What mRNA Abundances Can Tell us about Metabolism
Abstract
:1. Introduction
- the layer of RNA transcripts (as opposed to the layer of proteins, the layer of reaction fluxes, and the layer of metabolites) is the only layer where a complete quantitative snapshot of all molecular species is currently feasible. Reaction flux estimations currently cover only a tiny share of all reactions. Metabolite concentrations are currently measured for some 100 s metabolites but specific classes of metabolites such as lipids still present large challenges. Protein amount estimations at the genome-scale are now being done but the effort necessary is huge. The layer of DNA, whose information is a precondition for any transcription-based analysis, is not mentioned as qualitative information.
- transcript arrays are moderately priced in relation to the amount of data gathered,
- the experimental effort for the researcher is moderate due to an highly automatized process,
- the technology provides a low ambiguity and accurate estimates of the RNA amount changes [6]. The high number of probes allows to distinguish between the RNA of separate genes, with only few exceptions. Ambiguity of the peaks is the main problem of the estimation of metabolite concentrations by mass spectrometry. Ambiguity is also the largest challenge in flux estimations based on 13C marked substrates, and
2. Fundamental Studies
2.1. Gene Chip Intensities→mRNA
2.2. mRNA→Protein
2.3. Enzyme Concentration → Enzyme Activity
2.4. Enzyme Activity → Metabolic Flux
2.5. Crossing Several Layers
2.6. mRNA → Fluxes
2.7. Regulation of Metabolic Genes
2.8. Genetic Interactions
3. Systematic Comparison of Methods
3.1. Absolute/Relative/Coexpression
3.2. Thresholds
3.3. Representation of the Metabolic System
3.4. Type of Inference
3.5. Biological Focus of Studies
4. Available Software
5. Conclusions and Outlook
Acknowledgments
References
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Hoppe, A. What mRNA Abundances Can Tell us about Metabolism. Metabolites 2012, 2, 614-631. https://doi.org/10.3390/metabo2030614
Hoppe A. What mRNA Abundances Can Tell us about Metabolism. Metabolites. 2012; 2(3):614-631. https://doi.org/10.3390/metabo2030614
Chicago/Turabian StyleHoppe, Andreas. 2012. "What mRNA Abundances Can Tell us about Metabolism" Metabolites 2, no. 3: 614-631. https://doi.org/10.3390/metabo2030614