title: Characterization of TATA-containing genes and TATA-less genes in S. cerevisiae by network topologies and biological properties.
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.
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: Yingli
authors.initials: Y
authors.lastname: Lv
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: The National Research Center for Animal Transgenic Biotechnology, Inner Mongolia University, Hohhot 010021, PR China.
authors.forename: Yongchun
authors.initials: Y
authors.lastname: Zuo
authors.affiliation: Department of Neurology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin 150081, PR China. Electronic address: lixianghyd@163.com.
authors.forename: Xiang
authors.initials: X
authors.lastname: Li
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: D053263:Gene Regulatory Networks; D005800:Genes, Fungal; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D016385:TATA Box
keywords: Correlation profile; F-score; Perturbation sensitivity network; Yeast