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Gene. 2015 Mar 15;559(1):1-8. doi: 10.1016/j.gene.2015.01.003. Epub 2015 Jan 7.

Genome-wide characterization of essential, toxicity-modulating and no-phenotype genes in S. cerevisiae.

Author information

1
College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China.
2
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.
3
College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China. Electronic address: jiangwei@hrbmu.edu.cn.

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.

KEYWORDS:

Biological properties; DNA damage; Graph theory; Yeast

PMID:
25576218
DOI:
10.1016/j.gene.2015.01.003
[Indexed for MEDLINE]

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