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Volumn 107, Issue 5, 2010, Pages 865-875

Integrative analysis using proteome and transcriptome data from yeast to unravel regulatory patterns at post-transcriptional level

Author keywords

Correlation; Proteome; Saccharomyces cerevisiae; Transcriptome

Indexed keywords

AMINO ACID BIOSYNTHETIC PATHWAYS; CATEGORIZATION METHODS; CORRELATION; DATA SETS; GENE FUNCTION; GOOD CORRELATIONS; INTEGRATIVE ANALYSIS; POSITIVE CORRELATIONS; POST-TRANSCRIPTIONAL; PROTEIN LEVEL; PROTEOMES; REGULATORY PATTERNS; SACCHAROMYCES CEREVISIAE; TRANSCRIPTOME; TRANSCRIPTOMES; TRANSLATIONAL REGULATION; UNTRANSLATED REGIONS;

EID: 77958561690     PISSN: 00063592     EISSN: 10970290     Source Type: Journal    
DOI: 10.1002/bit.22868     Document Type: Article
Times cited : (15)

References (34)
  • 1
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • Aebersold R, Mann M. 2003. Mass spectrometry-based proteomics. Nature 422(6928): 198-207.
    • (2003) Nature , vol.422 , Issue.6928 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 2
    • 0041817645 scopus 로고    scopus 로고
    • Translational selection and yeast proteome evolution
    • Akashi H. 2003. Translational selection and yeast proteome evolution. Genetics 164(4): 1291-1303.
    • (2003) Genetics , vol.164 , Issue.4 , pp. 1291-1303
    • Akashi, H.1
  • 3
    • 1542399989 scopus 로고    scopus 로고
    • FatiGO: A web tool for finding significant associations of Gene Ontology terms with groups of genes
    • Al-Shahrour F, Diaz-Uriarte R, Dopazo J. 2004. FatiGO: A web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics 20(4): 578-580.
    • (2004) Bioinformatics , vol.20 , Issue.4 , pp. 578-580
    • Al-Shahrour, F.1    Diaz-Uriarte, R.2    Dopazo, J.3
  • 5
    • 33748377124 scopus 로고    scopus 로고
    • Quantification of protein half-lives in the budding yeast proteome
    • Belle A, Tanay A, Bitincka L, Shamir R, Oshea EK. 2006. Quantification of protein half-lives in the budding yeast proteome. Proc Natl Acad Sci USA 103(35): 13004-13009.
    • (2006) Proc Natl Acad Sci USA , vol.103 , Issue.35 , pp. 13004-13009
    • Belle, A.1    Tanay, A.2    Bitincka, L.3    Shamir, R.4    Oshea, E.K.5
  • 6
    • 10944232800 scopus 로고    scopus 로고
    • Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale
    • Beyer A, Hollunder J, Nasheuer HP, Willhelm T. 2004. Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale. Mol Cell Proteomics 3(11): 1083-1092.
    • (2004) Mol Cell Proteomics , vol.3 , Issue.11 , pp. 1083-1092
    • Beyer, A.1    Hollunder, J.2    Nasheuer, H.P.3    Willhelm, T.4
  • 7
    • 33645813378 scopus 로고    scopus 로고
    • Mass spectrometry and protein analysis
    • Domon B, Aebersold R. 2006. Mass spectrometry and protein analysis. Science 312(5771): 212-217.
    • (2006) Science , vol.312 , Issue.5771 , pp. 212-217
    • Domon, B.1    Aebersold, R.2
  • 8
    • 4644280499 scopus 로고    scopus 로고
    • Solving the riddle of codon usage preferences: A test for translational selection
    • dos Reis M, Savva R, Wernisch L. 2004. Solving the riddle of codon usage preferences: A test for translational selection. Nucleic Acid Res 39: 5036-5044.
    • (2004) Nucleic Acid Res , vol.39 , pp. 5036-5044
    • dos Reis, M.1    Savva, R.2    Wernisch, L.3
  • 10
    • 0035999672 scopus 로고    scopus 로고
    • Analysis of mRNA expression and protein abundance data: An approach for the comparison of the enrichment of features in the cellular population of protein and transcripts
    • Greenbaum D, Jansen R, Gerstein M. 2002. Analysis of mRNA expression and protein abundance data: An approach for the comparison of the enrichment of features in the cellular population of protein and transcripts. Bioinformatics 18(4): 585-596.
    • (2002) Bioinformatics , vol.18 , Issue.4 , pp. 585-596
    • Greenbaum, D.1    Jansen, R.2    Gerstein, M.3
  • 11
    • 0141920354 scopus 로고    scopus 로고
