{"database":"Cell Collective","file_versions":[],"scores":{"citationCount":18963,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"omics_type":["Models"],"submitter":["Audrey Crowther"],"version_name":[""],"full_dataset_link":["https://cellcollective.org/#4706/predicting-variabilities-in-cardiac-gene"],"model_score":["19.400000000000002"],"default_version":["1"],"ModelFormat":["SBML"],"submitter_affiliation":[""],"submitter_email":[""],"version_id":["1"],"repository":["Cell Collective"],"version_url":["https://cellcollective.org/#4706:1/predicting-variabilities-in-cardiac-gene"],"version_description":[""],"pubmed_abstract":["Gene interactions in cells can be represented by gene regulatory networks. A Boolean network models gene interactions according to rules where gene expression is represented by binary values (on / off or {1, 0}). In reality, however, the gene's state can have multiple values due to biological properties. Furthermore, the noisy nature of the experimental design results in uncertainty about a state of the gene. Here we present a new Boolean network paradigm to allow intermediate values on the interval [0, 1]. As in the Boolean network, fixed points or attractors of such a model correspond to biological phenotypes or states. We use our new extension of the Boolean network paradigm to model gene expression in first and second heart field lineages which are cardiac progenitor cell populations involved in early vertebrate heart development. By this we are able to predict additional biological phenotypes that the Boolean model alone is not able to identify without utilizing additional biological knowledge. The additional phenotypes predicted by the model were confirmed by published biological experiments. Furthermore, the new method predicts gene expression propensities for modelled but yet to be analyzed genes."],"pubmed_title":["Predicting Variabilities in Cardiac Gene Expression with a Boolean Network Incorporating Uncertainty."],"pubmed_authors":["Grieb Melanie M, Burkovski Andre A, Sträng J Eric JE, Kraus Johann M JM, Groß Alexander A, Palm Günther G, Kühl Michael M, Kestler Hans A HA"],"description_synonyms":["Experimental Designs, Networks, hematopoietic precursor cell, Research Technique, Modules, Gene Regulatory, Materials, Problem Formulations, Adjustments, Procedures, hemopoietic stem cell, Colony-Forming Units, Design, Error Sources, Matched Groups, Progenitor Cell, Gene, Scoring Method, Network, Technic, Techniques, Adjustment, method, hematopoietic progenitor cell, Circuit, Method, Scoring Methods, Sources, method used in an experiment, Transcriptional Networks, Mother Cells, Studies, Transcriptional Network, Gene Regulatory Network, DmF2, Fs(3)Hor, Technique, Progenitor, Module, Experimental Design, lod, Transcriptional, Group, Regulatory Network, Methodology, Circuits, DmelCG2684, Genetic, Gene Expressions, Scoring, CFU-S, Research, Proposals, Matched Group, Designs, Matched, Mother, Groups, experimental design, NTef2, Expressions, Research Strategy, Study, Methodological Studies, blutbildende Stammzelle, Reporting, Gene Network, Error Source, Research Techniques, Expression, Strategies, Data Reporting, Colony Forming Unit, Research Technic, Research Methodology, Progenitor Cells, SHF, Research Proposals, Formulation, HSC, Procedure, Cistrons, Cell, Gene Circuits, results, cardiac development, Research Proposal, predicted, Fs(3)Sz11, Research Strategies, Experimental, hemopoietic progenitor cell, Colony-Forming Unit, Stem Cell, Genetic Materials, Technics, Problem Formulation, Problem, fixed, Genetic Material, Proposal, Methods, Mother Cell, Epistemology, Gene Circuit, Gene Module, Source, Stem, Research Designs, Colony Forming Units, HSC cell, INSDC_feature:gene, Research Technics, Methodological, Lds, Methodological Study, early, Formulations, plan specification, Phenotypes, Data Adjustment, Gene Modules, Regulatory