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Systems-biology dissection of eukaryotic cell growth.

Przytycka TM, Andrews J - BMC Biol. (2010)

Bottom Line: A recent article in BMC Biology illustrates the use of a systems-biology approach to integrate data across the transcriptome, proteome and metabolome of budding yeast in order to dissect the relationship between nutrient conditions and cell growth.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Center for Biotechnology Information, NLM, NIH, 8000 Rockville Pike, Bethesda, MD 20814, USA.

ABSTRACT
A recent article in BMC Biology illustrates the use of a systems-biology approach to integrate data across the transcriptome, proteome and metabolome of budding yeast in order to dissect the relationship between nutrient conditions and cell growth.

Show MeSH
Analytical approaches. (a) Multivariate analysis of growth rate and nutrition conditions. Comparing cellular responses to varying growth rates and nutrition conditions allows the dissection of growth-rate effects (red), nutrition effects (green) and nutrition-specific growth effects (blue). (b) Systems-biology analysis of cellular responses. Assaying cell responses at the transcript, protein, and metabolite levels allows the analysis of transcriptional (red), protein expression (green), and metabolic (blue) responses. Comparing the transcription and protein-expression responses allows the inference of post-transcriptional responses (orange). Comparing the protein expression and metabolic responses allows the inference of enzyme-metabolite correlations (purple).
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Figure 1: Analytical approaches. (a) Multivariate analysis of growth rate and nutrition conditions. Comparing cellular responses to varying growth rates and nutrition conditions allows the dissection of growth-rate effects (red), nutrition effects (green) and nutrition-specific growth effects (blue). (b) Systems-biology analysis of cellular responses. Assaying cell responses at the transcript, protein, and metabolite levels allows the analysis of transcriptional (red), protein expression (green), and metabolic (blue) responses. Comparing the transcription and protein-expression responses allows the inference of post-transcriptional responses (orange). Comparing the protein expression and metabolic responses allows the inference of enzyme-metabolite correlations (purple).

Mentions: The multivariate analysis examines the response of yeast cells to different nutrition conditions and over differing growth rates. Cells were cultured in media limiting for either glucose, ammonium, phosphate, or sulfate; while the growth rates were set at doubling times of either 3.5, 7 or 10 hours. This allowed the effects of nutrition to be disentangled from secondary effects associated with altered growth rates (Figure 1a). Effects that were only associated with growth rate were identified as variation that was common to the different growth rate conditions across all limiting nutrients (red in Figure 1a). Effects that were only associated with different nutrient conditions were identified as variation that was specific to a nutrition treatment averaged across different growth rates (green in Figure 1a). Finally, nutrition-specific growth-rate effects were identified as growth-rate effects that were found in specific nutrient conditions (blue in Figure 1a).


Systems-biology dissection of eukaryotic cell growth.

Przytycka TM, Andrews J - BMC Biol. (2010)

Analytical approaches. (a) Multivariate analysis of growth rate and nutrition conditions. Comparing cellular responses to varying growth rates and nutrition conditions allows the dissection of growth-rate effects (red), nutrition effects (green) and nutrition-specific growth effects (blue). (b) Systems-biology analysis of cellular responses. Assaying cell responses at the transcript, protein, and metabolite levels allows the analysis of transcriptional (red), protein expression (green), and metabolic (blue) responses. Comparing the transcription and protein-expression responses allows the inference of post-transcriptional responses (orange). Comparing the protein expression and metabolic responses allows the inference of enzyme-metabolite correlations (purple).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2875221&req=5

Figure 1: Analytical approaches. (a) Multivariate analysis of growth rate and nutrition conditions. Comparing cellular responses to varying growth rates and nutrition conditions allows the dissection of growth-rate effects (red), nutrition effects (green) and nutrition-specific growth effects (blue). (b) Systems-biology analysis of cellular responses. Assaying cell responses at the transcript, protein, and metabolite levels allows the analysis of transcriptional (red), protein expression (green), and metabolic (blue) responses. Comparing the transcription and protein-expression responses allows the inference of post-transcriptional responses (orange). Comparing the protein expression and metabolic responses allows the inference of enzyme-metabolite correlations (purple).
Mentions: The multivariate analysis examines the response of yeast cells to different nutrition conditions and over differing growth rates. Cells were cultured in media limiting for either glucose, ammonium, phosphate, or sulfate; while the growth rates were set at doubling times of either 3.5, 7 or 10 hours. This allowed the effects of nutrition to be disentangled from secondary effects associated with altered growth rates (Figure 1a). Effects that were only associated with growth rate were identified as variation that was common to the different growth rate conditions across all limiting nutrients (red in Figure 1a). Effects that were only associated with different nutrient conditions were identified as variation that was specific to a nutrition treatment averaged across different growth rates (green in Figure 1a). Finally, nutrition-specific growth-rate effects were identified as growth-rate effects that were found in specific nutrient conditions (blue in Figure 1a).

Bottom Line: A recent article in BMC Biology illustrates the use of a systems-biology approach to integrate data across the transcriptome, proteome and metabolome of budding yeast in order to dissect the relationship between nutrient conditions and cell growth.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Center for Biotechnology Information, NLM, NIH, 8000 Rockville Pike, Bethesda, MD 20814, USA.

ABSTRACT
A recent article in BMC Biology illustrates the use of a systems-biology approach to integrate data across the transcriptome, proteome and metabolome of budding yeast in order to dissect the relationship between nutrient conditions and cell growth.

Show MeSH