Nonparametric simulation of signal transduction networks with semi-synchronized update.

Simulating signal transduction in cellular signaling networks provides predictions of network dynamics by quantifying the changes in concentration and activity-level of the individual proteins. Since numerical values of kinetic parameters might be difficult to obtain, it is imperative to develop non...

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Autores principales:	Isar Nassiri, Ali Masoudi-Nejad, Mahdi Jalili, Ali Moeini
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/8aed6c54bd9d4a1c98b3040455fb0848
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spelling	oai:doaj.org-article:8aed6c54bd9d4a1c98b3040455fb08482021-11-18T07:14:43ZNonparametric simulation of signal transduction networks with semi-synchronized update.1932-620310.1371/journal.pone.0039643https://doaj.org/article/8aed6c54bd9d4a1c98b3040455fb08482012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22737250/?tool=EBIhttps://doaj.org/toc/1932-6203Simulating signal transduction in cellular signaling networks provides predictions of network dynamics by quantifying the changes in concentration and activity-level of the individual proteins. Since numerical values of kinetic parameters might be difficult to obtain, it is imperative to develop non-parametric approaches that combine the connectivity of a network with the response of individual proteins to signals which travel through the network. The activity levels of signaling proteins computed through existing non-parametric modeling tools do not show significant correlations with the observed values in experimental results. In this work we developed a non-parametric computational framework to describe the profile of the evolving process and the time course of the proportion of active form of molecules in the signal transduction networks. The model is also capable of incorporating perturbations. The model was validated on four signaling networks showing that it can effectively uncover the activity levels and trends of response during signal transduction process.Isar NassiriAli Masoudi-NejadMahdi JaliliAli MoeiniPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 6, p e39643 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Isar Nassiri Ali Masoudi-Nejad Mahdi Jalili Ali Moeini Nonparametric simulation of signal transduction networks with semi-synchronized update.
description	Simulating signal transduction in cellular signaling networks provides predictions of network dynamics by quantifying the changes in concentration and activity-level of the individual proteins. Since numerical values of kinetic parameters might be difficult to obtain, it is imperative to develop non-parametric approaches that combine the connectivity of a network with the response of individual proteins to signals which travel through the network. The activity levels of signaling proteins computed through existing non-parametric modeling tools do not show significant correlations with the observed values in experimental results. In this work we developed a non-parametric computational framework to describe the profile of the evolving process and the time course of the proportion of active form of molecules in the signal transduction networks. The model is also capable of incorporating perturbations. The model was validated on four signaling networks showing that it can effectively uncover the activity levels and trends of response during signal transduction process.
format	article
author	Isar Nassiri Ali Masoudi-Nejad Mahdi Jalili Ali Moeini
author_facet	Isar Nassiri Ali Masoudi-Nejad Mahdi Jalili Ali Moeini
author_sort	Isar Nassiri
title	Nonparametric simulation of signal transduction networks with semi-synchronized update.
title_short	Nonparametric simulation of signal transduction networks with semi-synchronized update.
title_full	Nonparametric simulation of signal transduction networks with semi-synchronized update.
title_fullStr	Nonparametric simulation of signal transduction networks with semi-synchronized update.
title_full_unstemmed	Nonparametric simulation of signal transduction networks with semi-synchronized update.
title_sort	nonparametric simulation of signal transduction networks with semi-synchronized update.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/8aed6c54bd9d4a1c98b3040455fb0848
work_keys_str_mv	AT isarnassiri nonparametricsimulationofsignaltransductionnetworkswithsemisynchronizedupdate AT alimasoudinejad nonparametricsimulationofsignaltransductionnetworkswithsemisynchronizedupdate AT mahdijalili nonparametricsimulationofsignaltransductionnetworkswithsemisynchronizedupdate AT alimoeini nonparametricsimulationofsignaltransductionnetworkswithsemisynchronizedupdate
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Nonparametric simulation of signal transduction networks with semi-synchronized update.

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