Integrated genomic and proteomic analyses of gene expression in mammalian cells

Molecular and Cellular Proteomics

Volumn 3, Issue 10, 2004, Pages 960-969

  Tian, Qiang ^a   Stepaniants, Serguei B ^b   Mao, Mao ^b   Weng, Lee ^b   Feetham, Megan C ^a   Doyle, Michelle J ^a   Yi, Eugene C ^a   Dai, Hongyue ^b   Thorsson, Vesteinn ^a   Eng, Jimmy ^a   Goodlett, David ^a   Berger, Joel P ^b   Gunter, Bert ^b   Linseley, Peter S ^b   Stoughton, Roland B ^b   Aebersold, Ruedi ^a   Collins, Steven J ^c   Hanlon, William A ^b   Hood, Leroy E ^a  

^a INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^b ROSETTA INPHARMATICS   (United States)

^c Fred Hutchinson Cancer Research Center   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

2,4 THIAZOLIDINEDIONE DERIVATIVE; DNA; MESSENGER RNA; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR AGONIST; PIRINIXIC ACID; PROTEIN; REAGENT; ROSIGLITAZONE; 2,4 THIAZOLIDINEDIONE; 2,4-THIAZOLIDINEDIONE; PEROXISOME PROLIFERATOR; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR; PYRIMIDINE DERIVATIVE;

ANALYTICAL ERROR; ANIMAL CELL; ANIMAL EXPERIMENT; ARTICLE; BONE MARROW CELL; CELL DIFFERENTIATION; CELL LINE; CELL MATURATION; CONTROLLED STUDY; CORRELATION ANALYSIS; DNA MICROARRAY; DOWN REGULATION; DRUG RESPONSE; DRUG STRUCTURE; GENE EXPRESSION PROFILING; GENOMICS; HEMATOPOIETIC CELL; LIVER CELL; MALE; MAMMAL CELL; MASS SPECTROMETRY; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN PROCESSING; PROTEOMICS; QUANTITATIVE ANALYSIS; REGULATORY MECHANISM; TWO DIMENSIONAL GEL ELECTROPHORESIS; UPREGULATION; ANIMAL; C57BL MOUSE; CULTURE MEDIUM; CYTOLOGY; DRUG EFFECT; DRUG POTENTIATION; GENE EXPRESSION REGULATION; GENETIC VARIABILITY; HEMATOPOIETIC STEM CELL; KINETICS; LIVER; METABOLISM; MYELOID PROGENITOR CELL; MYELOPOIESIS;

MAMMALIA;

ANIMALS; CELL LINE; CULTURE MEDIA, CONDITIONED; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; GENE EXPRESSION REGULATION; GENOMICS; HEMATOPOIETIC STEM CELLS; KINETICS; LIVER; MALE; MASS SPECTROMETRY; MICE; MICE, INBRED C57BL; MYELOID PROGENITOR CELLS; MYELOPOIESIS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PEROXISOME PROLIFERATOR-ACTIVATED RECEPTORS; PEROXISOME PROLIFERATORS; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEINS; PROTEOMICS; PYRIMIDINES; RNA, MESSENGER; THIAZOLIDINEDIONES; VARIATION (GENETICS);

EID: 20144368638     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.M400055-MCP200     Document Type: Article

References (25)

