Gene expression module-based chemical function similarity search

doi:10.1093/nar/gkn610

CORC > 上海药物研究所 > 中国科学院上海药物研究所 > 药物发现与设计中心

	Gene expression module-based chemical function similarity search
	Li, Yun 3,4; Hao, Pei 3,4; Zheng, Siyuan 3; Tu, Kang 3; Fan, Haiwei 4; Zhu, Ruixin 4; Ding, Guohui 3; Dong, Changzheng 3; Wang, Chuan 3; Li, Xuan 4
刊名	NUCLEIC ACIDS RESEARCH
	2008-11
卷号	36 期号:20
ISSN号	0305-1048
DOI	10.1093/nar/gkn610
文献子类	Article
英文摘要	Investigation of biological processes using selective chemical interventions is generally applied in biomedical research and drug discovery. Many studies of this kind make use of gene expression experiments to explore cellular responses to chemical interventions. Recently, some research groups constructed libraries of chemical related expression profiles, and introduced similarity comparison into chemical induced transcriptome analysis. Resembling sequence similarity alignment, expression pattern comparison among chemical intervention related expression profiles provides a new way for chemical function prediction and chemical-gene relation investigation. However, existing methods place more emphasis on comparing profile patterns globally, which ignore noises and marginal effects. At the same time, though the whole information of expression profiles has been used, it is difficult to uncover the underlying mechanisms that lead to the functional similarity between two molecules. Here a new approach is presented to perform biological effects similarity comparison within small biologically meaningful gene categories. Regarding gene categories as units, a reduced similarity matrix is generated for measuring the biological distances between query and profiles in library and pointing out in which modules do chemical pairs resemble. Through the modularization of expression patterns, this method reduces experimental noises and marginal effects and directly correlates chemical molecules with gene function modules.
资助项目	863 Hi-Tech Program of China[2007AA02Z304] ; 863 Hi-Tech Program of China[2007AA02Z332] ; 863 Hi-Tech Program of China[2006AA02Z344] ; 863 Hi-Tech Program of China[2006AA02Z334] ; 863 Hi-Tech Program of China[2006AA020406] ; Shanghai Committee of Science and Technology[07dz22004] ; National Key Basic Research Program (973)[2006CB910700] ; National Key Basic Research Program (973)[2004CB720103] ; National Key Basic Research Program (973)[2004CB518606] ; National Key Basic Research Program (973)[2003CB715901] ; Research Program of CAS[KSCX2-YW-R-112] ; BMBF[CHN07/38]
WOS关键词	BREAST-CANCER CELLS ; UNDERLYING MOLECULAR-MECHANISMS ; HISTONE DEACETYLASE INHIBITOR ; MAMMALIAN TARGET ; PROFILES ; APOPTOSIS ; RAPAMYCIN ; PATHWAYS ; HYPOXIA ; RESISTANCE
WOS研究方向	Biochemistry & Molecular Biology
语种	英语
出版者	OXFORD UNIV PRESS
WOS记录号	WOS:000260977500008
内容类型	期刊论文
源URL	[http://119.78.100.183/handle/2S10ELR8/272770]
专题	药物发现与设计中心中科院受体结构与功能重点实验室新药研究国家重点实验室
通讯作者	Li, Yixue
作者单位	1.Univ Rostock, Inst Immunol, D-18055 Rostock, Germany; 2.Chinese Acad Sci, Shanghai Inst Biol Sci, Shanghai Inst Mat Med, State Key Lab Drug Res,Drug Discovery & Design Ct, Shanghai 201203, Peoples R China 3.Chinese Acad Sci, Shanghai Inst Biol Sci, Key Lab Syst Biol, Shanghai 200031, Peoples R China; 4.Shanghai Ctr Bioinformat Technol, Shanghai 200235, Peoples R China; 5.Univ Michigan, Med Ctr, Dept Internal Med, Ctr Cardiovasc, Ann Arbor, MI 48109 USA;
推荐引用方式 GB/T 7714	Li, Yun,Hao, Pei,Zheng, Siyuan,et al. Gene expression module-based chemical function similarity search[J]. NUCLEIC ACIDS RESEARCH,2008,36(20).
APA	Li, Yun.,Hao, Pei.,Zheng, Siyuan.,Tu, Kang.,Fan, Haiwei.,...&Li, Yixue.(2008).Gene expression module-based chemical function similarity search.NUCLEIC ACIDS RESEARCH,36(20).
MLA	Li, Yun,et al."Gene expression module-based chemical function similarity search".NUCLEIC ACIDS RESEARCH 36.20(2008).