi, P.5    Ramponi, G.6
  • 8
    • 17044409660 scopus 로고    scopus 로고
    • UAUG and uORFs in human and rodent 5' untranslated mRNAs
    • 10.1016/j.gene.2004.11.041, 15777708
    • Iacono M, Mignone F, Pesole G. uAUG and uORFs in human and rodent 5' untranslated mRNAs. Gene 2005, 349:97-105. 10.1016/j.gene.2004.11.041, 15777708.
    • (2005) Gene , vol.349 , pp. 97-105
    • Iacono, M.1    Mignone, F.2    Pesole, G.3
  • 9
    • 0034459468 scopus 로고    scopus 로고
    • Upstream Open Reading Frames as Regulators of mRNA Translation
    • 10.1128/MCB.20.23.8635-8642.2000, 86464, 11073965
    • Morris DR, Geballe AP. Upstream Open Reading Frames as Regulators of mRNA Translation. Mol Cell Biol 2000, 20(23):8635-8642. 10.1128/MCB.20.23.8635-8642.2000, 86464, 11073965.
    • (2000) Mol Cell Biol , vol.20 , Issue.23 , pp. 8635-8642
    • Morris, D.R.1    Geballe, A.P.2
  • 10
    • 0025930710 scopus 로고
    • AUG codons in the RNA leader sequences of the yeast PET genes CBS1 and SCO1 have no influence on translation efficiency
    • 10.1007/BF00334773, 1782674
    • Krummeck G, Gottenöf T, Rödel G. AUG codons in the RNA leader sequences of the yeast PET genes CBS1 and SCO1 have no influence on translation efficiency. Curr Genet 1991, 20:465-469. 10.1007/BF00334773, 1782674.
    • (1991) Curr Genet , vol.20 , pp. 465-469
    • Krummeck, G.1    Gottenöf, T.2    Rödel, G.3
  • 11
    • 0026342613 scopus 로고
    • An Analysis of Vertebrate mRNA Sequences: Intimations of Translational Control
    • 10.1083/jcb.115.4.887, 2289952, 1955461
    • Kozak M. An Analysis of Vertebrate mRNA Sequences: Intimations of Translational Control. J Cell Biol 1991, 115(4):887-903. 10.1083/jcb.115.4.887, 2289952, 1955461.
    • (1991) J Cell Biol , vol.115 , Issue.4 , pp. 887-903
    • Kozak, M.1
  • 12
    • 0032967120 scopus 로고    scopus 로고
    • Translational control of growth factor and proto-oncogene expression
    • 10.1016/S1357-2725(98)00133-2, 10216945
    • Willis AE. Translational control of growth factor and proto-oncogene expression. Int J Biochem Cell Biol 1999, 31:73-86. 10.1016/S1357-2725(98)00133-2, 10216945.
    • (1999) Int J Biochem Cell Biol , vol.31 , pp. 73-86
    • Willis, A.E.1
  • 13
    • 84870741733 scopus 로고    scopus 로고
    • Cancer Research UK
    • Cancer Research UK. , http://www.cancerhelp.org.uk/help/default.asp?page=6412
  • 14
    • 0033061571 scopus 로고    scopus 로고
    • Initiation of translation in prokaryotes and eukaryotes
    • 10.1016/S0378-1119(99)00210-3, 10395892
    • Kozak M. Initiation of translation in prokaryotes and eukaryotes. Gene 1999, 234:187-208. 10.1016/S0378-1119(99)00210-3, 10395892.
    • (1999) Gene , vol.234 , pp. 187-208
    • Kozak, M.1
  • 15
    • 0031975482 scopus 로고    scopus 로고
    • An activating splice donor mutation in the thrombopoietin gene causes hereditary thrombocythaemia
    • 10.1038/ng0198-49, 9425899
    • Wiestner A, Schlemper RJ, Maas APC, Skoda RC. An activating splice donor mutation in the thrombopoietin gene causes hereditary thrombocythaemia. Nat Genet 1998, 18:49-52. 10.1038/ng0198-49, 9425899.
