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- Growth control of the eukaryote cell: a systems biology investigation into yeast
Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell-growth regulation. Comprehensive studies at the transcriptional, proteomic and metabolic levels under defined controlled conditions are currently lacking.
This investigation shows public data taken from the BioInvestigation Index. (http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-1)
Organism: Saccharomyces Cerevisiae
SEEK ID: https://demo.fairdomhub.org/investigations/2
Projects: SysMO DB
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Created: 16th Oct 2009 at 13:08
Last updated: 29th Nov 2011 at 16:32

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- People (1)
- Projects (1)
- Studies (2+1)
- Assays (5)
- Data files (4)
- Models (1+1)
- SOPs (1+1)
- Publications (1)
Expertise: Biochemistry, Bioinformatics, Data Management
Tools: Data Management, Transcriptomics, Databases, Workflows, Web services, Taverna, Ontologies
I am a Research Fellow at the University of Manchester, working in Bioinformatics and Computer Science. I am also a guest researcher at the Vrije Universiteit.My research interests include scientific workflows, semantic discovery, and applying ontology technologies to biological data
The main objectives of SysMO-DB are to: facilitate the web-based exchange of data between research groups within- and inter- consortia, and to provide an integrated platform for the dissemination of the results of the SysMO projects to the scientific community. We aim to devise a progressive and scalable solution to the data management needs of the SysMO initiative, that:
* facilitates and maximises the potential for data exchange between SysMO research groups;
* maximises the ‘shelf life’ and
...
Programme: SysMO
Public web page: http://www.sysmo-db.org/
Organisms: Saccharomyces cerevisiae, Lactic Acid Bacteria
Comprehensive high-throughput analyses at the levels of mRNAs, proteins, and metabolites, and studies on gene expression patterns are required for systems biology studies of cell growth [4,26-29]. Although such comprehensive data sets are lacking, many studies have pointed to a central role for the target-of-rapamycin (TOR) signal transduction pathway in growth control. TOR is a serine/threonine kinase that has been conserved from yeasts to mammals; it integrates signals from nutrients or growth
...
Person responsible: Katy Wolstencroft
Snapshots: No snapshots
Investigation: Growth control of the eukaryote cell: a systems...
Scales: Not specified
This study examines whether the in vivo behavior of yeast glycolysis can be understood in terms of the in vitro kinetic properties of the constituent enzymes.
Person responsible: Jacky Snoep
Snapshots: No snapshots
Investigation: Growth control of the eukaryote cell: a systems...
Scales: Not specified
Assay to measure gene expression of Saccharomyces cerevisiae (yeast) under different nutrient limitations
Limiting Nutrients:
ethanol, nitrogen, glucose, phosphorus, carbon, sulfur, sulphur
This data is public data taken from the BioInvestigation Index.
(http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-1)
Submitter: Katy Wolstencroft
Assay type: Transcriptional Profiling
Technology type: Microarray
Snapshots: No snapshots
Investigation: Growth control of the eukaryote cell: a systems...
Study: 1 hidden item
Organisms: Saccharomyces cerevisiae
SOPs: 1 hidden item
Data files: a_transcriptome from BII-S-1
Scales: Not specified
Assay to measure metabolites of yeast saccharomyces cerevisiae under different nutrient limitations
Limiting Nutrients:
ethanol, nitrogen, glucose, phosphorus, carbon, sulfur, sulphur
This data is public data taken from the BioInvestigation Index. (http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-1)
Submitter: Katy Wolstencroft
Assay type: Metabolite Profiling
Technology type: Mass Spectrometry
Snapshots: No snapshots
Investigation: Growth control of the eukaryote cell: a systems...
Study: 1 hidden item
Organisms: Saccharomyces cerevisiae
SOPs: No SOPs
Data files: a_metabolome_BII-S-1
Scales: Not specified
Assay to measure protein expression in yeast saccharomyces cerevisiae under different nutrient limitations
Limiting Nutrients:
ethanol, nitrogen, glucose, phosphorus, carbon, sulfur, sulphur
This data is public data taken from the BioInvestigation Index. (http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-1)
Submitter: Katy Wolstencroft
Assay type: Protein Expression Profiling
Technology type: Mass Spectrometry
Snapshots: No snapshots
Investigation: Growth control of the eukaryote cell: a systems...
Study: 1 hidden item
Organisms: Saccharomyces cerevisiae
SOPs: No SOPs
Data files: a_proteome from BII-S-1
Scales: Not specified
Assay for transcriptional profiling time course in yeast treated with rapamycin
This is public data from the BioInvestigation Index (http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-2)
Submitter: Katy Wolstencroft
Assay type: Transcriptional Profiling
Technology type: Microarray
Snapshots: No snapshots
Investigation: Growth control of the eukaryote cell: a systems...
Study: A time course analysis of transcription respon...
Organisms: Saccharomyces cerevisiae
SOPs: Nutrient_limited_stationary
Data files: a_microarray from BII-S-2
Scales: Not specified
Glycolysis in Saccharomyces cerevisiae
Investigation: Growth control of the eukaryote cell: a systems...
Study: Can yeast glycolysis be understood in terms of ...
Organisms: Saccharomyces cerevisiae (chemostat)
Models: Teusink and 1 hidden item
SOPs: No SOPs
Data files: No Data files
Scales: Not specified
Results of transcriptional profile in Saccharomyces cerevisiae after rapamycin treatment
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
Investigations: Growth control of the eukaryote cell: a systems...
Scales: Not specified
Results of proteomics profile in Saccharomyces cerevisiae under different experimental conditions
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
Investigations: Growth control of the eukaryote cell: a systems...
Studies: 1 hidden item
Assays: Changes in flux on the proteome
Scales: Not specified
results of metabolic profiling of Saccharomyces cerevisiae in different conditions
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
Investigations: Growth control of the eukaryote cell: a systems...
Studies: 1 hidden item
Scales: Not specified
Results of transcriptional profile in saccharomyces cerevisiae under different experimental conditions
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
Investigations: Growth control of the eukaryote cell: a systems... and 1 hidden item
Studies: 2 hidden items
Assays: Changes in flux on the transcriptome and 1 hidden item
Scales: Not specified
This model is for a paper that examines whether the in vivo behavior of yeast glycolysis can be understood in terms of the in vitro kinetic properties of the constituent enzymes. In non-growing, anaerobic, compressed Saccharomyces cerevisiae the values of the kinetic parameters of most glycolytic enzymes were determined. For the other enzymes appropriate literature values were collected. By inserting these values into a kinetic model for glycolysis, fluxes and metabolites were calculated. Under
...
Creator: Stuart Owen
Submitter: Stuart Owen
Model type: Not specified
Model format: SBML
Environment: Not specified
Organism: Saccharomyces cerevisiae
Investigations: Growth control of the eukaryote cell: a systems...
Studies: Can yeast glycolysis be understood in terms of ...
Modelling analyses: Glycolysis in Saccharomyces cerevisiae
A stationary-phase culture (10ml) was used to inoculate the fermenter vessel.
Taken from ArrayExpress:
http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-MEXP-115
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
Investigations: Growth control of the eukaryote cell: a systems...
Scales: Not specified
Abstract (Expand)
Authors: Firstname Lastname, J Passarge, C A Reijenga, E Esgalhado, C C van der Weijden, M Schepper, M C Walsh, B M Bakker, K van Dam, H V Westerhoff, Firstname Lastname
Date Published: 22nd Aug 2000
Publication Type: Not specified
PubMed ID: 10951190
Citation:
Scales: Not specified