{"database":"Cell Collective","file_versions":[],"scores":{"citationCount":29288,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"omics_type":["Models"],"submitter":["Tomas Helikar"],"version_name":[""],"full_dataset_link":["https://cellcollective.org/#2423/budding-yeast-cell-cycle-2009"],"model_score":["28.0736"],"default_version":["1"],"ModelFormat":["SBML"],"submitter_affiliation":[""],"submitter_email":[""],"version_id":["1"],"repository":["Cell Collective"],"version_url":["https://cellcollective.org/#2423:1/budding-yeast-cell-cycle-2009"],"version_description":[""],"pubmed_abstract":["The budding yeast Saccharomyces cerevisiae is a model organism that is commonly used to investigate control of the eukaryotic cell cycle. Moreover, because of the extensive experimental data on wild type and mutant phenotypes, it is also particularly suitable for mathematical modelling and analysis. Here, I present a new Boolean model of the budding yeast cell cycle. This model is consistent with a wide range of wild type and mutant phenotypes and shows remarkable robustness against perturbations, both to reaction times and the states of component genes/proteins. Because of its simple logical nature, the model is suitable for sub-network analysis, which can be used to identify a four node core regulatory circuit underlying cell cycle regulation. Sub-network analysis can also be used to identify key sub-dynamics that are essential for viable cell cycle control, as well as identifying the sub-dynamics that are most variable between different mutants."],"pubmed_title":["Logical analysis of the budding yeast cell cycle."],"pubmed_authors":["Irons D J DJ"],"description_synonyms":["AT1G11140, MGC130048, multi-cellular organism, Materials, SGCG_HUMAN, tumor suppressor, experimental, determination, Cell Cycle Control, Brewer's, A4, baker's yeast, Gene, regulation of cell cycle transition, broad, Saccharomyces italicus, TYPE, dIKK-gamma, Arrests, prevention, CG12298, DAGA4, SUB, Endomycetale, Cell Cycle-Transition Points, cell cycle regulator, variable., DmelCG12298, dorsal marginal zone, DmIKK-gamma, yeast, Cycle, 35DAG, Gene Products, SCRAMBLED, Cell Cycle Transition Points, dmIKKgamma, MAM, gamma-SG, IKK[[gamma]], animal, prevention and control, SCG3, KIF20A, IKKg, lager beer yeast, KEY, Key, Cell Division Cycles, Cycles, gamma sarcoglycan, network topology analysis, methods, Genetic, reference sample, nodus primitivus, experimental section, mei-1794, Cell Division Cycle, cell-division cycle, Saccharomyes cerevisiae, Baker, Cell Division, Saccharomyces uvarum var. melibiosus, S. cerevisiae, preventive measures, reaction, S cerevisiae, Abstract, Budding Yeast, Candida robusta, control of cell cycle progression, Endomycopses, IKK, regulation of progression through cell cycle, Saccharomyces capensis, regulation of cell cycle progression, stem node, Cell Cycles, Baker's, gamma-sarcoglycan, Checkpoint, Mycoderma cerevisiae, SRF9, Cell Cycle, 1883, species, Cell Cycle-Transition, brewer's yeast, Cell Cycle Arrest, SIMPLE, negative regulation of cell cycle arrest, Budding, Controlled, TP53I7, Budding Yeasts, Saccharomycetale, cell cycle modulation, Controlling, preventive therapy, wide/broad, 35 kDa dystrophin-associated glycoprotein, Cell Cycle-Transition Point, Saccharomyces cerevisiae 'var. diastaticus', body, cell cycle arrest, Proteins, SG-gamma, STRUBBELIG, whole body, Cistrons, Saccaromyces cerevisiae, Cell, Division Cycles, SGCG, LGMD2C, STRUBBELIG-RECEPTOR FAMILY 9, Baker's Yeasts, Sccharomyces cerevisiae, IKKgamma, organism, positive regulation of cell cycle arrest, DmIKKgamma, Checkpoints, Saccharomyces diastaticus, arrest of mitotic cell cycle progression, dIKK, PIG7, chemical analysis, Protein, Kenny, modulation of cell cycle progression, core, Genetic Materials, Henson's node, sarcoglycan, Cell Cycle Arrests, Genetic Material, Saccharomyces oviformis, Yeasts, Yeast, Arrest, whole organism, DMDA1, Division Cycle, nodal stem, cell cycle control, Cell Cycle Controls, Dmikkgamma, prophylaxis, Dub, IKK-gamma, Control, Controls, gamma (35kDa dystrophin-associated glycoprotein), CG16910, experimental procedures, mitotic cell cycle arrest, Cell Cycle Checkpoint, Protein Gene Products, Phenotypes, Gene Proteins, Saccharomyces cerevisiae (Desm.) Meyen ex E.C. Hansen, Cycle-Transition Point, wide, DMDA, DmelCG16910, control, Material, 35kD dystrophin-associated glycoprotein, Point, Endomycopsis, Koerper, SCARMD2, DMZ, regulation of cell cycle arrest, Cistron, assay, Baker's Yeast, T19D16.8, Brewer's Yeast, Endomycetales, SCM, cell cycle regulation, Baker Yeast"],"pubmed_title_synonyms":["Budding Yeasts, Saccharomycetale, Yeasts, Cell Division Cycles, Cycles, Endomycetale, Yeast, Budding