FBA-PRCC. Partial Rank Correlation Coefficient (PRCC) Global Sensitivity Analysis (GSA) in Application to Constraint-Based Models
Background: Whole-genome models (GEMs) have become a versatile tool for systems biology, biotechnology, and medicine. GEMs created by automatic and semi-automatic approaches contain a lot of redundant reactions. At the same time, the nonlinearity of the model makes it difficult to evaluate the signi...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-03-01
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| Series: | Biomolecules |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2218-273X/13/3/500 |
| _version_ | 1797613203528613888 |
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| author | Anatoly Sorokin Igor Goryanin |
| author_facet | Anatoly Sorokin Igor Goryanin |
| author_sort | Anatoly Sorokin |
| collection | DOAJ |
| description | Background: Whole-genome models (GEMs) have become a versatile tool for systems biology, biotechnology, and medicine. GEMs created by automatic and semi-automatic approaches contain a lot of redundant reactions. At the same time, the nonlinearity of the model makes it difficult to evaluate the significance of the reaction for cell growth or metabolite production. Methods: We propose a new way to apply the global sensitivity analysis (GSA) to GEMs in a straightforward parallelizable fashion. Results: We have shown that Partial Rank Correlation Coefficient (PRCC) captures key steps in the metabolic network despite the network distance from the product synthesis reaction. Conclusions: FBA-PRCC is a fast, interpretable, and reliable metric to identify the sign and magnitude of the reaction contribution to various cellular functions. |
| first_indexed | 2024-03-11T06:52:32Z |
| format | Article |
| id | doaj.art-621d490216084c42b7fad2e778c9f3ea |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-03-11T06:52:32Z |
| publishDate | 2023-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomolecules |
| spelling | doaj.art-621d490216084c42b7fad2e778c9f3ea2023-11-17T09:52:10ZengMDPI AGBiomolecules2218-273X2023-03-0113350010.3390/biom13030500FBA-PRCC. Partial Rank Correlation Coefficient (PRCC) Global Sensitivity Analysis (GSA) in Application to Constraint-Based ModelsAnatoly Sorokin0Igor Goryanin1Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, JapanOkinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, JapanBackground: Whole-genome models (GEMs) have become a versatile tool for systems biology, biotechnology, and medicine. GEMs created by automatic and semi-automatic approaches contain a lot of redundant reactions. At the same time, the nonlinearity of the model makes it difficult to evaluate the significance of the reaction for cell growth or metabolite production. Methods: We propose a new way to apply the global sensitivity analysis (GSA) to GEMs in a straightforward parallelizable fashion. Results: We have shown that Partial Rank Correlation Coefficient (PRCC) captures key steps in the metabolic network despite the network distance from the product synthesis reaction. Conclusions: FBA-PRCC is a fast, interpretable, and reliable metric to identify the sign and magnitude of the reaction contribution to various cellular functions.https://www.mdpi.com/2218-273X/13/3/500whole-genome modelconstraint-based modelmetabolic networkglobal sensitivity analysisFBA |
| spellingShingle | Anatoly Sorokin Igor Goryanin FBA-PRCC. Partial Rank Correlation Coefficient (PRCC) Global Sensitivity Analysis (GSA) in Application to Constraint-Based Models Biomolecules whole-genome model constraint-based model metabolic network global sensitivity analysis FBA |
| title | FBA-PRCC. Partial Rank Correlation Coefficient (PRCC) Global Sensitivity Analysis (GSA) in Application to Constraint-Based Models |
| title_full | FBA-PRCC. Partial Rank Correlation Coefficient (PRCC) Global Sensitivity Analysis (GSA) in Application to Constraint-Based Models |
| title_fullStr | FBA-PRCC. Partial Rank Correlation Coefficient (PRCC) Global Sensitivity Analysis (GSA) in Application to Constraint-Based Models |
| title_full_unstemmed | FBA-PRCC. Partial Rank Correlation Coefficient (PRCC) Global Sensitivity Analysis (GSA) in Application to Constraint-Based Models |
| title_short | FBA-PRCC. Partial Rank Correlation Coefficient (PRCC) Global Sensitivity Analysis (GSA) in Application to Constraint-Based Models |
| title_sort | fba prcc partial rank correlation coefficient prcc global sensitivity analysis gsa in application to constraint based models |
| topic | whole-genome model constraint-based model metabolic network global sensitivity analysis FBA |
| url | https://www.mdpi.com/2218-273X/13/3/500 |
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