Identification of Smaug-bound mRNAs. The average, across three biological replicates and one technical replicate, of the microarray signal intensities of each expressed transcript in the Smaug and control RIPs divided by the signal intensities of each transcript in the immunoprecipitation inputs, were plotted against one another. SAM analysis allowed for the identification of 384 transcripts (blue dots) representing 339 genes that are enriched in the Smaug RIPs versus control RIPs at an FDR of <5%. The dots representing Smaug’s two known target mRNAs, nanos and Hsp83, are indicated. The dark dashed line represents no enrichment and the light dashed diagonal lines represent two-fold enrichment or depletion.