A Standardized Brain Molecular Atlas: A Resource for Systems Modeling and Simulation

Accurate molecular concentrations are essential for reliable analyses of biochemical networks and the creation of predictive models for molecular and systems biology, yet protein and metabolite concentrations used in such models are often poorly constrained or irreproducible. Challenges of using dat...

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Autores principales:	Polina Shichkova, Jay S. Coggan, Henry Markram, Daniel Keller
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	molecular concentrations neuroproteomics quantitative resource data integration mouse brain systems modelling and simulation Neurosciences. Biological psychiatry. Neuropsychiatry RC321-571
Acceso en línea:	https://doaj.org/article/217ae044f21c411faa158fedb031ecc6
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spelling	oai:doaj.org-article:217ae044f21c411faa158fedb031ecc62021-11-10T06:51:31ZA Standardized Brain Molecular Atlas: A Resource for Systems Modeling and Simulation1662-509910.3389/fnmol.2021.604559https://doaj.org/article/217ae044f21c411faa158fedb031ecc62021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fnmol.2021.604559/fullhttps://doaj.org/toc/1662-5099Accurate molecular concentrations are essential for reliable analyses of biochemical networks and the creation of predictive models for molecular and systems biology, yet protein and metabolite concentrations used in such models are often poorly constrained or irreproducible. Challenges of using data from different sources include conflicts in nomenclature and units, as well as discrepancies in experimental procedures, data processing and implementation of the model. To obtain a consistent estimate of protein and metabolite levels, we integrated and normalized data from a large variety of sources to calculate Adjusted Molecular Concentrations. We found a high degree of reproducibility and consistency of many molecular species across brain regions and cell types, consistent with tight homeostatic regulation. We demonstrated the value of this normalization with differential protein expression analyses related to neurodegenerative diseases, brain regions and cell types. We also used the results in proof-of-concept simulations of brain energy metabolism. The standardized Brain Molecular Atlas overcomes the obstacles of missing or inconsistent data to support systems biology research and is provided as a resource for biomolecular modeling.Polina ShichkovaJay S. CogganHenry MarkramHenry MarkramDaniel KellerFrontiers Media S.A.articlemolecular concentrationsneuroproteomicsquantitative resourcedata integrationmouse brainsystems modelling and simulationNeurosciences. Biological psychiatry. NeuropsychiatryRC321-571ENFrontiers in Molecular Neuroscience, Vol 14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	molecular concentrations neuroproteomics quantitative resource data integration mouse brain systems modelling and simulation Neurosciences. Biological psychiatry. Neuropsychiatry RC321-571
spellingShingle	molecular concentrations neuroproteomics quantitative resource data integration mouse brain systems modelling and simulation Neurosciences. Biological psychiatry. Neuropsychiatry RC321-571 Polina Shichkova Jay S. Coggan Henry Markram Henry Markram Daniel Keller A Standardized Brain Molecular Atlas: A Resource for Systems Modeling and Simulation
description	Accurate molecular concentrations are essential for reliable analyses of biochemical networks and the creation of predictive models for molecular and systems biology, yet protein and metabolite concentrations used in such models are often poorly constrained or irreproducible. Challenges of using data from different sources include conflicts in nomenclature and units, as well as discrepancies in experimental procedures, data processing and implementation of the model. To obtain a consistent estimate of protein and metabolite levels, we integrated and normalized data from a large variety of sources to calculate Adjusted Molecular Concentrations. We found a high degree of reproducibility and consistency of many molecular species across brain regions and cell types, consistent with tight homeostatic regulation. We demonstrated the value of this normalization with differential protein expression analyses related to neurodegenerative diseases, brain regions and cell types. We also used the results in proof-of-concept simulations of brain energy metabolism. The standardized Brain Molecular Atlas overcomes the obstacles of missing or inconsistent data to support systems biology research and is provided as a resource for biomolecular modeling.
format	article
author	Polina Shichkova Jay S. Coggan Henry Markram Henry Markram Daniel Keller
author_facet	Polina Shichkova Jay S. Coggan Henry Markram Henry Markram Daniel Keller
author_sort	Polina Shichkova
title	A Standardized Brain Molecular Atlas: A Resource for Systems Modeling and Simulation
title_short	A Standardized Brain Molecular Atlas: A Resource for Systems Modeling and Simulation
title_full	A Standardized Brain Molecular Atlas: A Resource for Systems Modeling and Simulation
title_fullStr	A Standardized Brain Molecular Atlas: A Resource for Systems Modeling and Simulation
title_full_unstemmed	A Standardized Brain Molecular Atlas: A Resource for Systems Modeling and Simulation
title_sort	standardized brain molecular atlas: a resource for systems modeling and simulation
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/217ae044f21c411faa158fedb031ecc6
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A Standardized Brain Molecular Atlas: A Resource for Systems Modeling and Simulation

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