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Fig. s3 A. Venn diagram showing the overlap of genes that are significantly upregulated in EJC mutant embryos and upf1 morphant embryos at 24 hpf [55]. Hypergeometric test p-values for each comparison are also shown. B. MA plot showing the genes that are altered in expression (fold change > 1.5 and FDR < 0.05 in red and unchanged genes in gray) in upf1 morphant embryos compared to control embryos at 12 hpf. The number of significantly upregulated genes is at the top right and the number of downregulated genes is at the bottom right. C. Venn diagram showing the overlap of significantly upregulated genes in upf1 morphant embryos at 24 hpf [55] and upf1 morphant embryos at 12 hpf. Hypergeometric test p-value for the comparison is indicated. D. Empirical CDF plot showing the fold changes in upf1 morphant embryos (24 hpf) [55] of upregulated (blue) and unchanged genes (black) in 21 hpf magoh mutant embryos. Kolmogorov-Smirnov (KS) test p-value for differences in the two distributions are indicated at the bottom of the class descriptions. E. Empirical CDF plot as in S3D for upregulated (red) and unchanged genes (black) in rbm8a mutant embryos at 21 hpf. F. Empirical CDF plot as in S3D for upregulated (red) and unchanged genes (black) in rbm8a mutant embryos at 27 hpf. G. Empirical CDF plot showing the fold changes in upf1 morphants (12 hpf) of upregulated (red) and unchanged genes (black) in rbm8a mutant embryos at 21 hpf. H and I. Proportion of uORF-containing (H) or 3′UI-containing (I) genes in the total number of genes showing significant (FDR < 0.05) fold changes in rbm8a mutant, magoh mutant and upf1 morphant embryos. Genes are divided into four categories based on their log2 fold change: >1.5, 1.5 to 0, 0 to -1.5 and < 1.5.