Extended Data Fig. 5: Correlations between transcriptomes, proteomes and phosphoproteomes.
From: Mass-spectrometry-based draft of the Arabidopsis proteome
a, Median PTRs across tissues plotted against the inter-tissue variation of these PTRs (expressed as MAD; proteins and transcripts had to be detected in at least 10 matching tissues to be included in the analysis). Arrows denote examples of genes with high PTRs (rbcL and petA) and low PTRs (IAA8 and IAA13). Bar plot shows the MAD range segmented into five quantiles, each containing the same number of genes (coloured bars and dashed lines). Most genes have reasonably stable PTRs across tissues. b, As in a (dataset n = 14,069) but for transcript (left) and protein (right) measurements. There is more variation in protein levels across tissues than there is mRNA variation (80% of all transcripts show a MAD of <1; 80% of all proteins show a MAD of 1.2). There is also more variation in the protein levels across tissues for low abundant proteins. This may in part be due to technical limitations as low abundance proteins can generally be less accurately quantified. c, As in a but for the ratio of phosphorylation site versus protein abundance. P-sites and proteins had to be detected in at least 10 matching tissues to be included in the analysis (n = 13,793). d, As in b (dataset n = 13,793) but for P-site abundance. P-site abundance shows greater variation across tissues than protein abundance (60% of all P-sites show MAD <1 compared with 80% of all proteins; see b). Again, this may in part be due to technical limitations as P-site quantification is performed on a peptide level and does not benefit from aggregating multiple peptide quantifications into one value for protein quantification.
