Comparing protein abundance and mRNA expression levels on a genomic scale

Genome Biology

Volumn 4, Issue 9, 2003, Pages

  Greenbaum, Dov ^a   Colangelo, Christopher ^b   Williams, Kenneth ^b   Gerstein, Mark ^b,c  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b YALE UNIVERSITY   (United States)

^c Yale University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; MESSENGER RNA; PROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN;

CATION EXCHANGE; CODON USAGE; CONTROLLED STUDY; CORRELATION ANALYSIS; FLUORESCENCE ANALYSIS; GENOMICS; ISOELECTRIC FOCUSING; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NONHUMAN; OPEN READING FRAME; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN EXPRESSION; PROTEIN PROCESSING; PROTEOMICS; QUANTITATIVE ANALYSIS; REVERSED PHASE HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; REVIEW; RNA ANALYSIS; RNA TRANSCRIPTION; RNA TRANSLATION; SACCHAROMYCES CEREVISIAE; TANDEM MASS SPECTROMETRY; TWO DIMENSIONAL GEL ELECTROPHORESIS; YEAST;

ANIMALS; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; GENE EXPRESSION; GENOMICS; HUMANS; MASS SPECTROMETRY; PROTEINS; PROTEOMICS; RNA, MESSENGER;

EUKARYOTA; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0141920354     PISSN: 14656906     EISSN: None     Source Type: Journal    
DOI: 10.1186/gb-2003-4-9-117     Document Type: Review

References (52)

