Interplay of transcriptomics and proteomics

Current Opinion in Biotechnology

Volumn 14, Issue 6, 2003, Pages 647-651

  Hegde, Priti S ^a   White, Ian R ^b   Debouck, Christine ^a  

^a GLAXOSMITHKLINE   (United States)

^b GLAXOSMITHKLINE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

AUTOMATION; COST EFFECTIVENESS ANALYSIS; DNA MICROARRAY; ENZYME LINKED IMMUNOSORBENT ASSAY; HYDROPHOBICITY; IMMUNOHISTOCHEMISTRY; PRIORITY JOURNAL; PROTEIN MODIFICATION; PROTEIN SYNTHESIS; PROTEOMICS; REVIEW; RNA SPLICING; WESTERN BLOTTING;

EID: 0344687398     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.copbio.2003.10.006     Document Type: Review

References (33)

1. Anderson L., Seilhamer J. A comparison of selected mRNA and protein abundances in human liver. Electrophoresis. 18:1997;533-537.
2. Gygi S.P., Rochon Y., Franza B.R., Aebersold R. Correlation between protein and mRNA abundance in yeast. Mol Cell Biol. 19:1999;1720-1730.
3. Ross J. mRNA stability in mammalian cells. Microbiol Rev. 59:1995;423-450.
4. Guhaniyogi J., Brewer G. Regulation of mRNA stability in mammalian cells. Gene. 265:2001;11-23.
5. Zong Q., Schummer M., Hood L., Morris D.R. Messenger RNA translation state: the second dimension of high-throughput expression screening. Proc Natl Acad Sci USA. 96:1999;10632-10636.
6. Pratt J.M., Petty J., Riba-Garcia I., Robertson D.H., Gaskell S.J., Oliver S.G., Beynon R.J. Dynamics of protein turnover, a missing dimension in proteomics. Mol Cell Proteomics. 1:2002;579-591.
7. Ideker T., Thorsson V., Ranish J.A., Christmas R., Buhler J., Eng J.K., Bumgarner R., Goodlett D.R., Aebersold R., Hood L. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science. 292:2001;929-934 An in-depth comparison of gene expression and protein expression to demonstrate the utilization of a systems approach to biology.
8. Griffin T.J., Gygi S.P., Ideker T., Rist B., Eng J., Hood L., Aebersold R. Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol Cell Proteomics. 1:2002;323-333.
9. Chen G., Gharib T.G., Huang C.C., Taylor J.M., Misek D.E., Kardia S.L., Giordano T.J., Iannettoni M.D., Orringer M.B., Hanash S.M., Beer D.G. Discordant protein and mRNA expression in lung adenocarcinomas. Mol Cell Proteomics. 1:2002;304-313.
10. Washburn M.P., Koller A., Oshira G., Ulaszek R.R., Plouffe D., Cediu C., Winzeler E., Yates J.R. III Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae. Proc Natl Acad Sci USA. 100:2003;3107-3112.
11. Greenbaum D., Jansen R., Gerstein M. Analysis of mRNA expression and protein abundance data: an approach for the comparison of enrichment of features in the cellular population of proteins and transcripts. Bioinformatics. 18:2002;585-596.
12. The Genome International Sequencing Consortium: Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921.
13. van de Vijver M.J., He Y.D., van't Veer L.J., Dai H., Hart A.A., Voskuil D.W., Schreiber G.J., Peterse J.L., Roberts C., Marton M.J.et al. A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med. 347:2002;1999-2009 An independent validation of results obtained from a previous study that identified a gene expression fingerprint as a predictor of survival in breast cancer.
14. Yeoh E.J., Ross M.E., Shurtleff S.A., Williams W.K., Patel D., Mahfouz R., Behm F.G., Raimondi S.C., Relling M.V., Patel A.et al. Classification, subtype discovery and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling. Cancer Cell. 1:2002;133-143.
15. Chang J.C., Wooten E.C., Tsimelzon A., Hilsenbeck S.G., Gutierrez M.C., Elledge R., Mohsin S., Osborne C.K., Chamness G.C., Allred D.C.et al. Gene expression profiling for the prediction of therapeutic response to docetaxel in patients with breast cancer. Lancet. 362:2003;362-369.
16. Zhou W., Sokoll L.J., Bruzek D.J., Zhang L., Velculescu V.E., Goldin S.B., Hruban R.H., Kern S.E., Hamilton S.R., Chan D.W.et al. Identifying markers for pancreatic cancer by gene expression analysis. Cancer Epidemiol Biomarkers Prev. 7:1998;109-112.
17. Mok S.C., Chao J., Skates S., Wong K., Yiu G.K., Muto M.G., Berkowitz R.S., Cramer D.W. Prostatin, a potential serum marker for ovarian cancer: identification through microarray technology. J Natl Cancer Inst. 93:2001;1458-1464.
