Dynamic changes in subgraph preference profiles of crucial transcription factors

doi:10.1371/journal.pcbi.0020047

	Dynamic changes in subgraph preference profiles of crucial transcription factors
	Zhang, Zhihua ; Liu, Changning ; Skogerbo, Geir ; Zhu, Xiaopeng ; Lu, Hongchao ; Chen, Lan ; Shi, Baochen ; Zhang, Yong ; Wang, Jie ; Wu, Tao ; Chen, Runsheng
	2006-05-01
发表期刊	PLOS COMPUTATIONAL BIOLOGY
ISSN	1553-734X
卷号	2 期号:5 页码:383-391
摘要	Transcription factors with a large number of target genes - transcription hub( s), or THub( s) - are usually crucial components of the regulatory system of a cell, and the different patterns through which they transfer the transcriptional signal to downstream cascades are of great interest. By profiling normalized abundances ( AN) of basic regulatory patterns of individual THubs in the yeast Saccharomyces cerevisiae transcriptional regulation network under five different cellular states and environmental conditions, we have investigated their preferences for different basic regulatory patterns. Subgraph-normalized abundances downstream of individual THubs often differ significantly from that of the network as a whole, and conversely, certain over-represented subgraphs are not preferred by any THub. The THub preferences changed substantially when the cellular or environmental conditions changed. This switching of regulatory pattern preferences suggests that a change in conditions does not only elicit a change in response by the regulatory network, but also a change in the mechanisms by which the response is mediated. The THub subgraph preference profile thus provides a novel tool for description of the structure and organization between the large- scale exponents and local regulatory patterns.
DOI	10.1371/journal.pcbi.0020047
收录类别	SCI
语种	英语
WOS研究方向	Biochemistry & Molecular Biology ; Mathematical & Computational Biology
WOS类目	Biochemical Research Methods ; Mathematical & Computational Biology
WOS记录号	WOS:000239493900007
出版者	PUBLIC LIBRARY SCIENCE
引用统计	被引频次：7[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/10721
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Chen, Runsheng
作者单位	1.Chinese Acad Sci, Inst Biophys, Bioinformat Lab, Beijing, Peoples R China 2.Chinese Acad Sci, Natl Lab Biomacromol, Beijing, Peoples R China 3.Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, Bioinformat Res Grp, Beijing, Peoples R China 4.Chinese Acad Sci, Grad Sch, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Zhihua,Liu, Changning,Skogerbo, Geir,et al. Dynamic changes in subgraph preference profiles of crucial transcription factors[J]. PLOS COMPUTATIONAL BIOLOGY,2006,2(5):383-391.
APA	Zhang, Zhihua.,Liu, Changning.,Skogerbo, Geir.,Zhu, Xiaopeng.,Lu, Hongchao.,...&Chen, Runsheng.(2006).Dynamic changes in subgraph preference profiles of crucial transcription factors.PLOS COMPUTATIONAL BIOLOGY,2(5),383-391.
MLA	Zhang, Zhihua,et al."Dynamic changes in subgraph preference profiles of crucial transcription factors".PLOS COMPUTATIONAL BIOLOGY 2.5(2006):383-391.