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Application of One Sided t-tests and a Generalized Experiment Wise Error Rate to High-Density Oligonucleotide Microarray Experiments: An Example Using Arabidopsis
並列摘要
Motivation: A formidable challenge in the analysis of microarray data is the identification of those genes that exhibit differential expression. The objectives of this research were to examine the utility of simple ANOVA, one sided t tests, natural log transformation, and a generalized experiment wise error rate methodology for analysis of such experiments. As a test case, we analyzed a Affymetrix GeneChip microarray experiment designed to test for the effect of a CHD3 chromatin remodeling factor, PICKLE, and an inhibitor of the plant hormone gibberellin (GA), on the expression of 8256 Arabidopsis thaliana genes. Results: The GFWER(k) is defined as the probability of rejecting k or more true null hypothesis at a given p level. Computing probabilities by GFWER(k) was shown to be simple to apply and, depending on the value of k, can greatly increase power. A k value as small as 2 or 3 was concluded to be adequate for large or small experiments respectively. A one sided t-test along with GFWER(2)=.05 identified 43 genes as exhibiting PICKLE-dependent expression. Expression of all 43 genes was re-examined by qRT-PCR, of which 36 (83.7%) were confirmed to exhibit PICKLE-dependent expression.
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延伸閱讀
- 李源芳（2012）。Studies on the Involvement of Arabidopsis thaliana Heptahelical Protein 1 in Stoma and Primary Root Responses to Abscisic Acid〔碩士論文，國立臺灣大學〕。華藝線上圖書館。https://doi.org/10.6342/NTU.2012.02046
- 李孟兒 (2012). Molecular Cloning, Protein Expression and Activity Assay of Triterpenoid Tailoring Cytochrome P450 Hydroxylases from Glycyrrhiza glabra and Arabidopsis thaliana [master's thesis, National Chiao Tung University]. Airiti Library. https://doi.org/10.6842/NCTU.2012.00978
- Wang, C. T. (2020). Using deep learning to predict gene structures of the coding genes in DNA sequences of Arabidopsis thaliana [master's thesis, National Taiwan University]. Airiti Library. https://doi.org/10.6342/NTU202002143
- Wang, 王. C. (2012). Using a forward genetic approach for the identification of novel heat tolerance determinants and characterization of their protecting mechanisms in Arabidopsis [doctoral dissertation, National Central University]. Airiti Library. https://www.airitilibrary.com/Article/Detail?DocID=U0031-1903201314433524
- Geisler, M., Gibson, D. J., Lindsey, K. J., Millar, K., & J.\dWood, A. (2012). Upregulation of Photosynthesis Genes, and Downregulation of Stress Defense Genes, is the Response of Arabidopsis Thaliana Shoots to Intraspecific Competition. Botanical Studies, 53(1), 85-96. https://www.airitilibrary.com/Article/Detail?DocID=1817406X-201201-201203050011-201203050011-86-97