title: Characterization of essential genes by topological properties in the perturbation sensitivity network.
abstract: Genes that are indispensable for survival are called essential genes. In recent years, the analysis of essential genes has become extremely important for understanding the way a cell functions. With the advent of large-scale gene expression profiling technologies, it is now possible to profile transcriptional changes in the entire genome of Saccharomyces cerevisiae. Notwithstanding the accumulation of gene expression profiling in recent years, only a few studies have used these data to construct the network for S. cerevisiae. In this paper, based on the transcriptional profiling of the S. cerevisiae genome in hundreds of different gene disruptions, the perturbation sensitivity (PS) network is constructed. A scale-free topology with node degree following a power-law distribution is shown in the PS network. Twelve topological properties are used to investigate the characteristics of essential and non-essential genes in the PS network. Most of the properties are found to be statistically discriminative between essential and non-essential genes. In addition, the F-score is used to estimate the essentiality of each property, and the core number demonstrates the highest F-score among all properties.
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: Jizhe
authors.initials: J
authors.lastname: Wang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China.
authors.forename: Huiping
authors.initials: H
authors.lastname: Wang
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 National Research Center for Animal Transgenic Biotechnology, 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: D017353:Gene Deletion; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D020043:Genes, Essential; D005800:Genes, Fungal; D016681:Genome, Fungal; D060066:Protein Interaction Maps; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics
chemical_list: D029701:Saccharomyces cerevisiae Proteins
keywords: Biological network; Essential gene; Statistical test; Yeast