  Large scale surveys in mammalian tissue culture cells suggest that the
protein expressed at the median abundance is present at 8,000 - 16,000
molecules per cell and that differences in mRNA expression between genes
explain only 10-40% of the differences in protein levels. We find, however,
that these surveys have significantly underestimated protein abundances and the
relative importance of transcription. Using individual measurements for 61
housekeeping proteins to rescale whole proteome data from Schwanhausser et al.,
we find that the median protein detected is expressed at 170,000 molecules per
cell and that our corrected protein abundance estimates show a higher
correlation with mRNA abundances than do the uncorrected protein data. In
addition, we estimated the impact of further errors in mRNA and protein
abundances, showing that mRNA levels explain at least 56% of the differences in
protein abundance for the genes detected by Schwanhausser et al., though
because one major source of error could not be estimated the true percent
contribution could be higher. We also employed a second, independent strategy
to determine the contribution of mRNA levels to protein expression. We show
that the variance in translation rates directly measured by ribosome profiling
is only 12% of that inferred by Schwanhausser et al. and that the measured and
inferred translation rates correlate only poorly (R2=0.13). Based on this, our
second strategy suggests that mRNA levels explain ~81% of the variance in
protein levels. We also determined the percent contributions of transcription,
RNA degradation, translation and protein degradation to the variance in protein
abundances using both of our strategies. While the magnitudes of the two
estimates vary, they both suggest that transcription plays a more important
role than the earlier studies implied and translation a much smaller role.
