title: In silico prediction of yeast deletion phenotypes.
abstract: Analysis of gene deletions is a fundamental approach for investigating gene function. We evaluated an algorithm that uses classification techniques to predict the phenotypic effects of gene deletions in yeast. We used a modified simulated annealing algorithm for feature selection and weighting. The selected features with high weights were phylogenetic conservation scores for bacteria, fungi (excluding Ascomycota), Ascomycota (excluding Saccharomyces cerevisiae), plants, and mammals, degree of paralogy, and number of protein-protein interactions. Classification was performed by weighted k-nearest neighbor and with support vector machine algorithms. To demonstrate how this approach might complement existing experimental procedures, we applied our algorithm to predict essential genes and genes causing morphological alterations in yeast.
authors.affiliation: Department of Computer Science, North Carolina State University, Raleigh, NC, USA.
authors.forename: Soma
authors.initials: S
authors.lastname: Saha
authors.forename: Steffen
authors.initials: S
authors.lastname: Heber
mesh_terms: D000465:Algorithms; D000818:Animals; D017353:Gene Deletion; D005800:Genes, Fungal / Q000235:genetics*; D009154:Mutation; D010641:Phenotype; D015003:Yeasts / Q000235:genetics*