    • (1998) Nat Genet , vol.18 , pp. 49-52
    • Wiestner, A.1    Schlemper, R.J.2    Maas, A.P.C.3    Skoda, R.C.4
  • 16
    • 34548512248 scopus 로고    scopus 로고
    • Identification of putative regulatory upstream ORFs in the yeast genome using heuristics and evolutionary conservation
    • 10.1186/1471-2105-8-295, 1964767, 17686169
    • Cvijovic M, Dalevi D, Bilsland E, Kemp GJL, Sunnerhagen P. Identification of putative regulatory upstream ORFs in the yeast genome using heuristics and evolutionary conservation. BMC Bioinformatics 2007, 8:295. 10.1186/1471-2105-8-295, 1964767, 17686169.
    • (2007) BMC Bioinformatics , vol.8 , pp. 295
    • Cvijovic, M.1    Dalevi, D.2    Bilsland, E.3    Kemp, G.J.L.4    Sunnerhagen, P.5
  • 17
    • 50549102501 scopus 로고    scopus 로고
    • A First Step towards Learning which uORFs Regulate Gene Expression
    • Selpi, Bryant CH, Kemp GJL, Cvijovic M. A First Step towards Learning which uORFs Regulate Gene Expression. Journal of Integrative Bioinformatics 2006, 3(2):31., http://journal.imbio.de/index.php?paper_id=31
    • (2006) Journal of Integrative Bioinformatics , vol.3 , Issue.2 , pp. 31
    • Selpi1    Bryant, C.H.2    Kemp, G.J.L.3    Cvijovic, M.4
  • 18
    • 33845223334 scopus 로고    scopus 로고
    • A large-scale full-length cDNA analysis to explore the budding yeast transcriptome
    • 10.1073/pnas.0605645103, 1693835, 17101987
    • Miura F, Kawaguchi N, Sese J, Toyoda A, Hattori M, Morishita S. A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. Proc Natl Acad Sci USA 2006, 103(47):17846-17851. 10.1073/pnas.0605645103, 1693835, 17101987.
    • (2006) Proc Natl Acad Sci USA , vol.103 , Issue.47 , pp. 17846-17851
    • Miura, F.1    Kawaguchi, N.2    Sese, J.3    Toyoda, A.4    Hattori, M.5    Morishita, S.6
  • 19
    • 2542454374 scopus 로고    scopus 로고
    • The Aleph Manual
    • Srinivasan A. The Aleph Manual. 1999, , http://web.comlab.ox.ac.uk/oucl/research/areas/machlearn/Aleph/
    • (1999)
    • Srinivasan, A.1
  • 20
    • 0028429573 scopus 로고
    • Inductive Logic Programming: Theory and Methods
    • Muggleton S, Raedt LD. Inductive Logic Programming: Theory and Methods. J Log Program 1994, 19/20:629-679.
    • (1994) J Log Program , vol.19-20 , pp. 629-679
    • Muggleton, S.1    Raedt, L.D.2
  • 21
    • 0004080766 scopus 로고
    • Inductive Logic Programming: Techniques and Applications
    • Lavrač N, Džeroski S. Inductive Logic Programming: Techniques and Applications. Ellis Horwood 1994,
    • (1994) Ellis Horwood
    • Lavrač, N.1    Džeroski, S.2
  • 23
    • 0029407394 scopus 로고
    • Applications of Inductive Logic Programming
    • Bratko I, Muggleton SH. Applications of Inductive Logic Programming. Commun ACM 1995, 38(11):65-70.
    • (1995) Commun ACM , vol.38 , Issue.11 , pp. 65-70
    • Bratko, I.1    Muggleton, S.H.2
  • 24
    • 0009720964 scopus 로고    scopus 로고
    • Scientific Knowledge Discovery Using Inductive Logic Programming
    • Muggleton S. Scientific Knowledge Discovery Using Inductive Logic Programming. Commun ACM 1999, 42(11):42-46.
