Multifactorial experimental design and the transitivity of ratios with spotted DNA microarrays

BMC Genomics

Volumn 4, Issue , 2003, Pages

  Townsend, Jeffrey P ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; DYE; MESSENGER RNA;

ANALYTICAL ERROR; ARTICLE; BAYES THEOREM; CORRELATION ANALYSIS; DNA HYBRIDIZATION; DNA MICROARRAY; GENE EXPRESSION; GENE EXPRESSION PROFILING; METHODOLOGY; OPEN READING FRAME; POLYMERASE CHAIN REACTION; SERIAL ANALYSIS OF GENE EXPRESSION; EVALUATION; REPRODUCIBILITY;

GENE EXPRESSION PROFILING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OPEN READING FRAMES; REPRODUCIBILITY OF RESULTS; RESEARCH DESIGN; RNA, MESSENGER;

EID: 9444291270     PISSN: 14712164     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2164-4-41     Document Type: Article

References (25)

1. Kerr M. Kathleen and Churchill Gary A.: Statistical design and the analysis of gene expression microarray data. Genetical Research 2001, 77:123-128.
2. Jin W, Riley RM, Wolfinger RD, White KP, Passador-Gurgel G and Gibson G: The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster. Nature Genetics 2001, 29:389-395.
3. Liang Mingyu, Briggs Amy G., Rute Elizabeth, Greene Andrew S. and Cowley Allen W.: Quantitative assessment of the importance of dye switching and biological replication in cDNA microarray studies. Physiological Genomics 2003, 14:199-207.
4. Ideker T, Thorsson V, Siegel AF and Hood LE: Testing for differentially-expressed genes by maximum-likelihood analysis of microarray data. JOURNAL OF COMPUTATIONAL BIOLOGY 2000, 7: 05-817.
5. Baldi Pierre and Long Anthony: A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics 2001, 17:509-519.
6. Theilhaber Joachim, Bushnell Steven, Jackson Amanda and Fuchs Rainer: Bayesian estimation of fold-changes in the analysis of gene expression: the PFOLD algorithm. Journal of Computational Biology 2001, 8:585-614.
7. Tseng George C., Oh Min-Kyu, Rohlin Lars, Liao James C. and Wong Wing Hung: Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Research 2001, 29:2549-2557.
8. DeRisi JL, Iyer VR and Brown PO: Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 1997, 278:680-686.
9. Gasch Audry P., Spellman Paul T., Kao Camillo M., Carmel-Harel Orna,, Eisen Michael B., Storz Gisela, Botstein David and Brown Patrick O.: Genomic expression programs in the response of yeast cells to environmental changes. Molecular Biology of the Cell 2000, 11:4241-4257.
10. White Kevin P., Rifkin Scott A., Hurban Patrick and Hogness David: Microarray analysis of Drosophila development during metamorphosis. Science 1999, 286:2179-2184.
11. Kerr M. Kathleen, Martin Mitchell and Churchill Gary A.: Analysis of variance for gene expression microarray data. Journal of Computational Biology 2000, 7:819-837.
12. Yang Yee Hwa and Speed Terry: Design issues for cDNA microarray experiments. Nature Reviews 2002, 3:579-588.
13. Arbeitman Michelle N., Furlong Eileen E. M., Imam Farhad, Johnson Eric, Null Brian H., Baker Bruce S., Krasnow Mark A., Scott Matthew P., Davis Ronald W. and White Kevin P.: Gene expression during the life cycle of Drosophila melanogaster. Science 2002, 297: 270-2275.
14. Peng Xuejun, Wood Constance, Blalock Eric M., Chen Kuey Chu, Landfield Philip W. and Stromberg Arnold J.: Statistical implications of pooling RNA samples for microarray experiments. BMC Bioinformatics 2003, 4:26.
15. Oleksiak MF, Churchill Gary A. and Crawford DL: Variation in gene expression within and among natural populations. Nature Genetics 2002, 32:261-266.
16. Townsend Jeffrey P., Cavalieri Duccio and Hartl Daniel L.: Population genetic variation in genome-wide gene expression. Molecular Biology and Evolution 2003, 20:955-963.
17. Ranz JM, Castillo-Davis CI, Meiklejohn Colin D. and Hartl Daniel L.: Sex-dependent gene expression and evolution of the Drosophila transcriptome. Science 2003, 300:1742-1745.
18. Wolfinger Russell D., Gibson Greg, Wolfinger Elizabeth D., Bennett Lee, Hamadeh Hisham, Bushel Pierre, Afshari Cynthia and Paules Richard S.: Assessing gene significance from cDNA microarray expression data via mixed models. Journal of Computational Biology 2001, 8:625-637.
19. Townsend Jeffrey P. and Hartl Daniel L.: Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple treatments or samples. Genome Biology 2002, 3:research0071.1-71.16.
20. Velculescu Victor E., Zhang Lin, Zhou Wei, Vogelstein Jacob, Basrai Munira, Bassett Douglas E., Hieter Phil, Vogelstein Bert and Kinzler Kenneth W.: Characterization of the yeast transcriptome. Cell 1997, 88:243-251.
21. Shamji Alykhan, Kuruvilla Finny G. and Schreiber Stuart: Partitioning the transcriptional program induced by rapamycin among the effectors of the Tor proteins. Current Biology 2000, 10: 574-1580.
22. Furlong Eileen E. M., Andersen Erik C., Null Brian, White Kevin P. and Scott Matthew P.: Patterns of gene expression during drosophila mesoderm development. Science 2001, 293:.
23. Kerr M. Kathleen and Churchill Gary A.: Experimental design for gene expression microarrays. Biostatistics 2001, 2:183-201.
24. Eisen MB and Brown PO: DNA arrays for analysis of gene expression. Methods Enzymol. 1999, 303:179-205.
25. Velculescu Victor E., Zhang Lin, Vogelstein Bert and Kinzler Kenneth: Serial analysis of gene expression. Science 1995, 270:484-487.