Fig. 4

Microarray filtering strategy of differentially expressed genes (DEGs): The microarray experiment is based on two biologically independent sample sets (1st, 2nd set) of two mouse lines (FL2, Ctrl). The 1st set analyzed for differential gene expression, while the 2nd set experimentally confirmed differential expression (see section microarray experimental design Material & Methods). The gene chip MTA 1.0 (Affymetrix) is equipped with 65,770 probe sets (PS). Using the gene expression detection the number of expressed genes within each sample set was evaluated and served as first filter criteria. (a) The Venn diagram illustrates the number of differentially expressed genes (FL2 vs. Ctrl) detected in 1st, 2nd and both sample sets independent of statistical filter (of 1st array set ANOVA, FDR, Bonferroni). (b) Experimentally verified DEGs were defined as: FC > 1.5; FC < −1.5 (of 1st and 2nd set); one-way ANOVA (of 1st set). The number and percentage of DEGs of the 1st set recovered in the 2nd set are given in table (c)