Figure 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. 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). (C) Boxplot depicting the distribution of protein-RNA correlation (x-axis) as a function of subcellular location (y-axis). Rank plots of median RNA-protein r_Pearson across (D) protein complexes or (E) biochemical pathways. Colors indicate databases from which the module sets were curated. (F) Representative examples of RNA-protein discordance profiles (for any given gene, mean across replicate is shown) for various stages. (G) Boxplot depicting the distributions of RNA-protein discordances (for any given gene, mean across replicates is shown) for various mouse stages. (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. Color scale indicates the p-value adjusted using the Benjamini-Hochberg procedure and sizes of dots indicate the number of genes detected within each term. (I) Median RNA-protein discordances of members of protein complexes at each stage of mouse gastruloid development. (J) Comparison of the RNA and protein log₂-scaled fold-changes between early vs. late mouse gastruloids in the Mediator complex (left), intraflagellar transport complex B (middle), and mitochondrial Complex I of the oxidative phosphorylation pathway. Significance testing on RNA and protein distributions was performed using a standard t-test.