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 - PubMed (original) (raw)
. 2001 Jun 8;276(23):19937-44.
doi: 10.1074/jbc.M010192200. Epub 2001 Mar 20.
Affiliations
- PMID: 11259426
- DOI: 10.1074/jbc.M010192200
Free article
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
A D Long et al. J Biol Chem. 2001.
Free article
Abstract
We describe statistical methods based on the t test that can be conveniently used on high density array data to test for statistically significant differences between treatments. These t tests employ either the observed variance among replicates within treatments or a Bayesian estimate of the variance among replicates within treatments based on a prior estimate obtained from a local estimate of the standard deviation. The Bayesian prior allows statistical inference to be made from microarray data even when experiments are only replicated at nominal levels. We apply these new statistical tests to a data set that examined differential gene expression patterns in IHF(+) and IHF(-) Escherichia coli cells (Arfin, S. M., Long, A. D., Ito, E. T., Tolleri, L., Riehle, M. M., Paegle, E. S., and Hatfield, G. W. (2000) J. Biol. Chem. 275, 29672-29684). These analyses identify a more biologically reasonable set of candidate genes than those identified using statistical tests not incorporating a Bayesian prior. We also show that statistical tests based on analysis of variance and a Bayesian prior identify genes that are up- or down-regulated following an experimental manipulation more reliably than approaches based only on a t test or fold change. All the described tests are implemented in a simple-to-use web interface called Cyber-T that is located on the University of California at Irvine genomics web site.
Similar articles
- Differential analysis of DNA microarray gene expression data.
Hatfield GW, Hung SP, Baldi P. Hatfield GW, et al. Mol Microbiol. 2003 Feb;47(4):871-7. doi: 10.1046/j.1365-2958.2003.03298.x. Mol Microbiol. 2003. PMID: 12581345 Review. - Global gene expression profiling in Escherichia coli K12. The effects of leucine-responsive regulatory protein.
Hung SP, Baldi P, Hatfield GW. Hung SP, et al. J Biol Chem. 2002 Oct 25;277(43):40309-23. doi: 10.1074/jbc.M204044200. Epub 2002 Jul 18. J Biol Chem. 2002. PMID: 12130640 - A Bayesian approach for decision making on the identification of genes with different expression levels: an application to Escherichia coli bacterium data.
Saraiva EF, Louzada F, Milan LA, Meira S, Cobre J. Saraiva EF, et al. Comput Math Methods Med. 2012;2012:953086. doi: 10.1155/2012/953086. Epub 2012 Mar 5. Comput Math Methods Med. 2012. PMID: 22474543 Free PMC article. - Cyber-T web server: differential analysis of high-throughput data.
Kayala MA, Baldi P. Kayala MA, et al. Nucleic Acids Res. 2012 Jul;40(Web Server issue):W553-9. doi: 10.1093/nar/gks420. Epub 2012 May 16. Nucleic Acids Res. 2012. PMID: 22600740 Free PMC article. - Applications of Bayesian statistical methods in microarray data analysis.
Yang D, Zakharkin SO, Page GP, Brand JP, Edwards JW, Bartolucci AA, Allison DB. Yang D, et al. Am J Pharmacogenomics. 2004;4(1):53-62. doi: 10.2165/00129785-200404010-00006. Am J Pharmacogenomics. 2004. PMID: 14987122 Review.
Cited by
- Gene selection and classification for cancer microarray data based on machine learning and similarity measures.
Liu Q, Sung AH, Chen Z, Liu J, Chen L, Qiao M, Wang Z, Huang X, Deng Y. Liu Q, et al. BMC Genomics. 2011 Dec 23;12 Suppl 5(Suppl 5):S1. doi: 10.1186/1471-2164-12-S5-S1. Epub 2011 Dec 23. BMC Genomics. 2011. PMID: 22369383 Free PMC article. - Pygo2 regulates histone gene expression and H3 K56 acetylation in human mammary epithelial cells.
Gu B, Watanabe K, Dai X. Gu B, et al. Cell Cycle. 2012 Jan 1;11(1):79-87. doi: 10.4161/cc.11.1.18402. Epub 2012 Jan 1. Cell Cycle. 2012. PMID: 22186018 Free PMC article. - Time-resolved determination of the CcpA regulon of Lactococcus lactis subsp. cremoris MG1363.
Zomer AL, Buist G, Larsen R, Kok J, Kuipers OP. Zomer AL, et al. J Bacteriol. 2007 Feb;189(4):1366-81. doi: 10.1128/JB.01013-06. Epub 2006 Oct 6. J Bacteriol. 2007. PMID: 17028270 Free PMC article. - Feature selection and classification of MAQC-II breast cancer and multiple myeloma microarray gene expression data.
Liu Q, Sung AH, Chen Z, Liu J, Huang X, Deng Y. Liu Q, et al. PLoS One. 2009 Dec 11;4(12):e8250. doi: 10.1371/journal.pone.0008250. PLoS One. 2009. PMID: 20011240 Free PMC article. - The PowerAtlas: a power and sample size atlas for microarray experimental design and research.
Page GP, Edwards JW, Gadbury GL, Yelisetti P, Wang J, Trivedi P, Allison DB. Page GP, et al. BMC Bioinformatics. 2006 Feb 22;7:84. doi: 10.1186/1471-2105-7-84. BMC Bioinformatics. 2006. PMID: 16504070 Free PMC article.
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources
Other Literature Sources