Yeast, Endomycopses, determination, Division Cycle, Endomycopsis, chemical analysis, Cycle, Cell Division Cycle, cell-division cycle, assay, Cell Division, Cell Cycles., Endomycetales, Budding, Cell, Division Cycles"],"name_synonyms":["Budding Yeasts, Saccharomycetale, Yeasts, Cell Division Cycles, Cycles, Endomycetale, Yeast, Budding Yeast, Endomycopses, Division Cycle, Endomycopsis, Cycle, Cell Division Cycle, cell-division cycle, Cell Division, Cell Cycles., Endomycetales, Budding, Cell, Division Cycles"],"pubmed_abstract_synonyms":["AT1G11140, MGC130048, multi-cellular organism, Materials, SGCG_HUMAN, tumor suppressor, experimental, determination, Cell Cycle Control, Brewer's, A4, baker's yeast, Gene, regulation of cell cycle transition, broad, Saccharomyces italicus, TYPE, dIKK-gamma, Arrests, prevention, CG12298, DAGA4, SUB, Endomycetale, Cell Cycle-Transition Points, cell cycle regulator, variable., DmelCG12298, dorsal marginal zone, DmIKK-gamma, yeast, Cycle, 35DAG, Gene Products, SCRAMBLED, Cell Cycle Transition Points, dmIKKgamma, MAM, gamma-SG, IKK[[gamma]], animal, prevention and control, SCG3, KIF20A, IKKg, lager beer yeast, KEY, Key, Cell Division Cycles, Cycles, gamma sarcoglycan, network topology analysis, methods, Genetic, reference sample, nodus primitivus, experimental section, mei-1794, Cell Division Cycle, cell-division cycle, Saccharomyes cerevisiae, Baker, Cell Division, Saccharomyces uvarum var. melibiosus, S. cerevisiae, preventive measures, reaction, S cerevisiae, Budding Yeast, Candida robusta, control of cell cycle progression, Endomycopses, IKK, regulation of progression through cell cycle, Saccharomyces capensis, regulation of cell cycle progression, stem node, Cell Cycles, Baker's, gamma-sarcoglycan, Checkpoint, Mycoderma cerevisiae, SRF9, Cell Cycle, 1883, species, Cell Cycle-Transition, brewer's yeast, Cell Cycle Arrest, SIMPLE, negative regulation of cell cycle arrest, Budding, Controlled, TP53I7, Budding Yeasts, Saccharomycetale, cell cycle modulation, Controlling, preventive therapy, wide/broad, 35 kDa dystrophin-associated glycoprotein, Cell Cycle-Transition Point, Saccharomyces cerevisiae 'var. diastaticus', body, cell cycle arrest, Proteins, SG-gamma, STRUBBELIG, whole body, Cistrons, Saccaromyces cerevisiae, Cell, Division Cycles, SGCG, LGMD2C, STRUBBELIG-RECEPTOR FAMILY 9, Baker's Yeasts, Sccharomyces cerevisiae, IKKgamma, organism, positive regulation of cell cycle arrest, DmIKKgamma, Checkpoints, Saccharomyces diastaticus, arrest of mitotic cell cycle progression, dIKK, PIG7, chemical analysis, Protein, Kenny, modulation of cell cycle progression, core, Genetic Materials, Henson's node, sarcoglycan, Cell Cycle Arrests, Genetic Material, Saccharomyces oviformis, Yeasts, Yeast, Arrest, whole organism, DMDA1, Division Cycle, nodal stem, cell cycle control, Cell Cycle Controls, Dmikkgamma, prophylaxis, Dub, IKK-gamma, Control, Controls, gamma (35kDa dystrophin-associated glycoprotein), CG16910, experimental procedures, mitotic cell cycle arrest, Cell Cycle Checkpoint, Protein Gene Products, Phenotypes, Gene Proteins, Saccharomyces cerevisiae (Desm.) Meyen ex E.C. Hansen, Cycle-Transition Point, wide, DMDA, DmelCG16910, control, Material, 35kD dystrophin-associated glycoprotein, Point, Endomycopsis, Koerper, SCARMD2, DMZ, regulation of cell cycle arrest, Cistron, assay, Baker's Yeast, T19D16.8, Brewer's Yeast, Endomycetales, SCM, cell cycle regulation, Baker Yeast"],"citation_count":["29288"],"additional_accession":[]},"is_claimable":false,"name":"Budding Yeast Cell Cycle 2009","description":"Abstract The budding yeast Saccharomyces cerevisiae is a model organism that is commonly used to investigate control of the eukaryotic cell cycle. Moreover, because of the extensive experimental data on wild type and mutant phenotypes, it is also particularly suitable for mathematical modelling and analysis. Here, I present a new Boolean model of the budding yeast cell cycle. This model is consistent with a wide range of wild type and mutant phenotypes and shows remarkable robustness against perturbations, both to reaction times and the states of component genes/proteins. Because of its simple logical nature, the model is suitable for sub-network analysis, which can be used to identify a four node core regulatory circuit underlying cell cycle regulation. Sub-network analysis can also be used to identify key sub-dynamics that are essential for viable cell cycle control, as well as identifying the sub-dynamics that are most variable between different mutants.","dates":{"created":"2014-06-18","publication":"","submission":"2016-03-29","last_modified":"2016-03-29"},"accession":"2423","cross_references":{"pubmed":["19185585"]}}