    • (1999) Commun ACM , vol.42 , Issue.11 , pp. 42-46
    • Muggleton, S.1
  • 27
    • 84888276476 scopus 로고    scopus 로고
    • ENSEMBL Database at BioMart
    • ENSEMBL Database at BioMart. , http://www.biomart.org/biomart/martview/
  • 28
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: The European Molecular Biology Open Software Suite
    • 10.1016/S0168-9525(00)02024-2, 10827456
    • Rice P, Longden I, Bleasby A. EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet 2000, 16(6):276-277. 10.1016/S0168-9525(00)02024-2, 10827456.
    • (2000) Trends Genet , vol.16 , Issue.6 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 29
    • 84874650886 scopus 로고    scopus 로고
    • Comparative Genomic Study of upstream Open Reading Frames
    • Chalmers University of Technology, Accessed 3 May 2006
    • Cvijovic M. Comparative Genomic Study of upstream Open Reading Frames. Online Masters Thesis 2005, Chalmers University of Technology, Accessed 3 May 2006., http://www.math.chalmers.se/Stat/Bioinfo/Master/Theses/2005/2.pdf
    • (2005) Online Masters Thesis
    • Cvijovic, M.1
  • 30
    • 0019852740 scopus 로고
    • Possible role of flanking nucleotides in recognition of the AUG initiator codon by eukaryotic ribosomes
    • 10.1093/nar/9.20.5233, 327517, 7301588
    • Kozak M. Possible role of flanking nucleotides in recognition of the AUG initiator codon by eukaryotic ribosomes. Nucleic Acids Res 1981, 9(20):5233-5252. 10.1093/nar/9.20.5233, 327517, 7301588.
    • (1981) Nucleic Acids Res , vol.9 , Issue.20 , pp. 5233-5252
    • Kozak, M.1
  • 31
    • 27144555357 scopus 로고    scopus 로고
    • Regulation of translation via mRNA structure in prokaryotes and eukaryotes
    • 10.1016/j.gene.2005.06.037, 16213112
    • Kozak M. Regulation of translation via mRNA structure in prokaryotes and eukaryotes. Gene 2005, 361:13-37. 10.1016/j.gene.2005.06.037, 16213112.
    • (2005) Gene , vol.361 , pp. 13-37
    • Kozak, M.1
  • 32
    • 27644556090 scopus 로고    scopus 로고
    • Identification and characterization of upstream open reading frames (uORF) in the 5' untranslated regions (UTR) of genes in Saccharomyces cerevisiae
    • 10.1007/s00294-005-0001-x, 16012843
    • Zhang Z, Dietrich FS. Identification and characterization of upstream open reading frames (uORF) in the 5' untranslated regions (UTR) of genes in Saccharomyces cerevisiae. Curr Genet 2005, 48:77-87. 10.1007/s00294-005-0001-x, 16012843.
    • (2005) Curr Genet , vol.48 , pp. 77-87
    • Zhang, Z.1    Dietrich, F.S.2
  • 34
    • 0038349948 scopus 로고    scopus 로고
    • Sequencing and comparison of yeast species to identify genes and regulatory elements
    • 10.1038/nature01644, 12748633
    • Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 2003, 423:241-254. 10.1038/nature01644, 12748633.
