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Integrative Gene Expression and Metabolic Analysis Tool IgemRNA
| Content Provider | MDPI |
|---|---|
| Author | Grausa, Kristina Mozga, Ivars Pleiko, Karlis Pentjuss, Agris |
| Copyright Year | 2022 |
| Description | Genome-scale metabolic modeling is widely used to study the impact of metabolism on the phenotype of different organisms. While substrate modeling reflects the potential distribution of carbon and other chemical elements within the model, the additional use of omics data, e.g., transcriptome, has implications when researching the genotype–phenotype responses to environmental changes. Several algorithms for transcriptome analysis using genome-scale metabolic modeling have been proposed. Still, they are restricted to specific objectives and conditions and lack flexibility, have software compatibility issues, and require advanced user skills. We classified previously published algorithms, summarized transcriptome pre-processing, integration, and analysis methods, and implemented them in the newly developed transcriptome analysis tool IgemRNA, which (1) has a user-friendly graphical interface, (2) tackles compatibility issues by combining previous data input and pre-processing algorithms in MATLAB, and (3) introduces novel algorithms for the automatic comparison of different transcriptome datasets with or without Cobra Toolbox 3.0 optimization algorithms. We used publicly available transcriptome datasets from Saccharomyces cerevisiae BY4741 and H4-S47D strains for validation. We found that IgemRNA provides a means for transcriptome and environmental data validation on biochemical network topology since the biomass function varies for different phenotypes. Our tool can detect problematic reaction constraints. |
| Starting Page | 586 |
| e-ISSN | 2218273X |
| DOI | 10.3390/biom12040586 |
| Journal | Biomolecules |
| Issue Number | 4 |
| Volume Number | 12 |
| Language | English |
| Publisher | MDPI |
| Publisher Date | 2022-04-16 |
| Access Restriction | Open |
| Subject Keyword | Biomolecules Mathematical and Computational Biology Genome-scale Metabolic Modeling Transcriptomics Software Engineering Cobra Toolbox 3.0 Matlab Flux Balance Analysis Flux Variability Analysis Omics Data Analysis |
| Content Type | Text |
| Resource Type | Article |
