Jun 23, 2016

Systematic analysis of transcriptional and post-transcriptional regulation of metabolism in yeast

BioRxiv : the Preprint Server for Biology
Emanuel GonçalvesJulio Saez-Rodriguez

Abstract

Cells react to extracellular perturbations with complex and intertwined responses. Systematic identification of the regulatory mechanisms that control these responses is still a challenge and requires tailored analyses integrating different types of molecular data. Here we acquired time-resolved metabolomics measurements in yeast under salt and pheromone stimulation and developed a machine learning approach to explore regulatory associations between metabolism and signal transduction. Existing phosphoproteomics measurements under the same conditions and kinase-substrate regulatory interactions were used to estimate the enzymatic activity of signalling kinases. Our approach identified informative associations between kinases and metabolic enzymes capable of predicting metabolic changes. We extended our analysis to two studies containing transcriptomics, phosphoproteomics and metabolomics measurements across a comprehensive panel of kinases/phosphatases knockouts and time-resolved perturbations to the nitrogen metabolism, conveying a total of 143 unique conditions. Our approach accurately estimated the change in activity of transcription factors, kinases and phosphatases and these were capable of building predictive models to inf...Continue Reading

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Mentioned in this Paper

Protein Kinase A Signaling Cascade
Metabolic Process, Cellular
Study
Phosphoric Monoester Hydrolases
Post-Transcriptional Regulation
Nitrogen Metabolism Pathway
Extracellular
Enzymes, antithrombotic
Acclimatization
Transcription, Genetic

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