TRIMER: Transcription Regulation Integrated with Metabolic Regulation

Summary: There has been extensive research in predictive modeling of genome-scale metabolic reaction networks. Living systems involve complex stochastic processes arising from interactions among different biomolecules. For more accurate and robust prediction of target metabolic behavior under differ...

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Autores principales:	Puhua Niu, Maria J. Soto, Byung-Jun Yoon, Edward R. Dougherty, Francis J. Alexander, Ian Blaby, Xiaoning Qian
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2021
Materias:	Bioinformatics Metabolomics Transcriptomics Science Q
Acceso en línea:	https://doaj.org/article/b253c942230f463e93206d40f5a39f37
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spelling	oai:doaj.org-article:b253c942230f463e93206d40f5a39f372021-11-20T05:08:23ZTRIMER: Transcription Regulation Integrated with Metabolic Regulation2589-004210.1016/j.isci.2021.103218https://doaj.org/article/b253c942230f463e93206d40f5a39f372021-11-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S258900422101186Xhttps://doaj.org/toc/2589-0042Summary: There has been extensive research in predictive modeling of genome-scale metabolic reaction networks. Living systems involve complex stochastic processes arising from interactions among different biomolecules. For more accurate and robust prediction of target metabolic behavior under different conditions, not only metabolic reactions but also the genetic regulatory relationships involving transcription factors (TFs) affecting these metabolic reactions should be modeled. We have developed a modeling and simulation pipeline enabling the analysis of Transcription Regulation Integrated with Metabolic Regulation: TRIMER. TRIMER utilizes a Bayesian network (BN) inferred from transcriptomes to model the transcription factor regulatory network. TRIMER then infers the probabilities of the gene states relevant to the metabolism of interest, and predicts the metabolic fluxes and their changes that result from the deletion of one or more transcription factors at the genome scale. We demonstrate TRIMER’s applicability to both simulated and experimental data and provide performance comparison with other existing approaches.Puhua NiuMaria J. SotoByung-Jun YoonEdward R. DoughertyFrancis J. AlexanderIan BlabyXiaoning QianElsevierarticleBioinformaticsMetabolomicsTranscriptomicsScienceQENiScience, Vol 24, Iss 11, Pp 103218- (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Bioinformatics Metabolomics Transcriptomics Science Q
spellingShingle	Bioinformatics Metabolomics Transcriptomics Science Q Puhua Niu Maria J. Soto Byung-Jun Yoon Edward R. Dougherty Francis J. Alexander Ian Blaby Xiaoning Qian TRIMER: Transcription Regulation Integrated with Metabolic Regulation
description	Summary: There has been extensive research in predictive modeling of genome-scale metabolic reaction networks. Living systems involve complex stochastic processes arising from interactions among different biomolecules. For more accurate and robust prediction of target metabolic behavior under different conditions, not only metabolic reactions but also the genetic regulatory relationships involving transcription factors (TFs) affecting these metabolic reactions should be modeled. We have developed a modeling and simulation pipeline enabling the analysis of Transcription Regulation Integrated with Metabolic Regulation: TRIMER. TRIMER utilizes a Bayesian network (BN) inferred from transcriptomes to model the transcription factor regulatory network. TRIMER then infers the probabilities of the gene states relevant to the metabolism of interest, and predicts the metabolic fluxes and their changes that result from the deletion of one or more transcription factors at the genome scale. We demonstrate TRIMER’s applicability to both simulated and experimental data and provide performance comparison with other existing approaches.
format	article
author	Puhua Niu Maria J. Soto Byung-Jun Yoon Edward R. Dougherty Francis J. Alexander Ian Blaby Xiaoning Qian
author_facet	Puhua Niu Maria J. Soto Byung-Jun Yoon Edward R. Dougherty Francis J. Alexander Ian Blaby Xiaoning Qian
author_sort	Puhua Niu
title	TRIMER: Transcription Regulation Integrated with Metabolic Regulation
title_short	TRIMER: Transcription Regulation Integrated with Metabolic Regulation
title_full	TRIMER: Transcription Regulation Integrated with Metabolic Regulation
title_fullStr	TRIMER: Transcription Regulation Integrated with Metabolic Regulation
title_full_unstemmed	TRIMER: Transcription Regulation Integrated with Metabolic Regulation
title_sort	trimer: transcription regulation integrated with metabolic regulation
publisher	Elsevier
publishDate	2021
url	https://doaj.org/article/b253c942230f463e93206d40f5a39f37
work_keys_str_mv	AT puhuaniu trimertranscriptionregulationintegratedwithmetabolicregulation AT mariajsoto trimertranscriptionregulationintegratedwithmetabolicregulation AT byungjunyoon trimertranscriptionregulationintegratedwithmetabolicregulation AT edwardrdougherty trimertranscriptionregulationintegratedwithmetabolicregulation AT francisjalexander trimertranscriptionregulationintegratedwithmetabolicregulation AT ianblaby trimertranscriptionregulationintegratedwithmetabolicregulation AT xiaoningqian trimertranscriptionregulationintegratedwithmetabolicregulation
_version_	1718419561938681856

TRIMER: Transcription Regulation Integrated with Metabolic Regulation

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