    • (2003) Nature , vol.423 , pp. 241-254
    • Kellis, M.1    Patterson, N.2    Endrizzi, M.3    Birren, B.4    Lander, E.S.5
  • 35
    • 84888276843 scopus 로고    scopus 로고
    • Upstream sequences of Sacchamomyces paradoxus
    • Upstream sequences of Sacchamomyces paradoxus. , ftp://genome-ftp.stanford.edu/pub/yeast/sequence/fungal_genomes/S_parado xus/MIT/orf_dna/utr5_500.fasta.gz
  • 36
    • 84888282369 scopus 로고    scopus 로고
    • Upstream sequences of Saccharomyces mikatae
    • Upstream sequences of Saccharomyces mikatae. , ftp://genome-ftp.stanford.edu/pub/yeast/sequence/fungal_genomes/S_mikata e/MIT/orf_dna/utr5_500.fasta.gz
  • 37
    • 84888282369 scopus 로고    scopus 로고
    • Upstream sequences of Saccharomyces bayanus
    • Upstream sequences of Saccharomyces bayanus. , ftp://genome-ftp.stanford.edu/pub/yeast/sequence/fungal_genomes/S_bayanu s/MIT/orf_dna/utr5_500.fasta.gz
  • 40
    • 84886470331 scopus 로고    scopus 로고
    • GO website
    • GO website. , http://www.geneontology.org/GO.downloads.ontology.shtml
  • 41
    • 84888274467 scopus 로고    scopus 로고
    • GO annotations for yeast genes
    • GO annotations for yeast genes. , ftp://genome-ftp.stanford.edu/pub/yeast/data_download/literature_curatio n/gene_association.sgd.gz
  • 43
    • 84874658531 scopus 로고    scopus 로고
    • GO Slim Mapper
    • GO Slim Mapper. , http://www.yeastgenome.org/help/goslimhelp.html
  • 44
    • 0345602742 scopus 로고    scopus 로고
    • Homodirectional changes in transcriptome composition and mRNA translation induced by rapamycin and heat shock
    • 10.1038/nsb1015, 14608375
    • Preiss T, Baron-Benhamou J, Ansorge W, Hentze MW. Homodirectional changes in transcriptome composition and mRNA translation induced by rapamycin and heat shock. Nat Struct Biol 2003, 10(12):1039-1047. 10.1038/nsb1015, 14608375.
    • (2003) Nat Struct Biol , vol.10 , Issue.12 , pp. 1039-1047
    • Preiss, T.1    Baron-Benhamou, J.2    Ansorge, W.3    Hentze, M.W.4
  • 45
    • 33749379882 scopus 로고    scopus 로고
    • Global Translational Responses to Oxidative Stress Impact upon Multiple Levels of Protein Synthesis
    • 10.1074/jbc.M601545200, 16849329
    • Shenton D, Smirnova JB, Selley JN, Carroll K, Hubbard SJ, Pavitt GD, Ashe MP, Grant CM. Global Translational Responses to Oxidative Stress Impact upon Multiple Levels of Protein Synthesis. J Biol Chem 2006, 281(39):29011-29021. 10.1074/jbc.M601545200, 16849329.
    • (2006) J Biol Chem , vol.281 , Issue.39 , pp. 29011-29021
    • Shenton, D.1    Smirnova, J.B.2    Selley, J.N.3    Carroll, K.4    Hubbard, S.J.5    Pavitt, G.D.6    Ashe, M.P.7    Grant, C.M.8
  • 46
    • 27144465421 scopus 로고    scopus 로고
    • Global Gene Expression Profiling Reveals Widespread yet Distinctive Translational Responses to Different Eukaryotic Translation Initiation Factor 2B-Targeting Stress Pathways
    • 10.1128/MCB.25.21.9340-9349.2005, 1265828, 16227585
    • Smirnova JB, Selley JN, Sanchez-Cabo F, Carroll K, Eddy AA, McCarthy JEG, Hubbard SJ, Pavitt GD, Grant CM, Ashe MP. Global Gene Expression Profiling Reveals Widespread yet Distinctive Translational Responses to Different Eukaryotic Translation Initiation Factor 2B-Targeting Stress Pathways. Mol Cell Biol 2005, 25(21):9340-9349. 10.1128/MCB.25.21.9340-9349.2005, 1265828, 16227585.