1. O'Farrell PH: High resolution two-dimensional electrophoresis of proteins. J Biol Chem 1975, 2504:4007-4021.
2. Klose J: Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals. Humangenetik 1975, 26:231-243.
3. Hatzimanikatis V, Choe LH, Lee KH: Proteomics: theoretical and experimental considerations. Biotechnol Prog 1999, 15:312-318.
4. Schena M, Heller RA, Theriault TP, Konrad K, Lachenmeier E, Davis RW: Microarrays: biotechnology's discovery platform for functional genomics. Trends Biotechnol 1998, 16:301-306.
5. McGall GH, Christians FC: High-density genechip oligonucleotide probe arrays. Adv Biochem Eng Biotechnol 2002, 77:21-42.
6. Brown PO, Botstein D: Exploring the new world of the genome with DNA microarrays. Nat Genet 1999, 21:33-37.
7. Gygi SP, Rochon Y, Franza BR, Aebersold R: Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 1999, 19:1720-1730.
8. Gygi SP, Corthals GL, Zhang Y, Rochon Y, Aebersold R: Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc Natl Acad Sci USA 2000, 97:9390-9395.
9. Tonge R, Shaw J, Middleton B, Rowlinson R, Rayner S, Young J, Pognan F, Hawkins E, Currie I, Davison M: Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology. Proteomics 2001, 1:377-396.
10. Gharbi S, Gaffney P, Yang A, Zvelebil MJ, Cramer R, Waterfield MD, Timms JF: Evaluation of two-dimensional differential gel electrophoresis for proteomic expression analysis of a model breast cancer cell system. Mol Cell Proteomics 2002, 1:91-98.
11. Zhou G, Li H, DeCamp D, Chen S, Shu H, Gong Y, Flaig M, Gillespie JW, Hu N, Taylor PR, et al.: 2D differential in-gel electrophoresis for the identification of esophageal scans cell cancer-specific protein markers. Mol Cell Proteomics 2002, 1:117-124.
12. Adam BL, Vlahou A, Semmes OJ, Wright GL Jr.: Proteomic approaches to biomarker discovery in prostate and bladder cancers. Proteomics 2001, 1:1264-1270.
13. Issaq HJ, Veenstra TD, Conrads TP, Felschow D: The SELDI-TOF MS approach to proteomics: protein profiling and biomarker identification. Biochem Biophys Res Commun 2002, 292:587-592.
14. Petricoin EF, Ardekani AM, Hitt BA, Levine PJ, Fusaro VA, Steinberg SM, Mills GB, Simone C, Fishman DA, Kohn EC, et al: Use of proteomic patterns in serum to identify ovarian cancer. Lancet 2002, 359:572-577.
15. Li J, Zhang Z, Rosenzweig J, Wang YY, Chan DW: Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clin Chem 2002, 48:1296-1304.
16. Wu B, Abbott T, Fishman D, McMurray W, Mor G, Stone K, Ward D, Williams K, Zhao H: Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data. Bioinformatics, in press.
17. SwissProt [http://www.expasy.ch/sprot/]
18. Han DK, Eng J, Zhou H, Aebersold R: Quantitative profiling of differentiation-induced microsomal proteins using isotopecoded affinity tags and mass spectrometry. Nat Biotechnol 2001, 19:946-951.
19. Wolters, DA Washburn MP, Yates JR 3rd: An automated multidimensional protein identification technology for shotgun proteomics. Anal Chem 2001, 73:5683-5690.
20. Washburn MP, Ulaszek R, Deciu C, Schieltz DM, Yates JR 3rd: Analysis of quantitative proteomic data generated via multidimensional protein identification technology. Anal Chem 2002, 74:1650-1657.
21. Washburn MP, Koller A, Oshiro G, Ulaszek RR, Plouffe D, Deciu C, Winzeler E, Yates JR 3rd: Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 2003, 100:3107-3112.
22. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, et al: Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 1999, 286:531-537.
23. Macgregor PF, Squire JA: Application of microarrays to the analysis of gene expression in cancer. Clin Chem 2002, 48:1170-1177.
24. Anderson L, Seilhamer J: A comparison of selected mRNA and protein abundances in human liver. Electrophoresis 1997, 18:533-537.
25. Lichtinghagen R, Musholt PB, Lein M, Romer A, Rudolph B, Kristiansen G, Hauptmann S, Schnorr D, Loening SA, Jung K: Different mRNA and protein expression of matrix metalloproteinases 2 and 9 and tissue inhibitor of metalloproteinases I in benign and malignant prostate tissue. Eur Ural 2002, 42:398-406.
26. Chen G, Gharib TG, Huang CC, Taylor JM, Misek DE, Kardia SL, Giordano TJ, Iannettoni MD, Orringer MB, Hanash SM, et al.: Discordant protein and mRNA expression in lung adenocarcinomas. Mol Cell Proteomics 2002, 1:304-313.
27. Orntoft TF, Thykjaer T, Waldman FM, Wolf H, Celis JE: Genomewide study of gene copy numbers, transcripts, and protein levels in pairs of non-invasive and invasive human transitional cell carcinomas. Mol Cell Proteomics 2002, 1:37-45.
28. Futcher B, Latter GI, Monardo P, McLaughlin CS, Garrels JI: A sampling of the yeast proteome. Mol Cell Biol 1999, 19:7357-7368.
29. Greenbaum D, Jansen R, Gerstein M: Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts. Bioinformatics 2002, 18:585-596.
30. Greenbaum D, Luscombe NM, Jansen R, Qian J, Gerstein M: Interrelating different types of genomic data, from proteome to secretome: 'oming in on function. Genome Res 2001, 11:1463-1468.
31. Washburn MP, Wolters D, Yates JR 3rd: Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 2001, 19:242-247.
32. Peng J, Elias JE, Thoreen CC, Licklider LJ, Gygi SP: Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J Proteome Res 2003, 2:43-50.
33. Gerstein Lab - Supplementary data tables [http://bioinfo.mbb.yale.edu/expression/mrna-v-protein/]
34. MIPS database [http://mips.gsf.de/]
35. Mewes HW, Frishman D, Guldener U, Mannhaupt G, Mayer K, Mokrejs M, Morgenstern B, Munsterkotter M, Rudd S, Weil B: MIPS: a database for genomes and protein sequences. Nucleic Acids Res 2002, 30:31-34.
36. Baldi P, Long AD: A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics 2001, 17:509-519.
37. Szallasi Z: Genetic network analysis in light of massively parallel biological data acquisition. Pac Symp Biocomput 1999, 5-16.
38. Cho RJ, Campbell MJ, Winzeler EA, Steinmetz L, Conway A, Wodicka L, Wolfsberg TG, Gabrielian AE, Landsman D, Lockhart DJ, et al.: A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell 1998, 2:65-73.
39. Arava Y, Wang Y, Storey JD, Liu CL, Brown PO, Herschlag D: Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 2003, 100:3889-3894.
40. Glickman MH, Ciechanover A: The ubiquitin-proteasome proteolytic pathway: destruction for the sake of construction. Physiol Rev 2002, 82:373-428.
41. Pratt JM, Petty J, Riba-Garcia I, Robertson DH, Gaskell SJ, Oliver SG, Beynon RJ: Dynamics of protein turnover, a missing dimension in proteomics. Mol Cell Proteomics 2002, 1:579-591.
42. Lian Z, Kluger Y, Greenbaum DS, Tuck D, Gerstein M, Berliner N, Weissman SM, Newburger PE: Genomic and proteomic analysis of the myeloid differentiation program: global analysis of gene expression during induced differentiation in the MPRO cell line. Blood 2002, 100:3209-3220.
43. Gerner C, Vejda S, Gelbmann D, Bayer E, Gotzmann J, Schulte-Hermann R, Mikulits W: Concomitant determination of absolute values of cellular protein amounts, synthesis rates, and turnover rates by quantitative proteome profiling. Mol Cell Proteomics 2002, 1:528-537.
44. Serikawa KA, Xu XL, MacKay VL, Law GL, Zong Q, Zhao LP, Bumgarner R, Morris DR: The transcriptome and its translation during recovery from cell cycle arrest in Saccharomyces cerevisiae. Mol Cell Proteomics 2003, 2:191-204.
45. Bennetzen JL, Hall BD: Codon selection in yeast. J Biol Chem 1982, 257:3026-3031.
46. Sharp PM, Li WH: The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 1987, 15:1281-1295.
47. Jansen R, Bussemaker HJ, Gerstein M: Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models. Nucleic Acids Res 2003, 31:2242-2251.
48. Coghlan A, Wolfe KH: Relationship of codon bias to mRNA concentration and protein length in Soccharomyces cerevisiae. Yeast 2000, 16:1131-1145.
49. Jansen R, Greenbaum D, Gerstein M: Relating whole-genome expression data with protein-protein interactions. Genome Res 2002, 12:37-46.
50. Qian J, Kluger Y, Yu H, Gerstein M: Identification and correction of spurious spatial correlations in microarray data. Biotechniques 2003, 35:42-44.
51. Yan, JX, Devenish, AT, Wait, R, Stone, T, Lewis, S, Fowler, S: Fluorescence two-dimensional difference gel electrophoresis and mass spectrometry based proteomic analysis of Escherichia coli. Proteomics 2002, 2:1682-98.
52. Kumar A, Agarwal S, Heyman JA, Matson S, Heidtman M, Piccirillo S, Umansky L, Drawid A, Jansen R, Liu Y, et al.: Subcellular localization of the yeast proteome. Genes Dev 2002, 16:707-719.