title: A Computational Method for Identifying Yeast Cell Cycle Transcription Factors.
abstract: The eukaryotic cell cycle is a complex process and is precisely regulated at many levels. Many genes specific to the cell cycle are regulated transcriptionally and are expressed just before they are needed. To understand the cell cycle process, it is important to identify the cell cycle transcription factors (TFs) that regulate the expression of cell cycle-regulated genes. Here, we describe a computational method to identify cell cycle TFs in yeast by integrating current ChIP-chip, mutant, transcription factor-binding site (TFBS), and cell cycle gene expression data. For each identified cell cycle TF, our method also assigned specific cell cycle phases in which the TF functions and identified the time lag for the TF to exert regulatory effects on its target genes. Moreover, our method can identify novel cell cycle-regulated genes as a by-product.
authors.affiliation: Department of Electrical Engineering, National Cheng Kung University, No. 1 Daxue Road, East District, Tainan City, 701, Taiwan, wessonwu@mail.ncku.edu.tw.
authors.forename: Wei-Sheng
authors.initials: WS
authors.lastname: Wu
mesh_terms: D001665:Binding Sites; D002453:Cell Cycle / Q000235:genetics*; D047369:Chromatin Immunoprecipitation; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling; D009154:Mutation; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D015003:Yeasts / Q000166:cytology* / Q000235:genetics / Q000378:metabolism*
chemical_list: D014157:Transcription Factors