Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae.

TitleLarge-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae.
Publication TypeJournal Article
Year of Publication2003
AuthorsFörster J, Famili I, Palsson BO, Nielsen J
JournalOMICS
Volume7
Issue2
Pagination193-202
Date Published2003 Summer
ISSN1536-2310
KeywordsComputational Biology, Databases, Genetic, Evaluation Studies as Topic, Gene Deletion, Gene Expression Regulation, Fungal, Genes, Fungal, Genome, Fungal, Saccharomyces cerevisiae, Software Validation
Abstract

A large-scale in silico evaluation of gene deletions in Saccharomyces cerevisiae was conducted using a genome-scale reconstructed metabolic model. The effect of 599 single gene deletions on cell viability was simulated in silico and compared to published experimental results. In 526 cases (87.8%), the in silico results were in agreement with experimental observations when growth on synthetic complete medium was simulated. Viable phenotypes were correctly predicted in 89.4% (496 out of 555) and lethal phenotypes were correctly predicted in 68.2% (30 out of 44) of the cases considered. The in silico evaluation was solely based on the topological properties of the metabolic network which is based on well-established reaction stoichiometry. No interaction or regulatory information was accounted for in the in silico model. False predictions were analyzed on a case-by-case basis for four possible inadequacies of the in silico model: (1) incomplete media composition, (2) substitutable biomass components, (3) incomplete biochemical information, and (4) missing regulation. This analysis eliminated a number of false predictions and suggested a number of experimentally testable hypotheses. A genome-scale in silico model can thus be used to systematically reconcile existing data and fill in our knowledge gaps about an organism.

DOI10.1089/153623103322246584
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/14506848?dopt=Abstract
Alternate JournalOMICS
PubMed ID14506848