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Predicting proteome dynamics using gene expression data

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dc.abstract.enWhile 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 response to posttranslational regulation, as we did for Clb2, a post-translationally regulated protein. The predicted changes in Clb2 abundance are consistent with earlier observations.
dc.affiliationUniwersytet Warszawski
dc.contributor.authorKudlicki, Andrzej
dc.contributor.authorKutner, Jan
dc.contributor.authorRowicka, Maga
dc.contributor.authorBiernacka, Anna
dc.contributor.authorTowpik, Joanna
dc.contributor.authorKuchta, Krzysztof
dc.contributor.authorGinalski, Krzysztof
dc.date.accessioned2024-01-25T17:32:30Z
dc.date.available2024-01-25T17:32:30Z
dc.date.issued2018
dc.description.financeNie dotyczy
dc.identifier.doi10.1038/S41598-018-31752-4
dc.identifier.issn2045-2322
dc.identifier.urihttps://repozytorium.uw.edu.pl//handle/item/116904
dc.identifier.weblinkhttps://www.nature.com/articles/s41598-018-31752-4
dc.languageeng
dc.pbn.affiliationbiological sciences
dc.relation.ispartofScientific Reports
dc.rightsClosedAccess
dc.sciencecloudnosend
dc.subject.en2018 Ginalski
dc.titlePredicting proteome dynamics using gene expression data
dc.typeJournalArticle
dspace.entity.typePublication