Assessing TF regulatory relationships of divergently transcribed genes

doi:10.1016/j.ygeno.2008.07.007

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	Assessing TF regulatory relationships of divergently transcribed genes
	Chen, Lan 2,3; Cai, Lun 2,3; Skogerbo, Geir 1; Zhao, Yi 1,2; Chen, Runsheng 1,2
刊名	GENOMICS
	2008-11-01
卷号	92 期号:5 页码:316-321
关键词	Divergently transcribed genes Gene regulation ChIP-chip data Microarray data
ISSN号	0888-7543
DOI	10.1016/j.ygeno.2008.07.007
英文摘要	Ambiguously located transcription factor (TF) binding sites may introduce a large number of potentially erroneous regulatory associations into models of transcriptional regulatory networks. We have used a two-step expression similarity strategy to distinguish between likely and unlikely regulatory associations for TFs located between divergently transcribed genes in the yeast genome. Most regulatory associations of divergently transcribed genes could be assigned to either high-confidence (HQ or low-confidence (LC) groups. In support of our result, we found that most of the previously characterized regulatory associations reported in the literature fell into the HC group rather than the LC group. Moreover, genomic distance analysis showed that TF binding sites tend to be located in relative proximity to the gene that is most likely to be regulated by this TF. Finally, removal of low-confidence (i.e., most probably erroneous) regulatory associations from the transcriptional regulatory network barely affected its basic architecture. (C) 2008 Elsevier Inc. All rights reserved.
资助项目	National Key Basic Research and Development Program (973)[2002CB713805] ; National Key Basic Research and Development Program (973)[2003CB715907] ; National Sciences Foundation of China[30630040] ; National Sciences Foundation of China[30570393] ; National Sciences Foundation of China[30600729] ; Data Sharing Network of China Essential Medicine Science[2005DKA32402]
WOS研究方向	Biotechnology & Applied Microbiology ; Genetics & Heredity
语种	英语
出版者	ACADEMIC PRESS INC ELSEVIER SCIENCE
WOS记录号	WOS:000260715400008
内容类型	期刊论文
源URL	[http://119.78.100.204/handle/2XEOYT63/11391]
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Zhao, Yi
作者单位	1.Chinese Acad Sci, Inst Biophys, Bioinformat Lab, Beijing 100101, Peoples R China 2.Chinese Acad Sci, Inst Comp Technol, Bioinformat Res Grp, Beijing 100190, Peoples R China 3.Chinese Acad Sci, Grad Sch, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Chen, Lan,Cai, Lun,Skogerbo, Geir,et al. Assessing TF regulatory relationships of divergently transcribed genes[J]. GENOMICS,2008,92(5):316-321.
APA	Chen, Lan,Cai, Lun,Skogerbo, Geir,Zhao, Yi,&Chen, Runsheng.(2008).Assessing TF regulatory relationships of divergently transcribed genes.GENOMICS,92(5),316-321.
MLA	Chen, Lan,et al."Assessing TF regulatory relationships of divergently transcribed genes".GENOMICS 92.5(2008):316-321.