Dynamical Analysis of Gene Networks Requires Both mRNA and Protein Expression Information

Metabolic Engineering

Volumn 1, Issue 4, 1999, Pages 275-281

  Hatzimanikatis, Vassily ^a   Lee, Kelvin H ^b  

^a CARGILL INC   (United States)

^b Cornell University   (United States)

Author keywords

circadian rhythms; functional genomics; microarray; Proteome

Indexed keywords

MESSENGER RNA; PROTEIN;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; CIRCADIAN RHYTHM; GENE EXPRESSION; GENETIC ENGINEERING; GENETICS; NONLINEAR SYSTEM;

ANIMALS; CIRCADIAN RHYTHM; GENE EXPRESSION; GENETIC ENGINEERING; MODELS, GENETIC; NONLINEAR DYNAMICS; PROTEINS; RNA, MESSENGER;

EID: 0033206211     PISSN: 10967176     EISSN: None     Source Type: Journal    
DOI: 10.1006/mben.1999.0115     Document Type: Article

References (37)

1. Antoch M. P., Song E. J., Chang A. M., Vitaterna M. H., Zhao Y., Wilsbacher L. D., Sangoram A. M., King D. P., Pinto L. H., Takahashi J. S. Functional identification of the mouse circadian Clock gene by transgenic BAC rescue. Cell. 89:1997;655-667.
2. Barinaga M. New clues found to circadian clocks - including mammals. Science. 276:1997;1030-1031.
3. Belasco J., Brawerman G. Control of Messenger RNA Stability. 1993;Academic Press, New York.
4. Bhalla U. S., Iyengar R. Emergent properties of networks of biological signaling pathways. Science. 283:1999;381-387.
5. Bremer H., Dennis P. Modulation of chemical composition and other parameters of the cellby growth rate. Neidhardt F. C., Ingraham J. C., Low K. B., Magasanik B., Schaechter M., Umbarger H. E. Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology. 1987;1527-1542 Am. Soc. Microbiol. Washington.
6. Carrier T. A., Keasling J. D. Controlling messenger RNA stability in bacteria: strategies for engineering gene expression. Biotech. Progr. 13:1997;699-708.
7. Chow J., Dennis P. Coupling between mRNA synthesis and mRNA stability in E. coli. Mol. Microbiol. 11:1994;919-931.
8. Crosthwaite S. K., Dunlap J. C., Loros J. J. Neurospora wc-1 and wc-2: transcription, photoresponses, and the origins of circadian rhythmicity. Science. 276:1997;763-769.
9. DeRisi J. L., Iyer V. R., Brown P. O. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science. 278:1997;608-686.
10. Dunlap J. C. Common threads in eukaryotic circadian systems. Curr. Op. Gene. Dev. 8:1998;400-406.
11. 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.
12. Hatzimanikatis V., Choe L. H., Lee K. H. Proteomics: theoretical and experimental considerations. Biotech. Prog. 15:1999.
13. Hardin P. E., Hall J. C., Rosbash M. Circadian oscillations in period gene mRNA levels are transcriptionally regulated. Proc. Natl. Acad. Sci. USA. 89:1992;11711-11715.
14. Hill, C. C, Hatzimanikatis, V, and, Lee, K. H. 1999. Manuscript in preparation.
15. Iost I., Dreyfus M. The stability of E. coli lacZ mRNA depends upon the simultaneity of its synthesis and translation. EMBO J. 14:1995;3252-3261.
16. Kauffman S. A. The Origins of Order. 1993;Oxford Univ. Press, New York.
17. Koshland D. E. The era of pathway quantification. Science. 280:1998;852-853.
18. Liang S., Fuhrman S., Somogyi R. REVEAL: a general reverse engineering algorithm for inference of genetic network architectures. Pacific Symp. Biocomput. 3:1998;18-29.
19. Lockhart D. J., Dong H., Byrne M. C., Follettie M. T., Gallo M. V., Chee M. S., Mittmann M., Wang C., Kobayashi M., Horton H., Brown E. L. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotech. 14:1996;1675-1680.
20. Loomis W. F., Sternberg P. W. Genetic networks. Science. 269:1995;649.
21. Maddox J. Cell-cycle regulation by numbers. Nature. 369:1994;6480.
22. Makarova O., Makarov E., Sousa R., Dreyfus M. Transcribing of E. coli genes with mutant T7 RNA polymerases: stability of lacZ mRNA inversely correlates with polymerase speed. Proc. Natl. Acad. Sci. USA. 92:1995;12250-12254.
23. McAdams H. H., Shapiro L. Circuit simulation of genetic networks. Science. 269:1995;650-656.
24. Michaels G. S., Carr D. B., Askenazi M., Fuhrman S., Wen X., Somogyi R. Cluster analysis and data visualization of large-scale gene expression data. Pacific Symp. Biocomput. 3:1998;42-53.
25. Murray J. D. Mathematical Biology. 1993;Springer-Verlag, New York.
26. Neidhardt F. C., Savageau M. A. Regulation beyond the operon. Neidhardt F. C. Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology. 1996;1310-1324 Am. Soc. Microbiol. Washington.
27. Popper K. R. The Logic of Scientific Discovery. 1992;Routledge, London.
28. Schena M., Shalon D., Davis R. W., Brown P. O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 270:1995;467-470.
29. Scheper T., Dlinkenberg D., Pennartz C., van Pelt J. A mathematical model for the intracellular circadian rhythm generator. J. Neurosci. 19:1999;40-47.
30. So W. V., Rosbash M. Post-transcriptional regulation contributes to Drosophila clock gene mRNA cycling. EMBO J. 16:1997;7146-7155.
31. Somers D. E., Devlin P. F., Kay S. A. Phytochromes and cryptochromes in the entrainment of the Arabidopsis clock. Science. 282:1998;1488-1490.
32. Suri V., Lanjuin A., Rosbash M. TIMELESS-dependent positive and negative autoregulation in the Drosophila circadian clock. EMBO J. 18:1999;675-686.
33. Thresher R. J., Vitaterna M. H., Miyamoto Y., Kazantsev A., Hsu D. S., Petit C., Selby C. P., Dawut L., Smithies O., Takahashi J. S., Sancar A. Role of mouse cryptochrome blue-light photoreceptor in circadian photoresponses. Science. 282:1998;1490-1494.
34. Thomas R. Kinetic Logic: A Boolean Approach to the Analysis of Complex Regulatory Systems. 1979;Springer-Verlag, New York.
35. Tyson J. J., Othmer H. G. The dynamics of feedback control circuits in biochemical pathways. Prog. Theor. Biol. 5:1978;1-62.
36. Wiggins S. Introduction to Applied Nonlinear Dynamical Systems and Chaos. 1990;Springer-Verlag, New York.
37. Winzeler E. A., Richards D. R., Conway A. R., Goldstein A. L., Kalman S., McCullough M. J., McCusker J. H., Stevens D. A., Wodicka L., Lockhart D. J., Davis R. W. Direct allelic variation scanning of the yeast genome. Science. 281:1998;1194-1197.