CpG islands or CpG clusters: how to identify functional GC-rich regions in a genome?

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	CpG islands or CpG clusters: how to identify functional GC-rich regions in a genome?
	Han L 1,2,3; Zhao ZM[*]2,4
刊名	BMC BIOINFORMATICS
	2009
卷号	10 期号:X 页码:e65
通讯作者	zzhao@vcu.edu
合作状况	其它
英文摘要	Background: CpG islands (CGIs), clusters of CpG dinucleotides in GC-rich regions, are often located in the 5' end of genes and considered gene markers. Hackenberg et al. ( 2006) recently developed a new algorithm, CpGcluster, which uses a completely different mathematical approach from previous traditional algorithms. Their evaluation suggests that CpGcluster provides a much more efficient approach to detecting functional clusters or islands of CpGs. Results: We systematically compared CpGcluster with the traditional algorithm by Takai and Jones ( 2002). Our comparisons of ( 1) the number of islands versus the number of genes in a genome, ( 2) the distribution of islands in different genomic regions, ( 3) island length, ( 4) the distance between two neighboring islands, and ( 5) methylation status suggest that Takai and Jones' algorithm is overall more appropriate for identifying promoter-associated islands of CpGs in vertebrate genomes. Conclusion: The generation of genome sequence and DNA methylation data is expected to accelerate greatly. The information in this study is important for its extensive utility in gene feature analysis and epigenomics including gene prediction and methylation chip design in different genomes.
收录类别	SCI
资助信息	This work was supported by a NIH grant (LM009598) from the National Library of Medicine, the Thomas F. and Kate Miller Jeffress Memorial Trust Fund, and Instituti
语种	英语
内容类型	期刊论文
源URL	[http://159.226.149.26:8080/handle/152453/10486]
专题	昆明动物研究所_比较基因组学昆明动物研究所_遗传资源与进化国家重点实验室
作者单位	1.State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, PR China 2.Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA, 3.Graduate School, Chinese Academy of Sciences, Beijing 100039, PR China 4.Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23284, USA
推荐引用方式 GB/T 7714	Han L,Zhao ZM[*]. CpG islands or CpG clusters: how to identify functional GC-rich regions in a genome?[J]. BMC BIOINFORMATICS,2009,10(X):e65.
APA	Han L,&Zhao ZM[*].(2009).CpG islands or CpG clusters: how to identify functional GC-rich regions in a genome?.BMC BIOINFORMATICS,10(X),e65.
MLA	Han L,et al."CpG islands or CpG clusters: how to identify functional GC-rich regions in a genome?".BMC BIOINFORMATICS 10.X(2009):e65.