Fig. 4: Gastruloid stages and gene modules exhibit varying degrees of RNA–protein discordance.

a, Histogram of correlations (r_Pearson) between protein and RNA expression for all genes detected at the transcript and protein level in our samplings of human and mouse gastruloid development. The dashed line indicates the mean r_Pearson across all genes. Representative genes with varying extents of correlation are highlighted. b, GO-term dotplot highlighting GO-defined biological processes exhibiting high RNA–protein correlation (r_Pearson ≥ 0.75) or anticorrelation (r_Pearson ≤ −0.75). The colour scale indicates the P value adjusted using the BH procedure (correcting for multiple hypothesis testing), and sizes of dots indicate the number of genes detected within each term. c, Boxplot depicting the distribution of protein–RNA correlation (x axis) across 6,010 genes as a function of subcellular location (y axis). d,e, Rank plots of median RNA–protein r_Pearson across protein complexes (d) or biochemical pathways (e). Colours indicate databases from which the module sets were curated. f, Representative examples of RNA–protein discordance profiles (for any given gene, the mean across replicates is shown) for various stages. g, Boxplot depicting the distributions of RNA–protein discordances (for any given gene, the mean across biological replicates is shown). Boxplots show the median (centre line), 25th–75th percentiles (box), 1.5× the interquartile range (line; end points signify maxima and minima). Mean protein and RNA abundance were calculated from three and two biological replicates, respectively, for various mouse stages. Significance was determined using a standard t-test. (NS, not significant; **P < 0.01, ***P < 0.001. h, Dotplot highlighting the biological processes significantly enriched in genes exhibiting protein-abundant (circles; discordance ≥ 1) or RNA-abundant (triangles; discordance ≤ −1) RNA–protein discordance. The colour scale indicates the P value adjusted using the BH procedure (correcting for multiple hypothesis testing), and sizes of dots indicate the number of genes detected within each term.