ONTOLOGY SOURCE REFERENCE
Term Source Name	NCBITAXON	OBI_BCGO	PATO	OBI	UO	CL	CHEBI	EFO	ROLEO
Term Source File	http://data.bioontology.org/ontologies/NCBITAXON	http://data.bioontology.org/ontologies/OBI_BCGO	http://data.bioontology.org/ontologies/PATO	http://data.bioontology.org/ontologies/OBI	http://data.bioontology.org/ontologies/UO	http://data.bioontology.org/ontologies/CL	http://data.bioontology.org/ontologies/CHEBI	http://data.bioontology.org/ontologies/EFO	http://data.bioontology.org/ontologies/ROLEO
Term Source Version	2	8	160	21	42	43	78	158	1
Term Source Description	National Center for Biotechnology Information (NCBI) Organismal Classification	Beta Cell Genomics Ontology	Phenotypic Quality Ontology	Ontology for Biomedical Investigations	Units of Measurement Ontology	Cell Ontology	Chemical Entities of Biological Interest Ontology	Experimental Factor Ontology	Role Ontology
Comment[Test]	1	2	3	4	5	6	7	8	9
INVESTIGATION
Investigation Identifier	BII-I-1
Investigation Title	Growth control of the eukaryote cell: a systems biology study in yeast
Investigation Description	Background 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. Results Metabolic control analysis is being exploited in a systems biology study of the eukaryotic cell. Using chemostat culture, we have measured the impact of changes in flux (growth rate) on the transcriptome, proteome, endometabolome and exometabolome of the yeast Saccharomyces cerevisiae. Each functional genomic level shows clear growth-rate-associated trends and discriminates between carbon-sufficient and carbon-limited conditions. Genes consistently and significantly upregulated with increasing growth rate are frequently essential and encode evolutionarily conserved proteins of known function that participate in many protein-protein interactions. In contrast, more unknown, and fewer essential, genes are downregulated with increasing growth rate; their protein products rarely interact with one another. A large proportion of yeast genes under positive growth-rate control share orthologs with other eukaryotes, including humans. Significantly, transcription of genes encoding components of the TOR complex (a major controller of eukaryotic cell growth) is not subject to growth-rate regulation. Moreover, integrative studies reveal the extent and importance of post-transcriptional control, patterns of control of metabolic fluxes at the level of enzyme synthesis, and the relevance of specific enzymatic reactions in the control of metabolic fluxes during cell growth. Conclusion This work constitutes a first comprehensive systems biology study on growth-rate control in the eukaryotic cell. The results have direct implications for advanced studies on cell growth, in vivo regulation of metabolic fluxes for comprehensive metabolic engineering, and for the design of genome-scale systems biology models of the eukaryotic cell.
Investigation Submission Date	2007-04-30
Investigation Public Release Date	2009-03-10
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INVESTIGATION PUBLICATIONS
Investigation PubMed ID	17439666	1231222	1234121
Investigation Publication DOI	doi:10.1186/jbiol54		
Investigation Publication Author List	Castrillo JI, Zeef LA, Hoyle DC, Zhang N, Hayes A, Gardner DC, Cornell MJ, Petty J, Hakes L, Wardleworth L, Rash B, Brown M, Dunn WB, Broadhurst D, O'Donoghue K, Hester SS, Dunkley TP, Hart SR, Swainston N, Li P, Gaskell SJ, Paton NW, Lilley KS, Kell DB, Oliver SG.	Piatnochka IT.	Monticelli G, Santori S.
Investigation Publication Title	Growth control of the eukaryote cell: a systems biology study in yeast.	Effect of prednisolone on the cardiovascular system in complex treatment of newly detected pulmonary tuberculosis	Indications for the use of prostheses in the treatment of pathological fractures due to primary malignant and metastatic tumours of bone.
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Investigation Publication Status	indexed in Pubmed	published	Published
Investigation Publication Status Term Accession Number		http://www.ebi.ac.uk/efo/EFO_0001796	
Investigation Publication Status Term Source REF		EFO	
INVESTIGATION CONTACTS
Investigation Person Last Name	Oliver	Juan	Leo
Investigation Person First Name	Stephen	Castrillo	Zeef
Investigation Person Mid Initials	G	I	A
Investigation Person Email	stephen.oliver@test.mail		
Investigation Person Phone		123456789	
Investigation Person Fax			+49 123456789
Investigation Person Address	Oxford Road, Manchester M13 9PT, UK	Oxford Road, Manchester M13 9PT, UK	Oxford Road, Manchester M13 9PT, UK
Investigation Person Affiliation	Faculty of Life Sciences, Michael Smith Building, University of Manchester	Faculty of Life Sciences, Michael Smith Building, University of Manchester	Faculty of Life Sciences, Michael Smith Building, University of Manchester
Investigation Person Roles	corresponding author	author	author
Investigation Person Roles Term Accession Number			http://purl.obolibrary.org/obo/RoleO_0000061
Investigation Person Roles Term Source REF			ROLEO
Comment[Investigation Person ORCID]	12345	0987654321	1357908642
Comment[Investigation Person REF]	personA	personB	personC

