Identification of yeast cell cycle regulated genes based on genomic features

BMC Systems Biology

Mark Gerstein¹  Linsheng Shen²  Yao Fu⁴  Chao Cheng³ 

[1] Department of Computer Science, Yale University, 260 Whitney Avenue, New Haven, CT 06520, USA;Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA;Institute for Quantitative Biomedical Sciences, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03766, USA;Program in Computational Biology and Bioinformatics, Yale University, 260 Whitney Avenue, New Haven, CT 06520, USA

关键词: Prediction;    Genomic features;    Cell cycle regulated genes;   

Others  :  1142469
DOI  :  10.1186/1752-0509-7-70

 received in 2013-02-14, accepted in 2013-07-09,  发布年份 2013

【 摘 要 】

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.

【 授权许可】

   
2013 Cheng et al.; licensee BioMed Central Ltd.

【 图 表 】

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