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Genomics. 2014 Dec;104(6 Pt B):562-71. doi: 10.1016/j.ygeno.2014.10.005. Epub 2014 Oct 14.

Characterization of TATA-containing genes and TATA-less genes in S. cerevisiae by network topologies and biological properties.

Author information

1
College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China.
2
The National Research Center for Animal Transgenic Biotechnology, Inner Mongolia University, Hohhot 010021, PR China.
3
Department of Neurology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin 150081, PR China. Electronic address: lixianghyd@163.com.
4
College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China. Electronic address: jiangwei@hrbmu.edu.cn.

Abstract

The TATA box is the core sequence of the promoter and the binding site of many transcription factors. Based on the presence or absence of TATA box, genes can be defined as TATA-containing or TATA-less genes. Many important stress-response functions and highly variable expression patterns are found to be correlated with the TATA box. However, until now, the relationships and differences between TATA-containing and TATA-less genes remain unclear. In this study, based on the transcriptional profiling of the Saccharomyces cerevisiae genome, the perturbation sensitivity (PS) network is constructed. The topological and biological properties are used to investigate differences between TATA-containing and TATA-less genes. Significant differences are found in all topological properties and most of the biological properties. Notably, the TF number, determined mathematically by the number of transcription factors regulating a gene, demonstrates the highest discrimination between TATA-containing and TATA-less genes when all properties are estimated by the F-score.

KEYWORDS:

Correlation profile; F-score; Perturbation sensitivity network; Yeast

PMID:
25451177
DOI:
10.1016/j.ygeno.2014.10.005
[Indexed for MEDLINE]
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