DOI: 10.5061/dryad.d644f
title: Data from: Accounting for experimental noise reveals that mRNA levels, amplified by post-transcriptional processes, largely determine steady-state protein levels in yeast

description: Cells 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.
description: S. cerevisiae raw mRNA
 and protein measurementsRaw mRNA and protein
 measurements for haploid budding yeast (S.cerevisiae) growing
 exponentially in rich medium with glucosescer-mrna-protein-raw.txtS. cerevisiae log-transformed SCM-normalized mRNA and protein measurementsSCM-normalized mRNA and protein measurements for haploid budding yeast (S.cerevisiae) growing exponentially in rich medium with glucosescer-mrna-protein-normalized.txtS. cerevisiae SCM estimates of mRNA and protein levels, log-transformed and unscaledSCM estimates of mRNA and protein levels, log-transformed and unscaled, for haploid budding yeast (S.cerevisiae) growing exponentially in rich medium with glucosescer-mrna-protein-unscaled-estimate.txtS. cerevisiae log-transformed SCM-normalized mRNA and protein measurements, with imputed valuesSCM-normalized mRNA and protein measurements, with imputed values, for haploid budding yeast (S.cerevisiae) growing exponentially in rich medium with glucosescer-mrna-protein-normalized-imputed.txtS. cerevisiae SCM estimates of mRNA and protein levels, log-transformed and unscaledSCM estimates of mRNA and protein levels, log-transformed and unscaled, for haploid budding yeast (S.cerevisiae) growing exponentially in rich medium with glucosescer-mrna-protein-unscaled-estimate.txtRibosome density, mRNA level, and translational efficiency measurements for haploid budding yeast (S.cerevisiae) growing exponentially in rich medium with glucoseMeasurements and summary statistics for RNA-seq mRNA levels, ribosome footprint density, and translational efficiency for haploid budding yeast (S.cerevisiae) growing exponentially in rich medium with glucosescer-translational-efficiency.txtS. cerevisiae sampled absolute mRNA and protein levels, scaled to (average) molecules per haploid cell, sampled from SCM estimatesmRNA and protein levels, scaled to (average) molecules per haploid cell, sampled according to SCM estimates, for haploid budding yeast (S.cerevisiae) growing exponentially in rich medium with glucosescer-mrna-protein-absolute-estimate-sample.txtS. cerevisiae absolute mRNA and protein levels, scaled to (average) molecules per haploid cell, estimated by SCMSCM estimates of absolute mRNA and protein levels, scaled to (average) molecules per haploid cell, for haploid budding yeast (S.cerevisiae) growing exponentially in rich medium with glucosescer-mrna-protein-absolute-estimate.txt