Quality criteria for finding genes with high mRNA-protein expression correlation and coexpression correlation

mRNA expression is widely used as a proxy for protein expression. However, their true relation is not known and two genes with the same mRNA levels might have different abundances of respective proteins. A related question is whether the coexpression of mRNA for gene pairs is reflected by the corresponding protein pairs.We examined the mRNA-protein correlation for both expression and coexpression. This analysis yielded insights into the relationship between mRNA and protein abundance, and allowed us to identify subsets of greater mRNA-protein coherence.The correlation between mRNA and protein was low for both expression and coexpression, 0.12 and 0.06 respectively. However, applying the best-performing quality measure, high-quality subsets reached a Spearman correlation of 0.31 for expression, 0.34 for coexpression and 0.49 for coexpression when restricted to functionally coupled genes. Our methodology can thus identify subsets for which the mRNA levels are expected to be the strongest correlated with protein levels.

► Coherence between mRNA and protein abundances has been shown to be low. ► A low coherence implies that using mRNA as a proxy for protein might be unsuitable. ► We show that subsets of genes with greater mRNA-protein coherence can be identified. ► This is accomplished using quality measures based on expression profiles. ► Using high quality subsets improves mRNA's reliability as a proxy for protein.