Figure 7

BRAT-associated mRNAs are globally upregulated in brat-mutant embryos. Scatterplots of RMA-normalized signal intensity in brat mutant versus w ¹¹¹⁸ embryos at (A) 0 to 1.5 h, (B) 1.5 to 3.0 h, (C) 3.0 to 4.5 h, and (D) 4.5 to 6.0 h post egglaying. Plots show all transcripts represented on the microarray that were defined as expressed (see Methods). Values represent averages from three independent biological replicates. The solid diagonal line represents no enrichment. Transcripts up or down in brat mutant embryos compared to wild-type embryos with an FDR <5% were defined as up- or downregulated transcripts, and are highlighted with orange and magenta, respectively. Beside each plot are Venn diagrams depicting the overlap between transcripts upregulated at the corresponding timepoint and the set of BRAT-associated mRNAs defined by our RIP-Chip (also see Table 4). Note that these comparisons suggest that the transcripts upregulated at 1.5 to 3.0, 3.0 to 4.5, and 4.5 to 6.0 h are directly regulated by BRAT as they are enriched for BRAT-associated mRNAs. In contrast, those upregulated at 0 to 1.5 h likely reflect changes resulting from secondary effects of the brat mutation. The total number of BRAT-associated transcripts (890) shown in this figure and Figure 8 differs from the number in Figure 1 (1,197) because of differences in the set of expressed genes defined for these two experiments. We only considered the subset of BRAT targets identified in Figure 1 that were also defined as expressed in the brat-mutant time-course shown here. Likewise, in the Venn diagrams in this figure and in Figure 8 the numbers of transcripts upregulated in brat mutants differ from the numbers in the associated plots. **P <10⁻¹¹ (Bonferroni-corrected Fisher’s exact test).