Figure 2

The differences in correlation between mRNA and protein expression values using novel categories. We see significant differences when looking at the highest and lowest ranking of groups of ORFs in the following categories: occupancy, CAI (codon adaptation index) value [45–47] and variability. Occupancy refers to the percentage of transcripts associated with ribosomes; we compared the correlation between the top 100 ORFs and the bottom 100 in terms of occupancy (r = 0.78 versus 0.30). For the CAI, we compared the correlation between mRNA and protein for those ORFs with the highest CAI and those with the lowest (r = 0.48 versus 0.02). Variability refers to the normalized standard deviation (that is, the standard deviation divided by the average expression level) for all ORFs in the cell-cycle expression dataset of Cho et al. [38]. Here, we compared the correlations between protein abundance and mRNA expression for the most variable compared with the least variable proteins (r = 0.89 versus 0.20). We found significant differences between the correlations of mRNA and protein levels for the top and bottom ranking populations for each of the comparisons.