Predicting proteome dynamics using gene expression data

Scientific Reports
Krzysztof KuchtaMaga Rowicka

Abstract

While protein concentrations are physiologically most relevant, measuring them globally is challenging. mRNA levels are easier to measure genome-wide and hence are typically used to infer the corresponding protein abundances. The steady-state condition (assumption that protein levels remain constant) has typically been used to calculate protein concentrations, as it is mathematically convenient, even though it is often not satisfied. Here, we propose a method to estimate genome-wide protein abundances without this assumption. Instead, we assume that the system returns to its baseline at the end of the experiment, which is true for cyclic phenomena (e.g. cell cycle) and many time-course experiments. Our approach only requires availability of gene expression and protein half-life data. As proof-of-concept, we predicted proteome dynamics associated with the budding yeast cell cycle, the results are available for browsing online at http://dynprot.cent.uw.edu.pl/ . The approach was validated experimentally by verifying that the predicted protein concentration changes were consistent with measurements for all proteins tested. Additionally, if proteomic data are available as well, we can also infer changes in protein half-lives in res...Continue Reading

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Citations

Nov 11, 2020·Nature Reviews. Genetics·Erick ArmingolNathan E Lewis
Dec 18, 2020·Molecular Systems Biology·Dominick MatteauSébastien Rodrigue

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Methods Mentioned

BETA
FACS

Software Mentioned

- Snap
SCEPTRANS webserver
Gene
MaxEnt
SCEPTRANS

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