18. Kim J.H., Skates S.J., Uede T., Wong Kk K.K., Schorge J.O., Feltmate C.M., Berkowitz R.S., Cramer D.W., Mok S.C. Osteopontin as a potential diagnostic biomarker for ovarian cancer. JAMA. 287:2002;1671-1679.
19. Tanwar M.K., Gilbert M.R., Holland E.C. Gene expression microarray analysis reveals YKL-40 to be a potential serum marker for malignant character in human glioma. Cancer Res. 62:2002;4364-4368.
20. Miller J.C., Zhou H., Kwekel J., Cavallo R., Burke J., Butler E.B., Teh B.S., Haab B.B. Antibody microarray profiling of human prostate cancer sera: antibody screening and identification of potential biomarkers. Proteomics. 3:2003;56-63.
21. Welsh J.B., Sapinoso L.M., Kern S.G., Brown D.A., Liu T., Bauskin A.R., Ward R.L., Hawkins N.J., Quinn D.I., Russell P.J.et al. Large-scale delineation of secreted protein biomarkers overexpressed in cancer tissue and serum. Proc Natl Acad Sci USA. 100:2003;3410-3415.
22. Shvartsman H.S., Lu K.H., Lee J., Lillie J., Deavers M.T., Clifford S., Wolf J.K., Mills G.B., Bast R.C. Jr., Gershenson D.M.et al. Overexpression of kallikrein 10 in epithelial ovarian carcinomas. Gynecol Oncol. 90:2003;44-50.
23. Petricoin E.F., Ardekani A.M., Hitt B.A., Levine P.J., Furaso V.A., Steinberg S.M., Milles G.B., Simone C., Fishman D.A., Kohn E.C., Liotta L.A. Use of proteomic patterns in serum to identify ovarian cancer. Lancet. 359:2002;572-577 A key study showing the potential of SELDI-TOF for the generation of disease-specific diagnostic protein profile patterns.
24. Banez L.L., Prasanna P., Sun L., Ali A., Zou Z., Adam B.L., McLeod D.G., Moul J.W., Srivastava S. Diagnostic potential of serum proteomic patterns in prostate cancer. J Urol. 170:2003;442-446.
25. Li J., Zhang Z., Rosenweig J., Wang Y.Y., Chan D.W. Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clin Chem. 48:2002;1296-1304.
26. Ye B., Cramer D.W., Skates S.J., Gygi S.P., Pratomo V., Fu L., Horick N.K., Licklider L.J., Schorge J.O., Berkowitz R.S., Mok S.C. Haptoglobin-α subunit as potential serum biomarker in ovarian cancer: identification and characterization using proteomic profiling and mass spectrometry. Clin Cancer Res. 9:2003;2904-2911.
27. Pieper R., Gatlin C.L., Makuski A.J., Russo P.S., Schatz C.R., Miller S.S., Su Q., McGrath A.M., Estock M.A., Parmar P.P.et al. The human serum proteome: display of nearly 3700 chromatographically separated protein spots on two-dimensional electrophoresis gels and identification of 325 distinct proteins. Proteomics. 3:2003;1345-1364 An extensive study that exemplifies many of the challenges associated with the search for serum-borne biomarkers.
28. Adkins J.N., Varnum S.M., Auberry K.J., Moore R.J., Angell N.H., Smith R.D., Springer D.L., Pounds J.G. Towards a human blood serum proteome: analysis by multidimensional separation coupled with mass spectrometry. Mol Cell Proteomics. 1:2002;947-955.
29. Drevs J., Medinger M., Schmidt-Gersbach C., Weber R., Unger C. Receptor tyrosine kinases: the main targets for new anticancer therapy. Curr Drug Targets. 4:2003;113-121.
30. Shin B.K., Wang K., Yim A.M., Le Naour F., Brichory F., Jang J.H., Zhao R., Puravs E., Tra J., Michael C.W.et al. Global profiling of the cell surface proteome of cancer cells uncovers an abundance of proteins with chaperone function. J Biol Chem. 278:2003;7607-7616.
31. Adam P.J., Boyd R., Tyson K.L., Fletcher G.C., Stampls A., Hudson L., Poyser H.R., Redpath N., Griffiths M., Steers G.et al. Comprehensive proteome analysis of breast cancer cell membranes reveals unique proteins with potential roles in clinical cancer. J Biol Chem. 278:2003;6482-6489.
32. Basik M., Mousses S., Trent J. Integration of genomic technologies for accelerated cancer drug development. Biotechniques. 35:2003;580-593.
33. Celis J.E., Gromov P., Gromova I., Moreira J.M., Cabezon T., Ambartsumian N., Grigorian M., Lukanidin E., Thor Straten P., Guldberg P.et al. Integrating proteomic and functional genomic technologies in discovery-driven translational breast cancer research. Mol Cell Proteomics. 2:2003;369-377.