Figure 3

Differential expression analysis during the transition from embryonic stage 16 to 17. (A) Analysis of the transcriptome of WT and Ho sall mutant embryos during the transition from stage 16 to 17. Scatter plot of log2 fold gene expression changes from the first to the second condition versus the mean counts for each compared pair. Unique counts normalized by the effective library size were used. Each point corresponds to a gene. Genes without significant change in their expression levels appear along the zero value of the y-axis (grey), and those whose transcription exceeds the threshold defined as statistically significant (p < 0.001, differentially expressed at 0.1% False Discovery Rate) are shown in red, above the y-axis zero value (genes upregulated at the transition from stage 16 to 17, number in black) or below (genes downregulated at this stage transition, number in grey). (B) Venn diagrams of differential expression overlap during the transition 16 to 17 of all genotypes analyzed. Genotypes analyzed: WT16 vs WT17, He16 vs He17, and Ho16 vs Ho17. Numbers indicate upregulated and downregulated genes for each comparison (top and bottom numbers, respectively) at stage 17 with respect to 16.