Csardi, GaborFranks, Alexander M.Choi, David S.Airoldi, EdoardoDrummond, D. Allan2015-06-022015Csárdi, Gábor, Alexander Franks, David S. Choi, Edoardo M. Airoldi, and D. Allan Drummond. 2015. “Accounting for Experimental Noise Reveals That mRNA Levels, Amplified by Post-Transcriptional Processes, Largely Determine Steady-State Protein Levels in Yeast.” PLoS Genetics 11 (5): e1005206. doi:10.1371/journal.pgen.1005206. http://dx.doi.org/10.1371/journal.pgen.1005206.1553-7390http://nrs.harvard.edu/urn-3:HUL.InstRepos:16120929Cells respond to their environment by modulating protein levels through mRNA transcription and post-transcriptional control. Modest observed correlations between global steady-state mRNA and protein measurements have been interpreted as evidence that mRNA levels determine roughly 40% of the variation in protein levels, indicating dominant post-transcriptional effects. However, the techniques underlying these conclusions, such as correlation and regression, yield biased results when data are noisy, missing systematically, and collinear---properties of mRNA and protein measurements---which motivated us to revisit this subject. Noise-robust analyses of 24 studies of budding yeast reveal that mRNA levels explain more than 85% of the variation in steady-state protein levels. Protein levels are not proportional to mRNA levels, but rise much more rapidly. Regulation of translation suffices to explain this nonlinear effect, revealing post-transcriptional amplification of, rather than competition with, transcriptional signals. These results substantially revise widely credited models of protein-level regulation, and introduce multiple noise-aware approaches essential for proper analysis of many biological phenomena.en-USJournal Article2015-06-0210.1371/journal.pgen.1005206