    • Comparing protein abundance and mRNA expression levels on a genomic scale
    • Greenbaum D, Colangelo C, Williams K, Gerstein M. 2003. Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol 4(9): 117.
    • (2003) Genome Biol , vol.4 , Issue.9 , pp. 117
    • Greenbaum, D.1    Colangelo, C.2    Williams, K.3    Gerstein, M.4
  • 12
    • 0036545614 scopus 로고    scopus 로고
    • Complementary profiling of gene expression at transcriptome and proteome levels in Saccharomyces cerevisiae
    • Griffin TL, Gygi SP, Ideker T, Rist B, Eng J, Hood L, Aebersold R. 2002. Complementary profiling of gene expression at transcriptome and proteome levels in Saccharomyces cerevisiae. Mol Cell Proteomics 1: 323-333.
    • (2002) Mol Cell Proteomics , vol.1 , pp. 323-333
    • Griffin, T.L.1    Gygi, S.P.2    Ideker, T.3    Rist, B.4    Eng, J.5    Hood, L.6    Aebersold, R.7
  • 13
    • 0033016717 scopus 로고    scopus 로고
    • Correlation between protein and mRNA abundance in yeast
    • Gygi SP, Rochon Y, Franza BR, Aebersold R. 1999. Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 19(3): 1720-1730.
    • (1999) Mol Cell Biol , vol.19 , Issue.3 , pp. 1720-1730
    • Gygi, S.P.1    Rochon, Y.2    Franza, B.R.3    Aebersold, R.4
  • 14
    • 65249176527 scopus 로고    scopus 로고
    • Stress-dependent coordination of transcriptome and translatome in yeast
    • Halbeisen RE, Gerber AP. 2009. Stress-dependent coordination of transcriptome and translatome in yeast. PLoS Biol 7(5): e1000105.
    • (2009) PLoS Biol , vol.7 , Issue.5
    • Halbeisen, R.E.1    Gerber, A.P.2
  • 15
    • 0031840530 scopus 로고    scopus 로고
    • Identification of gelseparatedproteins by liquid chromatography-electrospray tandem mass spectrometry: Comparison of methods and their limitations
    • Haynes PA, Fripp N, Aebersold R. 1998. Identification of gelseparatedproteins by liquid chromatography-electrospray tandem mass spectrometry: Comparison of methods and their limitations. Electrophoresis 19: 939-945.
    • (1998) Electrophoresis , vol.19 , pp. 939-945
    • Haynes, P.A.1    Fripp, N.2    Aebersold, R.3
  • 16
    • 0035997269 scopus 로고    scopus 로고
    • Proteomics and its trends facing nature's complexity
    • Hochstrasser D, Sanchez JC, Appel RD. 2002. Proteomics and its trends facing nature's complexity. Proteomics 2: 807-812.
    • (2002) Proteomics , vol.2 , pp. 807-812
    • Hochstrasser, D.1    Sanchez, J.C.2    Appel, R.D.3
  • 17
    • 1442329652 scopus 로고    scopus 로고
    • Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae
    • Hurowitz E, Brown P. 2003. Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae. Genome Biol 5(1): R2.
    • (2003) Genome Biol , vol.5 , Issue.1
    • Hurowitz, E.1    Brown, P.2
  • 19
    • 0035793042 scopus 로고    scopus 로고
    • Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection
    • Li C, Wong WH. 2001. Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection. Proc Natl Acad Sci 98: 31-36.
    • (2001) Proc Natl Acad Sci , vol.98 , pp. 31-36
    • Li, C.1    Wong, W.H.2
  • 20
    • 0037338365 scopus 로고    scopus 로고
    • Proteomic analysis of post-translational modifications
    • Mann M, Jensen ON. 2003. Proteomic analysis of post-translational modifications. Nat Biotechnol 21: 255-261.
    • (2003) Nat Biotechnol , vol.21 , pp. 255-261
    • Mann, M.1    Jensen, O.N.2
  • 21
    • 75349102148 scopus 로고    scopus 로고
    • Universal function-specificity of codon usage
    • Najafabadi HS, Goodarzi H, Salavati R. 2009. Universal function-specificity of codon usage. Nucleic Acids Res 37(21): 7014-7023.
    • (2009) Nucleic Acids Res , vol.37 , Issue.21 , pp. 7014-7023
    • Najafabadi, H.S.1    Goodarzi, H.2    Salavati, R.3
  • 22
    • 38349164135 scopus 로고    scopus 로고
    • Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae
    • Nielsen J, Jewett MC. 2008. Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae. FEMS Yeast Res 8(1): 122-131.
    • (2008) FEMS Yeast Res , vol.8 , Issue.1 , pp. 122-131
