Figure 2

(A, B) Genes identified as significantly differentially expressed (p < 0.05) in Arabidopsis thaliana, as a function of the gDNA hybridisation intensity threshold used to generate probe-mask files, for two AtGenExpress experiments [24]. (A) RNA was extracted from leaves 2, 4, 6, 8, 10 and 12, sampled from 17 d old plants (n = 3), labelled and hybridised to the A. thaliana ATH1-121501 GeneChip array, and data were normalised to the median expression value of each gene across all leaves. The number of genes identified as differentially expressed in one, two, three and four of the six conditions are represented by filled circles, squares, triangles and diamonds respectively. (B) RNA was extracted from whole rosettes of 7, 14, and 21 d old plants (n = 3), labelled and hybridised to the A. thaliana ATH1-121501 GeneChip array, and normalised to the median expression value of each gene across all time points. (C) Genes identified as significantly differentially expressed (p < 0.05) in the absence of a probe-mask, as a proportion of the sum of all genes significantly differentially expressed (p < 0.05) when analyses were conducted with and without a corresponding probe-mask. Filled circles represent Data Set A, open circles represent Data Set B.