Genome-Scale Analysis of Translation Elongation with a Ribosome Flow Model
Figure 3
Prediction of protein abundance of endogenous genes by the tAI [27] and by the ribosome flow model (RFM).
We compare the RFM to the tAI (insensitive to codon order), the RFM also outperformed other predictors, such as the Bottleneck and the Mean Speed (see definitions in the Methods section; see Figure S1). The predictions were obtained for groups of genes with different levels of protein abundance in different organisms; in each organism all bins are of equal size; organisms with a larger number of measurements enable more bins. A. Predicting protein abundance of E. coli endogenous genes. B. Predicting protein abundance for S. pombe endogenous genes C. Predicting protein abundance for S. cerevisiae endogenous genes [16]. D. Sensitivity to codon order vs. protein abundance in S. cerevisiae.