Dataset Information

Celiku_Friedenberg_2022 -- Probabilistic Model Checking of Cancer Metabolism

ABSTRACT: We provide a model of glycolysis and TCA cycle in cancers in which IDH is encountered both in its wild type form as well as mutated and capable of catalyzing an onco-metabolite. The model is constructed using the Probabilistic Symbolic Model Checker (PRISM,https://www.prismmodelchecker.org/) specification language, and properties are specified using a temporal-property specification language. The reaction rates are instantiated using both experimentally derived metabolic flux rate data (under normoxia and hypoxia conditions) as well as derived through a combination of these experimental rates and relative enzyme activity levels estimated using mRNA expression data from patient samples. We provide shell scripts for invoking the freely-available automatic model checker for reasoning about the specified properties.

SUBMITTER: Orieta Celiku

PROVIDER: MODEL2207180001 | BioModels | 2022-07-18

REPOSITORIES: BioModels

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Dataset's files

Source:

			Action	DRS
	MODEL2207180001?filename=prism_glycolysis_tca_maxamount_5.sh	Other
	MODEL2207180001?filename=prism_glycolysis_tca_maxamount_5_gln_varied.sh	Other
	MODEL2207180001?filename=prism_glycolysis_tca_maxamount_5_gluc_varied.sh	Other
	MODEL2207180001?filename=prism_glycolysis_tca_maxamount_5_nut_varied_cumulative.sh	Other
	MODEL2207180001?filename=prism_glycolysis_tca_maxamount_5_nut_varied_saturation.sh	Other

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Publications

Probabilistic model checking of cancer metabolism.

Friedenberg Meir D MD Lita Adrian A Gilbert Mark R MR Larion Mioara M Celiku Orieta O

Scientific reports 20221107 1

Cancer cell metabolism is often deregulated as a result of adaption to meeting energy and biosynthesis demands of rapid growth or direct mutation of key metabolic enzymes. Better understanding of such deregulation can provide new insights on targetable vulnerabilities, but is complicated by the difficulty in probing cell metabolism at different levels of resolution and under different experimental conditions. We construct computational models of glucose and glutamine metabolism with focus on the ...[more]

PMID: 36344581

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