Differential analysis of DNA microarray gene expression data

Molecular Microbiology

Volumn 47, Issue 4, 2003, Pages 871-877

  Hatfield, G Wesley ^a,b   Hung, She Pin ^a   Baldi, Pierre ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTICAL ERROR; BAYES THEOREM; BIOLOGICAL TRAIT; CALCULATION; CELL TYPE; CONTROLLED STUDY; DATA ANALYSIS; DNA MICROARRAY; ESCHERICHIA COLI; GENE CONTROL; GENE EXPRESSION; GENE IDENTIFICATION; GENOTYPE; HUMAN; NONHUMAN; PRIORITY JOURNAL; PROBABILITY; QUANTITATIVE ANALYSIS; SHORT SURVEY; STATISTICAL ANALYSIS; STUDENT T TEST; TECHNIQUE;

ANALYSIS OF VARIANCE; BAYES THEOREM; DATA INTERPRETATION, STATISTICAL; ESCHERICHIA COLI; FALSE NEGATIVE REACTIONS; FALSE POSITIVE REACTIONS; GENE EXPRESSION PROFILING; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROBABILITY;

ESCHERICHIA COLI;

EID: 0037323928     PISSN: 0950382X     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2958.2003.03298.x     Document Type: Short Survey

References (16)

1. Allison, D.B., Gadbury, G.L., Heo, M., Fernandez, J.R., Lee, C.K., Prolla, T.A., and Weindruch, R. (2002) A mixture model approach for the analysis of microarray gene expression data. Comput Stat Data Anal 39: 1-20.
2. Arfin, S.M., Long, A.D., Ito, E.T., Tolleri, L., Riehle, M.M., Paegle, E.S., and Hatfield, G.W. (2000) Global gene expression profiling in Escherichia coli K12. The effects of integration host factor. J Biol Chem 275: 29672-29684.
3. Baldi, P., and Hatfield, G.W. (2002) DNA Microarrays and Gene Expression: from Experiments to Data Analysis and Modelling. Cambridge: Cambridge University Press.
4. Baldi, P., and Long, A.D. (2001) A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics 17: 509-519.
5. Best, C.J., and Emmert-Buck, M.R. (2001) Molecular profiling of tissue samples using laser capture microdissection. Expert Rev Mol Diagn 1: 53-60.
6. Gross, C.A. (1996) Function and regulation of the heat shock proteins. In Escherichia coli and Salmonella. Cellular and Molecular Biology, Vol. 1. Neidhardt, F.C., Curtis, R.I., Ingraham, J.L., Lin, E.C.C., Low, K.B., Magasanik, B., et al. (eds). Washington, DC: American Society for Microbiology Press, pp. 1382-1399.
7. Higgins, C.F., Dorman, C.J., Stirling, D.A., Waddell, L., Booth, I.R., May, G., and Bremer, E. (1988) A physiological role for DNA supercoiling in the osmotic regulation of gene expression in S. typhimurium and E. coli. Cell 52: 569-584.
8. Hung, S.-P., Baldi, P., and Hatfield, G.W. (2002) Global gene expression profiling in Escherichia coli K12: the effects of leucine-responsive regulatory protein. J Biol Chem 277: 40309-40323.
9. Long, A.D., Mangalam, H.J., Chan, B.Y., Tolleri, L., Hatfield, G.W., and Baldi, P. (2001) Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J Biol Chem 276: 19937-19944.
10. McAdams, H.H., and Arkin, A. (1999) It's a noisy business! Genetic regulation at the nanomolar scale. Trends Genet 15: 65-69.
11. McLachlan, G.J., and Peel, D. (2000) Finite Mixture Models. New York: John Wiley & Sons.
12. Ninfa, A.J. (1996) Regulation of gene transcription by extracellular stimuli. In Escherichia coli and Salmonella. Cellular and Molecular Biology, Vol. 1. Neidhardt, F.C., Curtis, R.I., Ingraham, J.L., Lin, E.C.C., Low, K.B., Magasanik, B., et al. (eds). Washington, DC: American Society for Microbiology Press, pp. 1246-1262.
13. Olivas, W., and Parker, R. (2000) The Puf3 protein is a transcript-specific regulator of mRNA degradation in yeast. EMBO J 19: 6602-6611.
14. Schena, M., Shalon, D., Davis, R.W., and Brown, P.O. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467-470.
15. Titterington, D.M., Smith, A.F.M., and Markov, U.E. (1985) Statistical Analysis of Finite Mixture Distributions. New York: John Wiley & Sons.
16. Zien, A., Aigner, T., Zimmer, R., and Lengauer, T. (2001) Centralization: a new method for the normalization of gene expression data. Bioinformatics 17: S323-S331.