1. Young, R. A. (1995) Biomedical discovery with DNA arrays. Cell 102, 9-15
2. Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., and Aebersold, R. (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17, 994-999
3. Ideker, T., Thorsson, V., Ranish, J. A., Christmas, R., Buhler, J., Eng, J. K., Bumgarner, R., Goodlett, D. R., Aebersold, R., and Hood, L. (2001) Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292, 929-934
4. Griffin, T. J., Gygi, S. P., Ideker, T., Rist, B., Eng, J., Hood, L., and Aebersold, R. (2002) Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol. Cell. Proteomics 1, 323-333
5. Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V., and Hood, L. (2002) Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach. Proc. Natl. Acad. Sci. U. S. A. 99, 14913-14918
6. 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., and Beer, D. G. (2002) Discordant protein and mRNA expression in lung adenocarcinomas. Mol. Cell. Proteomics 1, 304-313
7. Tsai, S., Bartelmez, S., Sitnicka, E., and Collins, S. (1994) Lymphohematopoietic progenitors immortalized by a retroviral vector harboring a dominant-negative retinoic acid receptor can recapitulate lymphoid, myeloid, and erythroid development. Genes Dev. 8, 2831-2841
8. Tsai, S., and Collins, S. (1993) A dominant negative retinoic acid receptor blocks neutrophil differentiation at the promyelocyte stage. Proc. Natl. Acad. Sci. U. S. A. 90, 7153-7157
9. Hughes, T. R., Mao, M., Jones, A. R., Burchard, J., Marton, M. J., Shannon, K. W., Lefkowitz, S. M., Ziman, M., Schelter, J. M., Meyer, M. R., Kobayashi, S., Davis, C., Dai, H., He, Y. D., Stephaniants, S. B., Cavet, G., Walker, W. L., West, A., Coffey, E., Shoemaker, D. D., Stoughton, R., Blanchard, A. P., Friend, S. H., and Linsley, P. S. (2001) Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat. Biotechnol. 19, 342-347
10. Han, D. K., Eng, J., Zhou, H., and Aebersold, R. (2001) Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat. Biotechnol. 19, 946-951
11. Koyama, H., Boueres, J. K., Han, W., Metzger, E. J., Bergman, J. P., Gratale, D. F., Miller, D. J., Tolman, R. L., MacNaul, K. L., Berger, J. P., Doebber, T. W., Leung, K., Moller, D. E., Heck, J. V., and Sahoo, S. P. (2003) 5-Aryl thiazolidine-2,4-diones as selective PPARγ agonists. Bioorg. Med. Chem. Lett. 13, 1801-1804
12. Unlu, M., Morgan, M. E., and Minden, J. S. (1997) Difference gel electrophoresis: A single gel method for detecting changes in protein extracts. Eletrophoresis 18, 2071-2077
13. Roberts, C. J., Nelson, B., Marton, M. J., Stoughton, R., Meyer, M. R., Bennett, H. A., He, Y. D., Dai, H., Walker, W. L., Hughes, T. R., Tyers, M., Boone, C., and Friend, S. H. (2000) Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 287, 873-880
14. Stoughton, R. S., and Dai, H. (2002) Statistical combining of cell expression profiles. United States Patent No. 6,351,712
15. Keller, A., Nesvizhskii, A. I., Kolker, E., and Aebersold R. (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74, 5383-5392
16. Broudy, V. C. (1997) Stem cell factor and hematopoiesis. Blood 90, 1345-1364
17. Geijsen, N., Spaargaren, M., Raaijmakers, J. A., Lammers, J. W., Koenderman, L., and Coffer, P. J. (1999) Association of RACK1 and PKCβ with the common β-chain of the IL-5/IL-3/GM-CSF receptor. Oncogene 18, 5126-5130
18. de Heredia, M. L., Izquierdo, J. M., and Cuezva, J. M. (2000) A conserved mechanism for controlling the translation of β-F1-ATPase mRNA between the fetal liver and cancer cells. J. Biol. Chem. 275, 7430-7437
19. Press, W. H., Teukolsky, S. A., Vetterling, W. T, and Flannery, B. P. (1992) Numerical Recipes in C, The Art of Scientific Computing, 2nd Ed., University of Cambridge Press, Cambridge, United Kingdom
20. Box, G. E. P., Hunter, W. G., and Hunter, J. S. (1978) Statistics for Experimenters. An Introduction to Design, Data Analysis and Model Building. John Wiley & Sons, Inc., New York.
21. Yang, D., Li, Y., Yuan, X., Matoney, L., and Yan, B. (2001) Regulation of rat carboxylesterase expression by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD): A dose-dependent decrease in mRNA levels but a biphasic change in protein levels and activity. Toxicol. Sci. 64, 20-27
22. He, Y. D., Dai, H., Schadt, E. E., Cavet, G., Edwards, S. W., Stepaniants, S. B., Duenwald, S., Kleinhanz, R., Jones, A. R., Shoemaker, D. D., and Stoughton, R. B. (2003) Microarray standard data set and figures of merit for comparing data processing methods and experiment designs. Bioinformatics 19, 956-965
23. Tonge, R., Shaw, J., Middleton, B., Rowlinson, R., Rayner, S., Young, J., Pognan, F., Hawkins, E., Currie, I., and Davison, M. (2001) Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology. Proteomics 1, 377-396
24. Zhou, G., Li, H., DeCamp, D., Chen, S., Shu, H., Gong, Y., Flaig, M., Gillespie, J. W., Hu, N., Taylor, P. R., Emmert-Buck, M. R., Liotta, L. A., Petricoin, E. F., 3rd, and Zhao, Y. (2002) 2D differential in-gel electrophoresis for the identification of esophageal scans cell cancer-specific protein markers. Mol. Cell. Proteomics 1, 117-124
25. Gharbi, S., Gaffney, P., Yang, A., Zvelebil, M. J., Cramer, R., Waterfield, M. D., and Timms, J. F. (2002) Evaluation of two-dimensional differential gel electrophoresis for proteomic expression analysis of a model breast cancer cell system. Mol. Cell. Proteomics 1, 91-98