title: Genome-wide characterization of essential, toxicity-modulating and no-phenotype genes in S. cerevisiae.
abstract: Based on the requirements for an organism's viability, genes can be classified into essential genes and non-essential genes. Non-essential genes can be further classified into toxicity-modulating genes and no-phenotype genes based on the fitness phenotype of yeast cells when the gene is deleted under DNA-damaging conditions. In this study, graph theoretical approaches were used to characterize essential, toxicity-modulating and no-phenotype genes for S. cerevisiae in the physical interaction (PI) network and the perturbation sensitivity (PS) network. We also gained previously published biological datasets to gain a more complete understanding of the differences and relationships between essential, toxicity-modulating genes and no-phenotype genes. The analysis results indicate that toxicity-modulating genes have similar properties as essential genes, and toxicity-modulating genes might represent a middle ground between essential genes and no-phenotype genes, suggesting that cells initiate highly coordinated responses to damage that are similar to those needed for vital cellular functions. These findings may elucidate the mechanisms for understanding toxicity-modulating processes relevant to certain diseases.
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China.
authors.forename: Lei
authors.initials: L
authors.lastname: Yang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China.
authors.forename: Dapeng
authors.initials: D
authors.lastname: Hao
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China.
authors.forename: Yingli
authors.initials: Y
authors.lastname: Lv
authors.affiliation: The Key Laboratory of Mammalian Reproductive Biology and Biotechnology of the Ministry of Education, College of Life Sciences, Inner Mongolia University, Hohhot 010021, PR China. Electronic address: yczuo@imu.edu.cn.
authors.forename: Yongchun
authors.initials: Y
authors.lastname: Zuo
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China. Electronic address: jiangwei@hrbmu.edu.cn.
authors.forename: Wei
authors.initials: W
authors.lastname: Jiang
mesh_terms: D004249:DNA Damage / Q000235:genetics*; D030561:Databases, Nucleic Acid; D015966:Gene Expression Regulation, Fungal / Q000235:genetics*; D005800:Genes, Fungal; D055106:Genome-Wide Association Study; D012441:Saccharomyces cerevisiae
keywords: Biological properties; DNA damage; Graph theory; Yeast