Advanced fault diagnosis methods in molecular networks.

Analysis of the failure of cell signaling networks is an important topic in systems biology and has applications in target discovery and drug development. In this paper, some advanced methods for fault diagnosis in signaling networks are developed and then applied to a caspase network and an SHP2 ne...

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Autores principales:	Iman Habibi, Effat S Emamian, Ali Abdi
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/cd0cb0fa723f4717b61e515c45a3f0b9
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spelling	oai:doaj.org-article:cd0cb0fa723f4717b61e515c45a3f0b92021-11-25T05:57:39ZAdvanced fault diagnosis methods in molecular networks.1932-620310.1371/journal.pone.0108830https://doaj.org/article/cd0cb0fa723f4717b61e515c45a3f0b92014-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0108830https://doaj.org/toc/1932-6203Analysis of the failure of cell signaling networks is an important topic in systems biology and has applications in target discovery and drug development. In this paper, some advanced methods for fault diagnosis in signaling networks are developed and then applied to a caspase network and an SHP2 network. The goal is to understand how, and to what extent, the dysfunction of molecules in a network contributes to the failure of the entire network. Network dysfunction (failure) is defined as failure to produce the expected outputs in response to the input signals. Vulnerability level of a molecule is defined as the probability of the network failure, when the molecule is dysfunctional. In this study, a method to calculate the vulnerability level of single molecules for different combinations of input signals is developed. Furthermore, a more complex yet biologically meaningful method for calculating the multi-fault vulnerability levels is suggested, in which two or more molecules are simultaneously dysfunctional. Finally, a method is developed for fault diagnosis of networks based on a ternary logic model, which considers three activity levels for a molecule instead of the previously published binary logic model, and provides equations for the vulnerabilities of molecules in a ternary framework. Multi-fault analysis shows that the pairs of molecules with high vulnerability typically include a highly vulnerable molecule identified by the single fault analysis. The ternary fault analysis for the caspase network shows that predictions obtained using the more complex ternary model are about the same as the predictions of the simpler binary approach. This study suggests that by increasing the number of activity levels the complexity of the model grows; however, the predictive power of the ternary model does not appear to be increased proportionally.Iman HabibiEffat S EmamianAli AbdiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 10, p e108830 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Iman Habibi Effat S Emamian Ali Abdi Advanced fault diagnosis methods in molecular networks.
description	Analysis of the failure of cell signaling networks is an important topic in systems biology and has applications in target discovery and drug development. In this paper, some advanced methods for fault diagnosis in signaling networks are developed and then applied to a caspase network and an SHP2 network. The goal is to understand how, and to what extent, the dysfunction of molecules in a network contributes to the failure of the entire network. Network dysfunction (failure) is defined as failure to produce the expected outputs in response to the input signals. Vulnerability level of a molecule is defined as the probability of the network failure, when the molecule is dysfunctional. In this study, a method to calculate the vulnerability level of single molecules for different combinations of input signals is developed. Furthermore, a more complex yet biologically meaningful method for calculating the multi-fault vulnerability levels is suggested, in which two or more molecules are simultaneously dysfunctional. Finally, a method is developed for fault diagnosis of networks based on a ternary logic model, which considers three activity levels for a molecule instead of the previously published binary logic model, and provides equations for the vulnerabilities of molecules in a ternary framework. Multi-fault analysis shows that the pairs of molecules with high vulnerability typically include a highly vulnerable molecule identified by the single fault analysis. The ternary fault analysis for the caspase network shows that predictions obtained using the more complex ternary model are about the same as the predictions of the simpler binary approach. This study suggests that by increasing the number of activity levels the complexity of the model grows; however, the predictive power of the ternary model does not appear to be increased proportionally.
format	article
author	Iman Habibi Effat S Emamian Ali Abdi
author_facet	Iman Habibi Effat S Emamian Ali Abdi
author_sort	Iman Habibi
title	Advanced fault diagnosis methods in molecular networks.
title_short	Advanced fault diagnosis methods in molecular networks.
title_full	Advanced fault diagnosis methods in molecular networks.
title_fullStr	Advanced fault diagnosis methods in molecular networks.
title_full_unstemmed	Advanced fault diagnosis methods in molecular networks.
title_sort	advanced fault diagnosis methods in molecular networks.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/cd0cb0fa723f4717b61e515c45a3f0b9
work_keys_str_mv	AT imanhabibi advancedfaultdiagnosismethodsinmolecularnetworks AT effatsemamian advancedfaultdiagnosismethodsinmolecularnetworks AT aliabdi advancedfaultdiagnosismethodsinmolecularnetworks
_version_	1718414368145670144

Advanced fault diagnosis methods in molecular networks.

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