Networks, Error, Material, Data, Horka, Gene Networks, progenitor cell, Cells, CG2684, Fs(3)Horka, dorsal vessel development, Cistron, Genetic Material., Strategy, Data Adjustments, colony forming unit spleen"],"pubmed_title_synonyms":["Gene., Gene, Expression, Gene Expressions, Expressions"],"name_synonyms":["Genetic Materials, Cistron, Gene, INSDC_feature:gene, Materials, Genetic Material., Genetic, Material, Cistrons"],"pubmed_abstract_synonyms":["Experimental Designs, Networks, hematopoietic precursor cell, Research Technique, Modules, Gene Regulatory, Materials, Problem Formulations, Adjustments, Procedures, hemopoietic stem cell, Colony-Forming Units, Design, Error Sources, Matched Groups, Progenitor Cell, Gene, Scoring Method, Network, Technic, Techniques, Adjustment, method, hematopoietic progenitor cell, Circuit, Method, Scoring Methods, Sources, method used in an experiment, Transcriptional Networks, Mother Cells, Studies, Transcriptional Network, Gene Regulatory Network, DmF2, Fs(3)Hor, Technique, Progenitor, Module, Experimental Design, lod, Transcriptional, Group, Regulatory Network, Methodology, Circuits, DmelCG2684, Genetic, Gene Expressions, Scoring, CFU-S, Research, Proposals, Matched Group, Designs, Matched, Mother, Groups, experimental design, NTef2, Expressions, Research Strategy, Study, Methodological Studies, blutbildende Stammzelle, Reporting, Gene Network, Error Source, Research Techniques, Expression, Strategies, Data Reporting, Colony Forming Unit, Research Technic, Research Methodology, Progenitor Cells, SHF, Research Proposals, Formulation, HSC, Procedure, Cistrons, Cell, Gene Circuits, results, cardiac development, Research Proposal, predicted, Fs(3)Sz11, Research Strategies, Experimental, hemopoietic progenitor cell, Colony-Forming Unit, Stem Cell, Genetic Materials, Technics, Problem Formulation, Problem, fixed, Genetic Material, Proposal, Methods, Mother Cell, Epistemology, Gene Circuit, Gene Module, Source, Stem, Research Designs, Colony Forming Units, HSC cell, INSDC_feature:gene, Research Technics, Methodological, Lds, Methodological Study, early, Formulations, plan specification, Phenotypes, Data Adjustment, Gene Modules, Regulatory Networks, Error, Material, Data, Horka, Gene Networks, progenitor cell, Cells, CG2684, Fs(3)Horka, dorsal vessel development, Cistron, Genetic Material., Strategy, Data Adjustments, colony forming unit spleen"],"citation_count":["18963"],"additional_accession":[]},"is_claimable":false,"name":"Predicting Variabilities in Cardiac Gene","description":"Gene interactions in cells can be represented by gene regulatory networks. A Boolean network models gene interactions according to rules where gene expression is represented by binary values (on / off or {1, 0}). In reality, however, the genes state can have multiple values due to biological properties. Furthermore, the noisy nature of the experimental design results in uncertainty about a state of the gene. Here we present a new Boolean network paradigm to allow intermediate values on the interval [0, 1]. As in the Boolean network, fixed points or attractors of such a model correspond to biological phenotypes or states. We use our new extension of the Boolean network paradigm to model gene expression in first and second heart field lineages which are cardiac progenitor cell populations involved in early vertebrate heart development. By this we are able to predict additional biological phenotypes that the Boolean model alone is not able to identify without utilizing additional biological knowledge. The additional phenotypes predicted by the model were confirmed by published biological experiments. Furthermore, the new method predicts gene expression propensities for modelled but yet to be analyzed genes.","dates":{"created":"2016-07-21","publication":"","submission":"2017-02-13","last_modified":"2017-02-13"},"accession":"4706","cross_references":{"pubmed":["26207376"]}}