    • Nielsen, J.1    Jewett, M.C.2
  • 23
    • 14544268137 scopus 로고    scopus 로고
    • Uncovering transcriptional regulation of metabolism by using metabolic network topology
    • Patil KR, Nielsen J. 2005. Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proc Natl Acad Sci 102(8): 2685-2689.
    • (2005) Proc Natl Acad Sci , vol.102 , Issue.8 , pp. 2685-2689
    • Patil, K.R.1    Nielsen, J.2
  • 24
    • 0345602742 scopus 로고    scopus 로고
    • Homodirectional changes in transcriptome composition and mRNA translation induced by rapamycin and heat shock
    • Preiss T, Baron-Benhamou J, Ansorge W, Hentze WM. 2003. Homodirectional changes in transcriptome composition and mRNA translation induced by rapamycin and heat shock. Nat Struct Biol 10(12): 1039-1047.
    • (2003) Nat Struct Biol , vol.10 , Issue.12 , pp. 1039-1047
    • Preiss, T.1    Baron-Benhamou, J.2    Ansorge, W.3    Hentze, W.M.4
  • 25
    • 34548093996 scopus 로고    scopus 로고
    • A catalog of stability-associated sequence elements in 3' UTRs of yeast mRNAs
    • Shalgi R, Lapidot M, Shamir R, Pilpel Y. 2005. A catalog of stability-associated sequence elements in 3' UTRs of yeast mRNAs. Genome Biol 6(10): R86.
    • (2005) Genome Biol , vol.6 , Issue.10
    • Shalgi, R.1    Lapidot, M.2    Shamir, R.3    Pilpel, Y.4
  • 26
    • 0023650543 scopus 로고
    • The codon adaptation index-A measure of directional synonymous codon usage bias, and its potential applications
    • Sharp PM, Li WH. 1987. The codon adaptation index-A measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acid Res 15: 1281-1295.
    • (1987) Nucleic Acid Res , vol.15 , pp. 1281-1295
    • Sharp, P.M.1    Li, W.H.2
  • 28
    • 37849033856 scopus 로고    scopus 로고
    • Determinants of protein abundance and translation efficiency in S. cerevisiae
    • Tuller T, Kupiec M, Ruppin E. 2007. Determinants of protein abundance and translation efficiency in S. cerevisiae. PLoS Comput Biol 3(12): e248.
    • (2007) PLoS Comput Biol , vol.3 , Issue.12
    • Tuller, T.1    Kupiec, M.2    Ruppin, E.3
  • 29
    • 38649098761 scopus 로고    scopus 로고
    • Characterization of global yeast quantitative proteome data generated from the wild-type and glucose repression Saccharomyces cerevisiae strains: The comparison of two quantitative methods
    • Usaite R, Wohlschlegel J, Venable JD, Park SK, Nielsen J, Olsson L, Yates JR III. 2008. Characterization of global yeast quantitative proteome data generated from the wild-type and glucose repression Saccharomyces cerevisiae strains: The comparison of two quantitative methods. J Proteome Res 7: 266-275.
    • (2008) J Proteome Res , vol.7 , pp. 266-275
    • Usaite, R.1    Wohlschlegel, J.2    Venable, J.D.3    Park, S.K.4    Nielsen, J.5    Olsson, L.6    Yates III, J.R.7
  • 30
    • 73149091660 scopus 로고    scopus 로고
    • Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator
    • Usaite R, Jewett MC, Oliveira AP, Yates JR III, Olsson L, Nielsen J. 2009. Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator. Mol Syst Biol 5(319): 319.
    • (2009) Mol Syst Biol , vol.5 , Issue.319 , pp. 319
    • Usaite, R.1    Jewett, M.C.2    Oliveira, A.P.3    Yates III, J.R.4    Olsson, L.5    Nielsen, J.6
  • 33
    • 0242669945 scopus 로고    scopus 로고
    • Regulation of mRNA translation by 5'- and 3'-UTR-binding factors
    • Wilkie GS, Dickson KS, Gray NK. 2003. Regulation of mRNA translation by 5'- and 3'-UTR-binding factors. Trends Biochem Sci 28(4): 182-188.
    • (2003) Trends Biochem Sci , vol.28 , Issue.4 , pp. 182-188
    • Wilkie, G.S.1    Dickson, K.S.2    Gray, N.K.3
  • 34
    • 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 EJ, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, Kellis M. 2005. Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature 434(7031): 338-345.
    • (2005) Nature , vol.434 , Issue.7031 , 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


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