    • (2005) Mol Cell Biol , vol.25 , Issue.21 , pp. 9340-9349
    • Smirnova, J.B.1    Selley, J.N.2    Sanchez-Cabo, F.3    Carroll, K.4    Eddy, A.A.5    McCarthy, J.E.G.6    Hubbard, S.J.7    Pavitt, G.D.8    Grant, C.M.9    Ashe, M.P.10
  • 47
    • 84949207675 scopus 로고    scopus 로고
    • Learning from Positive Data. In Inductive Logic Programming Workshop, of Lect Notes Comput Sci
    • Springer, Muggleton S
    • Muggleton S. Learning from Positive Data. In Inductive Logic Programming Workshop, of Lect Notes Comput Sci. 1996, 1314:358-376. Springer, Muggleton S.
    • (1996) , vol.1314 , pp. 358-376
    • Muggleton, S.1
  • 48
    • 33646417617 scopus 로고    scopus 로고
    • Using Inductive Logic Programming for Predicting Protein-Protein Interactions from Multiple Genomic Data. In PKDD, of Lect Notes Comput Sci
    • Springer, Jorge A, Torgo L, Brazdil P, Camacho R, Gama J
    • Tran TN, Satou K, Ho TB. Using Inductive Logic Programming for Predicting Protein-Protein Interactions from Multiple Genomic Data. In PKDD, of Lect Notes Comput Sci. 2005, 3721:321-330. Springer, Jorge A, Torgo L, Brazdil P, Camacho R, Gama J.
    • (2005) , vol.3721 , pp. 321-330
    • Tran, T.N.1    Satou, K.2    Ho, T.B.3
  • 49
    • 0042128690 scopus 로고    scopus 로고
    • Functional Discrimination of Gene Expression Patterns in Terms of the Gene Ontology
    • Badea L. Functional Discrimination of Gene Expression Patterns in Terms of the Gene Ontology. Pacific Symposium on Biocomputing 2003, 565-576.
    • (2003) Pacific Symposium on Biocomputing , pp. 565-576
    • Badea, L.1
  • 50
    • 6944251719 scopus 로고    scopus 로고
    • Predicting gene function in Saccharomyces cerevisiae
    • Clare A, King RD. Predicting gene function in Saccharomyces cerevisiae. Bioinformatics 2003, 19(Suppl 2):ii42-ii49.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 2
    • Clare, A.1    King, R.D.2
  • 52
    • 34547774618 scopus 로고    scopus 로고
    • Dual Modes of Natural Selection on Upstream Open Reading Frames
    • 10.1093/molbev/msm093, 17494029
    • Neafsey DE, Galagan JE. Dual Modes of Natural Selection on Upstream Open Reading Frames. Mol Biol Evol 2007, 24(8):1744-1751. 10.1093/molbev/msm093, 17494029.
    • (2007) Mol Biol Evol , vol.24 , Issue.8 , pp. 1744-1751
    • Neafsey, D.E.1    Galagan, J.E.2
  • 53
    • 33646136452 scopus 로고    scopus 로고
    • Evidence for conservation and selection of upstream open reading frames suggests probable encoding of bioactive peptides
    • 1402274, 16438715
    • Crowe ML, Wang XQ, Rothnagel JA. Evidence for conservation and selection of upstream open reading frames suggests probable encoding of bioactive peptides. BMC Genomics 2006, 7(16). 1402274, 16438715.
    • (2006) BMC Genomics , vol.7 , Issue.16
    • Crowe, M.L.1    Wang, X.Q.2    Rothnagel, J.A.3
  • 54
    • 0023988840 scopus 로고
    • MRNA Structures Influencing Translation in the Yeast Saccharomyces cerevisiae
    • 363319, 2837649
    • Baim SB, Sherman F. mRNA Structures Influencing Translation in the Yeast Saccharomyces cerevisiae. Molecular and Cellular Biology 1988, 8(4):1591-1601. 363319, 2837649.
    • (1988) Molecular and Cellular Biology , vol.8 , Issue.4 , pp. 1591-1601
    • Baim, S.B.1    Sherman, F.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.