Extended Data Fig. 4: Relationships between transcript and protein levels.
From: Mass-spectrometry-based draft of the Arabidopsis proteome
a, Pearson’s correlation (r) of transcriptome and proteome expression (core datasets; n = 5,043) for each tissue. b, Pearson’s correlation between measured and predicted protein abundance levels in all tissues. Predicted protein abundance levels were obtained from the best fitting feature selection model for each tissue (Methods). The number of genes used for the correlation analysis is indicated for each tissue. c, Violin plots showing the spread in relative contribution of selected features to the prediction of gene-level protein abundance across tissues (n = 30 tissues) using our model. Violin shapes show the kernel density estimation of the data distribution and the median as white dot. Thick black bars denote the interquartile range. d, Specific nucleotide sequence motifs in 5′ UTRs of mRNAs contribute to the prediction of protein levels in a subset of tissues. Clustering tissues based on the presence or absence of detected 5′ UTR motifs shows that several features are repeatedly selected for inclusion in the model while others appear to be more tissue-specific. e, On the basis of the observation that the dN/dS ratio between orthologous of A. thaliana and A. lyrata contributed to the prediction of protein levels (c), we analysed this feature in more detail. Left, distribution of the dN/dS ratio for orthologous genes in A. thaliana and A. lyrata. The distribution is plotted for the example of ‘leaf distal’ (n = 6,447 genes). To compare evolutionarily conserved genes (defined by low dN/dS ratios) and genes that evolve neutrally or are under positive selection (high dN/dS ratios), we selected the bottom 5% and top 5% of the dN/dS ratio distribution, respectively. Right, evolutionarily conserved genes (low dN/dS ratio) show 10–20 times higher protein abundance than genes under evolutionary pressure. Boxes contain 50% of the data and show the median as a black line. Whiskers denote 1.5 times the interquartile range. Outliers were omitted from the plot for clarity. f, Time-course analysis of median protein abundance changes after treatment with CHX (translation block) or MG132 (proteasome block) versus time-matched DMSO control samples (Methods). Boxes contain 50% of the data and show medians as black lines. Whiskers denote 1.5 times the interquartile range. Outliers were omitted from the plot for clarity but were included in the statistical tests below. All proteins in the experiment (n = 8,920, grey), proteins that have a high PTR in seed (n = 425, red) or a low PTR in seed (n = 254, blue) (defined as in Fig. 3d) are shown. Differences between time points were tested for significance within each subset (all; high PTR; low PTR) using one-way ANOVA and the post hoc Tukey HSD test. ***P < 0.001 (all_CHX8–CHX16: P < 1 × 10−7; all_CHX8–CHX24: P < 1 × 10−7; all_CHX16–CHX24: P = 0.0002; highPTR_CHX8–CHX24: P = 0.0003; lowPTR_CHX8–CHX16: P = 0.0000004; lowPTR_CHX8–CHX24: P < 1 × 10−7; lowPTR_CHX16–CHX24: P < 1 × 10−7). g, Representative images of seeds after 4 days of incubation with CHX, MG132 or DMSO control medium (n = 1). Germination was completely inhibited by CHX and partially inhibited by MG132, showing that the drug treatments were effective.
