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Mean of the typical decoding rates: a new translation efficiency index based on the analysis of ribosome profiling data.

Dana A, Tuller T - G3 (Bethesda) (2014)

Bottom Line: The suggested translation efficiency index is based on the analysis of the organism's ribosome profiling data.This index could be used for example to predict changes in translation elongation efficiency of lowly expressed genes that usually have relatively low and/or biased ribosomal densities and protein levels measurements, or can be used for example for predicting translation efficiency of new genetically engineered genes.We demonstrate the usability of this index via the analysis of six organisms in different tissues and developmental stages.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Ramat Aviv 69978, Israel.

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Protein abundance (PA) vs. mean of the typical decoding rates (MTDR) and Spearman correlation between MTDR index and protein abundance for various organisms.
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fig3: Protein abundance (PA) vs. mean of the typical decoding rates (MTDR) and Spearman correlation between MTDR index and protein abundance for various organisms.

Mentions: The usability of the suggested MTDR index was validated for four different organisms that have abundant large scale protein and mRNA levels measurements (E. coli, B. subtilis, C. elegans, and S. cerevisiae). Spearman correlation between the MTDR index to various proxies of translation efficiency such as protein abundance resulted in significant correlations (0.32< r < 0.44; P < 3.8*10−87; see also Figure 3 and Table 3). Similarly, a significant partial Spearman correlation between protein abundance and MTDR index given mRNA levels (partial correlation) was observed (0.23 < r < 0.5; P < 4.2*10−86; see Table 3).


Mean of the typical decoding rates: a new translation efficiency index based on the analysis of ribosome profiling data.

Dana A, Tuller T - G3 (Bethesda) (2014)

Protein abundance (PA) vs. mean of the typical decoding rates (MTDR) and Spearman correlation between MTDR index and protein abundance for various organisms.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4291471&req=5

fig3: Protein abundance (PA) vs. mean of the typical decoding rates (MTDR) and Spearman correlation between MTDR index and protein abundance for various organisms.
Mentions: The usability of the suggested MTDR index was validated for four different organisms that have abundant large scale protein and mRNA levels measurements (E. coli, B. subtilis, C. elegans, and S. cerevisiae). Spearman correlation between the MTDR index to various proxies of translation efficiency such as protein abundance resulted in significant correlations (0.32< r < 0.44; P < 3.8*10−87; see also Figure 3 and Table 3). Similarly, a significant partial Spearman correlation between protein abundance and MTDR index given mRNA levels (partial correlation) was observed (0.23 < r < 0.5; P < 4.2*10−86; see Table 3).

Bottom Line: The suggested translation efficiency index is based on the analysis of the organism's ribosome profiling data.This index could be used for example to predict changes in translation elongation efficiency of lowly expressed genes that usually have relatively low and/or biased ribosomal densities and protein levels measurements, or can be used for example for predicting translation efficiency of new genetically engineered genes.We demonstrate the usability of this index via the analysis of six organisms in different tissues and developmental stages.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Ramat Aviv 69978, Israel.

Show MeSH