title: Identification of yeast cell cycle regulated genes based on genomic features.
abstract: BACKGROUND
  Time-course microarray experiments have been widely used to identify cell cycle regulated genes. However, the method is not effective for lowly expressed genes and is sensitive to experimental conditions. To complement microarray experiments, we propose a computational method to predict cell cycle regulated genes based on their genomic features - transcription factor binding and motif profiles.
  
  
  RESULTS
  Through integrating gene-expression data with ChIP-chip binding and putative binding sites of transcription factors, our method shows high accuracy in discriminating yeast cell cycle regulated genes from non-cell cycle regulated ones. We predict 211 novel cell cycle regulated genes. Our model rediscovers the main cell cycle transcription factors and provides new insights into the regulatory mechanisms. The model also reveals a regulatory circuit mediated by a number of key cell cycle regulators.
  
  
  CONCLUSIONS
  Our model suggests that the periodical pattern of cell cycle genes is largely coded in their promoter regions, which can be captured by motif and transcription factor binding data. Cell cycle is controlled by a relatively small number of master transcription factors. The concept of genomic feature based method can be readily extended to human cell cycle process and other transcriptionally regulated processes, such as tissue-specific expression.
authors.affiliation: Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA. chao.cheng@dartmouth.edu
authors.forename: Chao
authors.initials: C
authors.lastname: Cheng
authors.forename: Yao
authors.initials: Y
authors.lastname: Fu
authors.forename: Linsheng
authors.initials: L
authors.lastname: Shen
authors.forename: Mark
authors.initials: M
authors.lastname: Gerstein
mesh_terms: D002453:Cell Cycle / Q000235:genetics*; D023281:Genomics; D012441:Saccharomyces cerevisiae / Q000166:cytology / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic; D059467:Transcriptome
chemical_list: D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors
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