Dataset Information

Changes in the transcriptome, proteome and phosphoproteome in a cardiomyocyte model of nitroxidative stress

ABSTRACT: Cells adapt to stress via changes in gene expression, protein degradation and PTMs. However, compared to regulations via PTMs and protein turnover, gene expression is a relatively slow process. We used a multi-omic approach to investigate different dynamics of transcripts, proteins and phosphoproteins during nitroxidative stress.

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE100410 | GEO | 2020/06/22

REPOSITORIES: GEO

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Project description:This a model from the article: Modelling the response of FOXO transcription factors to multiple post-translational modifications made by ageing-related signalling pathways. Smith GR, Shanley DP. PLoS One. 2010 Jun 14;5(6):e11092. 20567500 , Abstract: FOXO transcription factors are an important, conserved family of regulators of cellular processes including metabolism, cell-cycle progression, apoptosis and stress resistance. They are required for the efficacy of several of the genetic interventions that modulate lifespan. FOXO activity is regulated by multiple post-translational modifications (PTMs) that affect its subcellular localization, half-life, DNA binding and transcriptional activity. Here, we show how a mathematical modelling approach can be used to simulate the effects, singly and in combination, of these PTMs. Our model is implemented using the Systems Biology Markup Language (SBML), generated by an ancillary program and simulated in a stochastic framework. The use of the ancillary program to generate the SBML is necessary because the possibility that many regulatory PTMs may be added, each independently of the others, means that a large number of chemically distinct forms of the FOXO molecule must be taken into account, and the program is used to generate them. Although the model does not yet include detailed representations of events upstream and downstream of FOXO, we show how it can qualitatively, and in some cases quantitatively, reproduce the known effects of certain treatments that induce various single and multiple PTMs, and allows for a complex spatiotemporal interplay of effects due to the activation of multiple PTM-inducing treatments. Thus, it provides an important framework to integrate current knowledge about the behaviour of FOXO. The approach should be generally applicable to other proteins experiencing multiple regulations. This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.. To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

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Changes in the transcriptome, proteome and phosphoproteome in a cardiomyocyte model of nitroxidative stress

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