Figure 1
BRAT and PUM each associate with hundreds of mRNAs in early Drosophila embryos. (A) BRAT associates with mRNAs from 1,197 genes, and (B) PUM associates with mRNAs from 641 genes. Plots show RMA-normalized signal intensity of all transcripts represented on the microarray that were defined as expressed in early embryos, in BRAT RIP or PUM RIP versus Control RIP. Values represent averages from three independent biological replicates. mRNAs with an average enrichment of at least 1.5-fold in the BRAT or PUM RIPs and with an FDR <5% are highlighted in blue or red, respectively. The solid diagonal line represents no enrichment, and dashed diagonal lines represent 1.5-fold enrichment or depletion. (C) Venn diagram demonstrating that there is a modest but statistically significant overlap between BRAT-associated and PUM-associated mRNAs. **Fisher’s exact test P value <10−13. (D) Plot of all transcripts represented on the microarray that were defined as expressed in early embryos, showing fold-enrichment in the BRAT RIP-Chip versus the PUM RIP-Chip. Transcripts associated exclusively with BRAT or PUM (that is, enriched >1.5-fold with an FDR <5%) are highlighted in blue and red, respectively, and transcripts associated with both BRAT and PUM are highlighted in green. Note that the majority of BRAT-associated transcripts show no indication of enrichment in the PUM RIP-Chip, and vice versa; this is further indicated by the negative Spearman’s correlation between the fold-enrichments from the two experiments when transcripts which are enriched in the control in both experiments (that is, the bottom left quadrant of the plot) and therefore expected to be correlated given that the same control was used in both cases, are excluded: Spearman’s rho = −0.188, P <10−37.