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Link to the Joint Probability Method
Our Array Data has been placed in the GEO database at NCBI under the
base platform GPL71 (not GPL244 as published) with the reference series GDS378. Note 1: Statistical Analysis of Array Data: The experimental design consisted
of four treatments with four replications per treatment, for a total of sixteen
chips. The treatment categories were
untreated wild type (Wt), untreated pkl
mutant (Pkl), uniconazole-P treated wild type (Uwt) and uniconazole-P treated pkl mutant (Upkl). The Affymetrix Differences in gene expression were evaluated in paired comparisons (Pkl vs. Wt and Upkl vs. Uwt). A t-test was generated for each gene pair using the Cyber-T (Long et al., 2001) web interface (http://genex.ncgr.org/genex/cybert). Probability values were generated with and without the Bonferroni correction for multiple comparisons. For the Bonferroni correction, the experiment-wide false positive rate (the probability of declaring an expression difference significant by chance alone) was set at 0.25. The set of genes examined in this paper occurred in the intersection of all of those genes that met criteria p < 0.05 without the Bonferroni correction for the two comparisons (Pkl vs. Wt p < 0.05 n Upkl vs. Uwt p < 0.05). 293 genes in total met these selection criteria. Those genes for which the corresponding transcript level is elevated two-fold or more in pkl seeds in both the absence and presence of uniconazole-P are listed in Table 1a (56 in total). The remaining 237 genes are listed in Table 1b. In addition, we include here the list of genes that occur in the intersection of all of those genes that met criteria p < 0.05 without the Bonferroni correction for the two comparisons (Pkl vs. Upkl p < 0.05 n Wt vs. Uwt p < 0.05) in Table 2, and the list of genes that occur in the intersection of all of those genes that met criteria p < 0.05 without the Bonferroni correction for the three comparisons (Wt vs. Upkl p < 0.05 n Pkl vs. Upkl p < 0.05 n Uwt vs. Upkl p < 0.05) in Table 3. Note 2: Supplementary information for qRT-PCR: Oligonucleotide primer sequences and primer concentrations used for qRT-PCR are available in Table 4. Relative expression values of genes were calculated from critical threshold values as described in ABI User Bulletin #2, part # 4303859B available at http://docs.appliedbiosystems.com/search.taf?_UserReference=6E00E667F6CFB2C43DE24701. Tables 5 through 10 list the critical threshold values for Figures 1, 3, 4, 5, 6, and 7 respectively from the manuscript. 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.
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analysis reported two values
for each gene: the average difference call and the absolute analysis or
presence/absence call (Affymetrix Microarray Suite v. 4.0).