Additional file 10.
Table 3: Analysis of stress responses for members of some functional classes.From the 1368 stress responsive probe sets we extracted the subsets associated with genes annotated in the GO database as a) glutathione transferases (GO:0004364), b) P450 cytochromes (from list at http://p450.antibes.inra.fr/) and c) proteasome component (GO:0004299). For each probe set k within one of these subsets, we calculated and reported in this table, for each stress condition, the mean ratio <Stress condition >k =<(AVstressi / AVref j)>i,j where AVstressi and AVrefj correspond to the average value measured for the ith sample in the stress condition and the jth sample respectively in the reference condition. To facilitate visual inspection, we used a color code (red corresponding to upregulation, green to downregulation) with thresholds corresponding to fold changes of 1.8 (dark colors), 1.5 (medium) and 1.25 (light). The standard error for each measurement is given in parenthesis. For each probe set, the mean detection p-value from MAS5 analysis of reference samples is reported in column 3 and cluster assignment in column 8. In column 9 additional information is reported for each class: in a) we indicate the GT class deduced from sequence comparison with human and mouse GTs and from  (D: delta, O: omega, T: theta, T2: distantly related to theta, Z: zeta); in b) the name of the genes are reported; in c) we indicate the proteasome subunit to which the genes defined in column 2 belong. Note that in c) a large number of genes not retained by SAM analysis (without cluster number) seem to be upregulated in P15 condition. Genes used for comparison between microarray and quantitative RT-PCR (Fig. 3) are outlined in bold character.
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Girardot et al. BMC Genomics 2004 5:74 doi:10.1186/1471-2164-5-74