Ontology type: schema:ScholarlyArticle Open Access: True
2008-12-17
AUTHORSKevin Kontos, Patrice Godard, Bruno André, Jacques van Helden, Gianluca Bontempi
ABSTRACTBackgroundNitrogen is an essential nutrient for all life forms. Like most unicellular organisms, the yeast Saccharomyces cerevisiae transports and catabolizes good nitrogen sources in preference to poor ones. Nitrogen catabolite repression (NCR) refers to this selection mechanism. All known nitrogen catabolite pathways are regulated by four regulators. The ultimate goal is to infer the complete nitrogen catabolite pathways. Bioinformatics approaches offer the possibility to identify putative NCR genes and to discard uninteresting genes.ResultsWe present a machine learning approach where the identification of putative NCR genes in the yeast Saccharomyces cerevisiae is formulated as a supervised two-class classification problem. Classifiers predict whether genes are NCR-sensitive or not from a large number of variables related to the GATA motif in the upstream non-coding sequences of the genes. The positive and negative training sets are composed of annotated NCR genes and manually-selected genes known to be insensitive to NCR, respectively. Different classifiers and variable selection methods are compared. We show that all classifiers make significant and biologically valid predictions by comparing these predictions to annotated and putative NCR genes, and by performing several negative controls. In particular, the inferred NCR genes significantly overlap with putative NCR genes identified in three genome-wide experimental and bioinformatics studies.ConclusionThese results suggest that our approach can successfully identify potential NCR genes. Hence, the dimensionality of the problem of identifying all genes involved in NCR is drastically reduced. More... »
PAGESs5
http://scigraph.springernature.com/pub.10.1186/1753-6561-2-s4-s5
DOIhttp://dx.doi.org/10.1186/1753-6561-2-s4-s5
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PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/19091052
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172 | grid-institutes:grid.4989.c | schema:alternateName | Laboratoire de Bioinformatique des Génomes et des Réseaux, Faculté des Sciences, ULB, Boulevard du Triomphe CP 263, 1050, Brussels, Belgium |
173 | ″ | ″ | Machine Learning Group, Département d'Informatique, Faculté des Sciences, Université Libre de Bruxelles (ULB), Boulevard du Triomphe CP 212, 1050, Brussels, Belgium |
174 | ″ | ″ | Physiologie Moléculaire de la Cellule, IBMM, Faculté des Sciences, ULB, Rue des Pr. Jeener et Brachet 12, 6041, Gosselies, Belgium |
175 | ″ | schema:name | Laboratoire de Bioinformatique des Génomes et des Réseaux, Faculté des Sciences, ULB, Boulevard du Triomphe CP 263, 1050, Brussels, Belgium |
176 | ″ | ″ | Machine Learning Group, Département d'Informatique, Faculté des Sciences, Université Libre de Bruxelles (ULB), Boulevard du Triomphe CP 212, 1050, Brussels, Belgium |
177 | ″ | ″ | Physiologie Moléculaire de la Cellule, IBMM, Faculté des Sciences, ULB, Rue des Pr. Jeener et Brachet 12, 6041, Gosselies, Belgium |
178 | ″ | rdf:type | schema:Organization |